Starting phenix.real_space_refine
on Tue Jan 14 09:52:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bcn_44431/01_2025/9bcn_44431.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bcn_44431/01_2025/9bcn_44431.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bcn_44431/01_2025/9bcn_44431.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bcn_44431/01_2025/9bcn_44431.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bcn_44431/01_2025/9bcn_44431.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bcn_44431/01_2025/9bcn_44431.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.262
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
     S      26      5.16       5
     Cl      2      4.86       5
     C    4248      2.51       5
     N    1128      2.21       5
     O    1202      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 6606
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3212
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 425, 3212
          Classifications: {'peptide': 425}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 27, 'TRANS': 397}
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 145
          Unresolved non-hydrogen dihedrals: 89
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 3, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 87
    Chain: "B"
      Number of atoms: 3208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 425, 3208
          Classifications: {'peptide': 425}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PTRANS': 27, 'TRANS': 397}
          Unresolved non-hydrogen bonds: 121
          Unresolved non-hydrogen angles: 150
          Unresolved non-hydrogen dihedrals: 92
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 4, 'ARG:plan': 3, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 91
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 15
          Unusual residues: {' CL': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 15
          Unusual residues: {' CL': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.38, per 1000 atoms: 0.66
  Number of scatterers: 6606
  At special positions: 0
  Unit cell: (98.5166, 84.4428, 86.608, 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)
     Cl      2     17.00
     S      26     16.00
     O    1202      8.00
     N    1128      7.00
     C    4248      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A  86 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 164 " - pdb=" SG  CYS A 213 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  60 " - pdb=" SG  CYS B  86 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 164 " - pdb=" SG  CYS B 213 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " NAG C   2 " - " MAN C   3 "
      " NAG D   2 " - " MAN D   3 "
      " NAG E   2 " - " MAN E   3 "
      " NAG F   2 " - " MAN F   3 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A1102 " - " ASN A 354 "
      " NAG B1102 " - " ASN B 354 "
      " NAG C   1 " - " ASN A  13 "
      " NAG D   1 " - " ASN A 395 "
      " NAG E   1 " - " ASN B  13 "
      " NAG F   1 " - " ASN B 395 "
  Time building additional restraints: 1.75
  Conformation dependent library (CDL) restraints added in 898.5 milliseconds
  

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1548

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 7 sheets defined
      42.7% alpha, 15.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 37
      Proline residue:  A  25  - end of helix
    Processing helix  chain 'A' and resid 64 through 77
    Processing helix  chain 'A' and resid 86 through 101
      removed outlier: 3.913A  pdb=" N   ALA A  91 " --> pdb=" O   VAL A  87 " (cutoff:3.500A)
      Proline residue:  A  92  - end of helix
    Processing helix  chain 'A' and resid 111 through 116
      removed outlier: 3.638A  pdb=" N   PHE A 114 " --> pdb=" O   ALA A 111 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   VAL A 116 " --> pdb=" O   GLY A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 145
      removed outlier: 3.938A  pdb=" N   LEU A 133 " --> pdb=" O   SER A 129 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   GLY A 134 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ASP A 135 " --> pdb=" O   ALA A 131 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ARG A 143 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 178
      removed outlier: 3.678A  pdb=" N   PHE A 166 " --> pdb=" O   GLU A 162 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ARG A 178 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 203
      removed outlier: 3.760A  pdb=" N   TYR A 196 " --> pdb=" O   ASP A 192 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   THR A 197 " --> pdb=" O   LEU A 193 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ARG A 201 " --> pdb=" O   THR A 197 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   THR A 202 " --> pdb=" O   ARG A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 229
    Processing helix  chain 'A' and resid 245 through 249
      removed outlier: 4.133A  pdb=" N   GLN A 249 " --> pdb=" O   GLN A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 274
      removed outlier: 3.557A  pdb=" N   GLN A 272 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 306
      removed outlier: 3.562A  pdb=" N   LEU A 291 " --> pdb=" O   ASN A 287 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   HIS A 299 " --> pdb=" O   LYS A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 336
      removed outlier: 3.513A  pdb=" N   ALA A 319 " --> pdb=" O   ASN A 315 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU A 326 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU A 336 " --> pdb=" O   VAL A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 339
      No H-bonds generated for 'chain 'A' and resid 337 through 339'
    Processing helix  chain 'A' and resid 344 through 350
    Processing helix  chain 'B' and resid 19 through 37
      Proline residue:  B  25  - end of helix
    Processing helix  chain 'B' and resid 64 through 77
    Processing helix  chain 'B' and resid 86 through 101
      removed outlier: 3.902A  pdb=" N   ALA B  91 " --> pdb=" O   VAL B  87 " (cutoff:3.500A)
      Proline residue:  B  92  - end of helix
    Processing helix  chain 'B' and resid 112 through 116
      removed outlier: 3.746A  pdb=" N   VAL B 116 " --> pdb=" O   GLY B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 145
      removed outlier: 3.775A  pdb=" N   GLY B 134 " --> pdb=" O   TYR B 130 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ASP B 135 " --> pdb=" O   ALA B 131 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ARG B 143 " --> pdb=" O   ALA B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 179
      removed outlier: 3.767A  pdb=" N   PHE B 166 " --> pdb=" O   GLU B 162 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASP B 177 " --> pdb=" O   MET B 173 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ARG B 178 " --> pdb=" O   ARG B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 202
      removed outlier: 3.674A  pdb=" N   ARG B 198 " --> pdb=" O   SER B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 207
      removed outlier: 3.718A  pdb=" N   LYS B 206 " --> pdb=" O   THR B 202 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLY B 207 " --> pdb=" O   MET B 203 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 202 through 207'
    Processing helix  chain 'B' and resid 215 through 229
    Processing helix  chain 'B' and resid 245 through 249
      removed outlier: 3.983A  pdb=" N   GLN B 249 " --> pdb=" O   GLN B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 274
    Processing helix  chain 'B' and resid 287 through 306
      removed outlier: 3.543A  pdb=" N   LEU B 291 " --> pdb=" O   ASN B 287 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   HIS B 299 " --> pdb=" O   LYS B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 338
    Processing helix  chain 'B' and resid 344 through 350
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 52
      removed outlier: 9.226A  pdb=" N   VAL A  80 " --> pdb=" O   ASN A   2 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   THR A   4 " --> pdb=" O   VAL A  80 " (cutoff:3.500A)
      removed outlier: 7.944A  pdb=" N   LEU A  82 " --> pdb=" O   THR A   4 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   ALA A   6 " --> pdb=" O   LEU A  82 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   PHE A  81 " --> pdb=" O   LEU A 105 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   LEU A 104 " --> pdb=" O   THR A 124 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 189
      removed outlier: 5.029A  pdb=" N   VAL A 209 " --> pdb=" O   GLN A 149 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ILE A 210 " --> pdb=" O   PHE A 239 " (cutoff:3.500A)
      removed outlier: 7.435A  pdb=" N   LEU A 241 " --> pdb=" O   ILE A 210 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   ILE A 212 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   PHE A 238 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   ILE A 280 " --> pdb=" O   PHE A 238 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   HIS A 240 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
      removed outlier: 8.361A  pdb=" N   TYR A 282 " --> pdb=" O   HIS A 240 " (cutoff:3.500A)
      removed outlier: 8.984A  pdb=" N   ALA A 277 " --> pdb=" O   MET A 381 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   MET A 381 " --> pdb=" O   ALA A 277 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   PHE A 376 " --> pdb=" O   ASN A 393 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   ASN A 393 " --> pdb=" O   PHE A 376 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   LEU A 378 " --> pdb=" O   VAL A 391 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ARG A 389 " --> pdb=" O   ASP A 380 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLU A 400 " --> pdb=" O   ASN A 395 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 359
    Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 52
      removed outlier: 9.152A  pdb=" N   VAL B  80 " --> pdb=" O   ASN B   2 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   THR B   4 " --> pdb=" O   VAL B  80 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   LEU B  82 " --> pdb=" O   THR B   4 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   ALA B   6 " --> pdb=" O   LEU B  82 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 106
      removed outlier: 6.159A  pdb=" N   LEU B 104 " --> pdb=" O   THR B 124 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 182 through 189
      removed outlier: 6.668A  pdb=" N   ILE B 210 " --> pdb=" O   PHE B 239 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   LEU B 241 " --> pdb=" O   ILE B 210 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   ILE B 212 " --> pdb=" O   LEU B 241 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   PHE B 238 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
      removed outlier: 7.326A  pdb=" N   ILE B 280 " --> pdb=" O   PHE B 238 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   HIS B 240 " --> pdb=" O   ILE B 280 " (cutoff:3.500A)
      removed outlier: 8.337A  pdb=" N   TYR B 282 " --> pdb=" O   HIS B 240 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   PHE B 376 " --> pdb=" O   ASN B 393 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   ASN B 393 " --> pdb=" O   PHE B 376 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   LEU B 378 " --> pdb=" O   VAL B 391 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 355 through 359

    275 hydrogen bonds defined for protein.
    798 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: 1.78

  Time building geometry restraints manager: 2.02 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1035
        1.32 -     1.44: 1982
        1.44 -     1.57: 3733
        1.57 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 6790
  Sorted by residual:
  bond pdb=" C5  MAN F   3 "
       pdb=" O5  MAN F   3 "
    ideal  model  delta    sigma   weight residual
    1.418  1.496 -0.078 2.00e-02 2.50e+03 1.53e+01
  bond pdb=" C5  MAN D   3 "
       pdb=" O5  MAN D   3 "
    ideal  model  delta    sigma   weight residual
    1.418  1.494 -0.076 2.00e-02 2.50e+03 1.44e+01
  bond pdb=" C1  NAG F   1 "
       pdb=" O5  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.481 -0.075 2.00e-02 2.50e+03 1.42e+01
  bond pdb=" C5  MAN E   3 "
       pdb=" O5  MAN E   3 "
    ideal  model  delta    sigma   weight residual
    1.418  1.492 -0.074 2.00e-02 2.50e+03 1.37e+01
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.478 -0.072 2.00e-02 2.50e+03 1.29e+01
  ... (remaining 6785 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 8994
        2.02 -     4.03: 220
        4.03 -     6.05: 53
        6.05 -     8.06: 13
        8.06 -    10.08: 3
  Bond angle restraints: 9283
  Sorted by residual:
  angle pdb=" C   GLU A 373 "
        pdb=" CA  GLU A 373 "
        pdb=" CB  GLU A 373 "
      ideal   model   delta    sigma   weight residual
     110.77  100.69   10.08 1.67e+00 3.59e-01 3.64e+01
  angle pdb=" C   GLU B 373 "
        pdb=" CA  GLU B 373 "
        pdb=" CB  GLU B 373 "
      ideal   model   delta    sigma   weight residual
     110.22  100.52    9.70 1.67e+00 3.59e-01 3.37e+01
  angle pdb=" CA  GLY B 207 "
        pdb=" C   GLY B 207 "
        pdb=" N   ARG B 208 "
      ideal   model   delta    sigma   weight residual
     114.58  119.56   -4.98 8.60e-01 1.35e+00 3.35e+01
  angle pdb=" O   GLY B 207 "
        pdb=" C   GLY B 207 "
        pdb=" N   ARG B 208 "
      ideal   model   delta    sigma   weight residual
     123.87  118.54    5.33 1.01e+00 9.80e-01 2.78e+01
  angle pdb=" N   THR B 197 "
        pdb=" CA  THR B 197 "
        pdb=" C   THR B 197 "
      ideal   model   delta    sigma   weight residual
     111.14  105.84    5.30 1.08e+00 8.57e-01 2.41e+01
  ... (remaining 9278 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.16: 3878
       24.16 -    48.31: 198
       48.31 -    72.47: 26
       72.47 -    96.63: 13
       96.63 -   120.79: 4
  Dihedral angle restraints: 4119
    sinusoidal: 1691
      harmonic: 2428
  Sorted by residual:
  dihedral pdb=" CB  CYS B  60 "
           pdb=" SG  CYS B  60 "
           pdb=" SG  CYS B  86 "
           pdb=" CB  CYS B  86 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  137.58  -44.58     1      1.00e+01 1.00e-02 2.76e+01
  dihedral pdb=" C   GLU A 373 "
           pdb=" N   GLU A 373 "
           pdb=" CA  GLU A 373 "
           pdb=" CB  GLU A 373 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.81  -12.79     0      2.50e+00 1.60e-01 2.62e+01
  dihedral pdb=" C   GLU B 373 "
           pdb=" N   GLU B 373 "
           pdb=" CA  GLU B 373 "
           pdb=" CB  GLU B 373 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.94  -12.66     0      2.50e+00 1.60e-01 2.56e+01
  ... (remaining 4116 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 1011
       0.107 -    0.214: 49
       0.214 -    0.321: 2
       0.321 -    0.427: 2
       0.427 -    0.534: 2
  Chirality restraints: 1066
  Sorted by residual:
  chirality pdb=" C1  NAG A1102 "
            pdb=" ND2 ASN A 354 "
            pdb=" C2  NAG A1102 "
            pdb=" O5  NAG A1102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.87   -0.53 2.00e-01 2.50e+01 7.13e+00
  chirality pdb=" C1  NAG B1102 "
            pdb=" ND2 ASN B 354 "
            pdb=" C2  NAG B1102 "
            pdb=" O5  NAG B1102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.88   -0.52 2.00e-01 2.50e+01 6.78e+00
  chirality pdb=" C4  NAG F   1 "
            pdb=" C3  NAG F   1 "
            pdb=" C5  NAG F   1 "
            pdb=" O4  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.15   -0.39 2.00e-01 2.50e+01 3.71e+00
  ... (remaining 1063 not shown)

  Planarity restraints: 1189
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B1102 "    0.049 2.00e-02 2.50e+03   3.97e-02 1.97e+01
        pdb=" C7  NAG B1102 "   -0.021 2.00e-02 2.50e+03
        pdb=" C8  NAG B1102 "    0.040 2.00e-02 2.50e+03
        pdb=" N2  NAG B1102 "   -0.058 2.00e-02 2.50e+03
        pdb=" O7  NAG B1102 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 200 "    0.020 2.00e-02 2.50e+03   4.03e-02 1.63e+01
        pdb=" C   LEU B 200 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   LEU B 200 "    0.026 2.00e-02 2.50e+03
        pdb=" N   ARG B 201 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 236 "   -0.016 2.00e-02 2.50e+03   2.12e-02 8.99e+00
        pdb=" CG  TYR A 236 "    0.017 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 236 "    0.033 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 236 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 236 "   -0.036 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 236 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 236 "   -0.015 2.00e-02 2.50e+03
        pdb=" OH  TYR A 236 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1186 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 181
        2.71 -     3.25: 6365
        3.25 -     3.80: 10206
        3.80 -     4.35: 13912
        4.35 -     4.90: 23450
  Nonbonded interactions: 54114
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 204 "
            pdb=" NH2 ARG B 208 "
     model   vdw
     2.156 3.120
  nonbonded pdb=" O3  NAG C   2 "
            pdb=" O7  NAG C   2 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" O3  NAG E   2 "
            pdb=" O7  NAG E   2 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   THR B  14 "
            pdb=" OG1 THR B  14 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   GLU A 190 "
            pdb=" OH  TYR A 196 "
     model   vdw
     2.319 3.040
  ... (remaining 54109 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 310 or (resid 311 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 312 through 345 or (resid 346 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 347 through 425 or resid 110 \ 
1 through 1102))
  selection = (chain 'B' and (resid 1 through 234 or (resid 235 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 236 through 425 or resid 1101 through 1102)) \ 

}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             0.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.100
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.078   6790  Z= 0.429
  Angle     :  0.805  10.078   9283  Z= 0.437
  Chirality :  0.056   0.534   1066
  Planarity :  0.006   0.046   1183
  Dihedral  : 15.344 120.785   2559
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  0.96 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.28), residues: 846
  helix:  0.22 (0.30), residues: 314
  sheet: -0.28 (0.41), residues: 162
  loop : -1.56 (0.28), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 379 
 HIS   0.006   0.001   HIS B 322 
 PHE   0.016   0.001   PHE A 172 
 TYR   0.036   0.002   TYR A 236 
 ARG   0.015   0.001   ARG B 389 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.721 
Fit side-chains
REVERT: A  119 GLU cc_start: 0.7097 (tt0) cc_final: 0.6841 (tt0)
REVERT: A  298 LYS cc_start: 0.8116 (mttt) cc_final: 0.7581 (mmtp)
REVERT: A  389 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8054 (pmt170)
  outliers start: 6
  outliers final: 2
  residues processed: 111
  average time/residue: 0.9470
  time to fit residues: 112.0028
Evaluate side-chains
  79 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  389 ARG
Chi-restraints excluded: chain B residue  208 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    0.3980
   chunk 63 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 42 optimal weight:    6.9990
   chunk 34 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 76 optimal weight:    0.7980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 246 GLN
A 338 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.124854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.093587 restraints weight = 7651.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 1.96
r_work: 0.2868 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2739 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.1152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6790  Z= 0.223
  Angle     :  0.689  11.510   9283  Z= 0.314
  Chirality :  0.047   0.340   1066
  Planarity :  0.005   0.039   1183
  Dihedral  : 13.238 108.777   1224
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  8.35 %
    Favored  : 90.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.29), residues: 846
  helix:  1.13 (0.31), residues: 316
  sheet: -0.46 (0.37), residues: 178
  loop : -1.13 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 100 
 HIS   0.006   0.001   HIS B 322 
 PHE   0.015   0.001   PHE A 172 
 TYR   0.011   0.001   TYR B 154 
 ARG   0.003   0.000   ARG B 262 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.658 
Fit side-chains
REVERT: A  173 MET cc_start: 0.8584 (mmm) cc_final: 0.8323 (mmt)
REVERT: A  192 ASP cc_start: 0.7400 (t70) cc_final: 0.6671 (t70)
  outliers start: 9
  outliers final: 5
  residues processed: 83
  average time/residue: 0.9837
  time to fit residues: 87.1269
Evaluate side-chains
  73 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain B residue  147 GLU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  208 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0060
   chunk 55 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0370
   chunk 53 optimal weight:    0.0770
   chunk 32 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.3632

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

Flipped N/Q/H residues before XYZ refinement:
A 246 GLN
A 338 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.127475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.096306 restraints weight = 7763.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.00
r_work: 0.2906 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2775 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6790  Z= 0.156
  Angle     :  0.621   9.939   9283  Z= 0.281
  Chirality :  0.045   0.319   1066
  Planarity :  0.004   0.034   1183
  Dihedral  : 12.775 110.601   1218
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 10.43 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.29), residues: 846
  helix:  1.42 (0.30), residues: 320
  sheet: -0.29 (0.36), residues: 184
  loop : -0.80 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 100 
 HIS   0.005   0.001   HIS B 322 
 PHE   0.015   0.001   PHE A 172 
 TYR   0.011   0.001   TYR B 154 
 ARG   0.004   0.000   ARG A  47 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.698 
Fit side-chains
REVERT: A  192 ASP cc_start: 0.7335 (t70) cc_final: 0.6623 (t70)
REVERT: A  298 LYS cc_start: 0.7515 (mttt) cc_final: 0.6962 (mmtp)
REVERT: B  344 ASP cc_start: 0.7517 (m-30) cc_final: 0.7283 (m-30)
  outliers start: 11
  outliers final: 4
  residues processed: 89
  average time/residue: 0.9115
  time to fit residues: 86.9478
Evaluate side-chains
  80 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain B residue  208 ARG
Chi-restraints excluded: chain B residue  341 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 42 optimal weight:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 3 optimal weight:    8.9990
   chunk 0 optimal weight:    7.9990
   chunk 80 optimal weight:    0.0370
   chunk 65 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   overall best weight:    1.2064

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

Flipped N/Q/H residues before XYZ refinement:
A 338 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.127111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.094933 restraints weight = 7800.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3014 rms_B_bonded: 2.05
r_work: 0.2896 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2765 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6790  Z= 0.209
  Angle     :  0.638  10.285   9283  Z= 0.286
  Chirality :  0.045   0.314   1066
  Planarity :  0.004   0.036   1183
  Dihedral  : 12.558 111.154   1218
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 12.52 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.29), residues: 846
  helix:  1.72 (0.31), residues: 314
  sheet: -0.24 (0.36), residues: 184
  loop : -0.82 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 353 
 HIS   0.007   0.001   HIS B 299 
 PHE   0.011   0.001   PHE B 188 
 TYR   0.011   0.001   TYR B 154 
 ARG   0.003   0.000   ARG A  47 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.716 
Fit side-chains
REVERT: A  192 ASP cc_start: 0.7407 (t70) cc_final: 0.6736 (t70)
REVERT: A  298 LYS cc_start: 0.7746 (mttt) cc_final: 0.7179 (mmtp)
REVERT: B  344 ASP cc_start: 0.7672 (m-30) cc_final: 0.7452 (m-30)
  outliers start: 16
  outliers final: 10
  residues processed: 90
  average time/residue: 0.8620
  time to fit residues: 83.4991
Evaluate side-chains
  79 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  208 ARG
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  347 ASN
Chi-restraints excluded: chain B residue  349 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 77 optimal weight:    0.0070
   chunk 47 optimal weight:    0.1980
   chunk 1 optimal weight:    0.9990
   chunk 56 optimal weight:   10.0000
   chunk 67 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0980
   overall best weight:    0.3798

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

Flipped N/Q/H residues before XYZ refinement:
A 338 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.129958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.099320 restraints weight = 7743.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 1.91
r_work: 0.2925 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2798 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6790  Z= 0.149
  Angle     :  0.604   9.878   9283  Z= 0.269
  Chirality :  0.044   0.292   1066
  Planarity :  0.004   0.037   1183
  Dihedral  : 12.293 110.421   1218
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 14.77 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.29), residues: 846
  helix:  1.81 (0.30), residues: 316
  sheet: -0.19 (0.36), residues: 184
  loop : -0.70 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 379 
 HIS   0.007   0.001   HIS B 299 
 PHE   0.014   0.001   PHE A 172 
 TYR   0.009   0.001   TYR B 154 
 ARG   0.005   0.000   ARG A  47 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.566 
Fit side-chains
REVERT: A  192 ASP cc_start: 0.7295 (t70) cc_final: 0.6620 (t70)
REVERT: A  298 LYS cc_start: 0.7537 (mttt) cc_final: 0.6940 (mmtp)
REVERT: B  344 ASP cc_start: 0.7539 (m-30) cc_final: 0.7302 (m-30)
  outliers start: 14
  outliers final: 8
  residues processed: 86
  average time/residue: 0.7818
  time to fit residues: 72.9983
Evaluate side-chains
  81 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  208 ARG
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  349 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 83 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 11 optimal weight:    0.3980
   chunk 8 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0970
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  77 ASN
A 195 HIS
A 338 HIS
B 299 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.129178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.097760 restraints weight = 7718.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 1.97
r_work: 0.2899 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6790  Z= 0.181
  Angle     :  0.615   9.734   9283  Z= 0.272
  Chirality :  0.044   0.292   1066
  Planarity :  0.004   0.037   1183
  Dihedral  : 12.202 109.962   1218
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 15.25 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.29), residues: 846
  helix:  1.91 (0.31), residues: 316
  sheet: -0.14 (0.36), residues: 184
  loop : -0.70 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 379 
 HIS   0.007   0.001   HIS B 299 
 PHE   0.009   0.001   PHE B 188 
 TYR   0.010   0.001   TYR B 154 
 ARG   0.004   0.000   ARG A  47 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.735 
Fit side-chains
REVERT: A  192 ASP cc_start: 0.7269 (t70) cc_final: 0.6533 (t0)
REVERT: A  195 HIS cc_start: 0.7300 (m-70) cc_final: 0.7020 (m-70)
REVERT: A  298 LYS cc_start: 0.7499 (mttt) cc_final: 0.6915 (mmtp)
REVERT: B  344 ASP cc_start: 0.7522 (m-30) cc_final: 0.7260 (m-30)
  outliers start: 13
  outliers final: 9
  residues processed: 85
  average time/residue: 0.9771
  time to fit residues: 88.9926
Evaluate side-chains
  79 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  185 HIS
Chi-restraints excluded: chain B residue  208 ARG
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  349 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 65 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
A  77 ASN
A 338 HIS
B 299 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.125646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.093489 restraints weight = 7680.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 2.04
r_work: 0.2840 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2708 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6790  Z= 0.234
  Angle     :  0.642  10.141   9283  Z= 0.285
  Chirality :  0.045   0.305   1066
  Planarity :  0.004   0.037   1183
  Dihedral  : 12.160 109.340   1218
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 2.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 16.85 %
    Favored  : 81.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.30), residues: 846
  helix:  1.88 (0.31), residues: 316
  sheet: -0.10 (0.37), residues: 180
  loop : -0.68 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  74 
 HIS   0.007   0.001   HIS B 299 
 PHE   0.013   0.001   PHE A 172 
 TYR   0.010   0.001   TYR A 154 
 ARG   0.004   0.000   ARG A  47 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A  192 ASP cc_start: 0.7055 (t70) cc_final: 0.6332 (t0)
REVERT: A  298 LYS cc_start: 0.7328 (mttt) cc_final: 0.6724 (mmtp)
REVERT: B  344 ASP cc_start: 0.7415 (m-30) cc_final: 0.7070 (m-30)
  outliers start: 12
  outliers final: 8
  residues processed: 78
  average time/residue: 0.8306
  time to fit residues: 70.1629
Evaluate side-chains
  76 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  208 ARG
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  349 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 27 optimal weight:    9.9990
   chunk 62 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A  77 ASN
A 338 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.127168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.095061 restraints weight = 7722.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 2.04
r_work: 0.2900 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6790  Z= 0.192
  Angle     :  0.623   9.970   9283  Z= 0.276
  Chirality :  0.044   0.299   1066
  Planarity :  0.004   0.037   1183
  Dihedral  : 12.056 108.797   1218
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 17.17 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.30), residues: 846
  helix:  1.89 (0.31), residues: 316
  sheet: -0.07 (0.37), residues: 180
  loop : -0.63 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  74 
 HIS   0.006   0.001   HIS B 322 
 PHE   0.010   0.001   PHE A 188 
 TYR   0.010   0.001   TYR B 154 
 ARG   0.004   0.000   ARG A  47 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.739 
Fit side-chains
REVERT: A  192 ASP cc_start: 0.7237 (t70) cc_final: 0.6517 (t70)
REVERT: A  298 LYS cc_start: 0.7696 (mttt) cc_final: 0.7104 (mmtp)
REVERT: B  344 ASP cc_start: 0.7674 (m-30) cc_final: 0.7402 (m-30)
  outliers start: 11
  outliers final: 9
  residues processed: 78
  average time/residue: 0.8167
  time to fit residues: 69.9225
Evaluate side-chains
  75 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  194 SER
Chi-restraints excluded: chain B residue  208 ARG
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  349 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0870
   chunk 78 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 81 optimal weight:    0.7980
   chunk 42 optimal weight:    7.9990
   chunk 65 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 48 optimal weight:    0.3980
   chunk 37 optimal weight:    4.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A  77 ASN
A 338 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.129262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.097595 restraints weight = 7811.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 1.99
r_work: 0.2936 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2807 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6790  Z= 0.158
  Angle     :  0.610  10.159   9283  Z= 0.269
  Chirality :  0.043   0.283   1066
  Planarity :  0.004   0.037   1183
  Dihedral  : 11.917 108.443   1218
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 17.66 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.30), residues: 846
  helix:  1.96 (0.31), residues: 316
  sheet: -0.07 (0.37), residues: 180
  loop : -0.57 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  74 
 HIS   0.005   0.001   HIS B 322 
 PHE   0.012   0.001   PHE A 172 
 TYR   0.010   0.001   TYR B 154 
 ARG   0.004   0.000   ARG A  47 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.727 
Fit side-chains
REVERT: A  192 ASP cc_start: 0.7165 (t70) cc_final: 0.6459 (t70)
REVERT: A  298 LYS cc_start: 0.7714 (mttt) cc_final: 0.7113 (mmtp)
REVERT: B  344 ASP cc_start: 0.7628 (m-30) cc_final: 0.7370 (m-30)
  outliers start: 10
  outliers final: 7
  residues processed: 77
  average time/residue: 0.8672
  time to fit residues: 72.5174
Evaluate side-chains
  77 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  147 GLU
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  349 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 14 optimal weight:    8.9990
   chunk 36 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  77 ASN
A 338 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.129148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.097300 restraints weight = 7830.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 2.00
r_work: 0.2910 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6790  Z= 0.171
  Angle     :  0.616   9.737   9283  Z= 0.270
  Chirality :  0.043   0.276   1066
  Planarity :  0.004   0.037   1183
  Dihedral  : 11.749 108.031   1214
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 17.82 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.30), residues: 846
  helix:  1.97 (0.31), residues: 316
  sheet: -0.05 (0.37), residues: 180
  loop : -0.58 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  74 
 HIS   0.005   0.001   HIS B 322 
 PHE   0.009   0.001   PHE A 188 
 TYR   0.010   0.001   TYR B 154 
 ARG   0.004   0.000   ARG A  47 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.997 
Fit side-chains
REVERT: A  192 ASP cc_start: 0.7123 (t70) cc_final: 0.6358 (t70)
REVERT: A  298 LYS cc_start: 0.7573 (mttt) cc_final: 0.6965 (mmtp)
REVERT: B  344 ASP cc_start: 0.7555 (m-30) cc_final: 0.7282 (m-30)
  outliers start: 9
  outliers final: 7
  residues processed: 77
  average time/residue: 0.8928
  time to fit residues: 74.3519
Evaluate side-chains
  78 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  349 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 7 optimal weight:    0.0010
   chunk 29 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:    0.2980
   chunk 70 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
A   2 ASN
A  77 ASN
A 338 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.130736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.099727 restraints weight = 7824.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 1.92
r_work: 0.2943 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2816 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6790  Z= 0.151
  Angle     :  0.602   9.386   9283  Z= 0.263
  Chirality :  0.043   0.265   1066
  Planarity :  0.004   0.037   1183
  Dihedral  : 11.633 108.008   1214
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 18.14 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.30), residues: 846
  helix:  1.96 (0.31), residues: 318
  sheet: -0.06 (0.37), residues: 184
  loop : -0.51 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  74 
 HIS   0.005   0.001   HIS B 322 
 PHE   0.013   0.001   PHE A 172 
 TYR   0.010   0.001   TYR B 154 
 ARG   0.004   0.000   ARG A  47 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4247.68 seconds
wall clock time: 76 minutes 36.83 seconds (4596.83 seconds total)