Starting phenix.real_space_refine
on Tue Aug  4 17:17:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9y63_72539/08_2026/9y63_72539.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9y63_72539/08_2026/9y63_72539.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9y63_72539/08_2026/9y63_72539.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9y63_72539/08_2026/9y63_72539.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9y63_72539/08_2026/9y63_72539.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9y63_72539/08_2026/9y63_72539.cif"
  }
  resolution = 2.3
  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=   0.033
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: 4
    Type Number    sf(0)   Gaussians
     S       3      5.16       5
     C    3352      2.51       5
     N     864      2.21       5
     O     960      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5179
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1726
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 16, 'TRANS': 213}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "B"
      Number of atoms: 1741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1741
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 16, 'TRANS': 213}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 15
    Chain: "C"
      Number of atoms: 1712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1712
          Classifications: {'peptide': 227}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 15, 'TRANS': 211}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 24
  Time building chain proxies: 1.52, per 1000 atoms: 0.29
  Number of scatterers: 5179
  At special positions: 0
  Unit cell: (90.865, 90.865, 69.485, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       3     16.00
     O     960      8.00
     N     864      7.00
     C    3352      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
  Time building additional restraints: 0.42
  Conformation dependent library (CDL) restraints added in 216.1 milliseconds
  

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1292

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 10 sheets defined
      6.0% alpha, 63.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 161 through 165
    Processing helix  chain 'A' and resid 174 through 180
    Processing helix  chain 'B' and resid 152 through 154
      No H-bonds generated for 'chain 'B' and resid 152 through 154'
    Processing helix  chain 'B' and resid 161 through 165
    Processing helix  chain 'B' and resid 174 through 179
    Processing helix  chain 'C' and resid 152 through 154
      No H-bonds generated for 'chain 'C' and resid 152 through 154'
    Processing helix  chain 'C' and resid 161 through 165
    Processing helix  chain 'C' and resid 174 through 180
    Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 78
      removed outlier: 7.358A  pdb=" N   THR A  35 " --> pdb=" O   SER A 111 " (cutoff:3.500A)
      removed outlier: 8.383A  pdb=" N   LEU A 113 " --> pdb=" O   THR A  35 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   LYS A  37 " --> pdb=" O   LEU A 113 " (cutoff:3.500A)
      removed outlier: 7.823A  pdb=" N   LEU A 115 " --> pdb=" O   LYS A  37 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   HIS A  39 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   LEU A 117 " --> pdb=" O   HIS A  39 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   SER A  41 " --> pdb=" O   LEU A 117 " (cutoff:3.500A)
      removed outlier: 4.802A  pdb=" N   SER A 114 " --> pdb=" O   ALA B 123 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ALA B 123 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
      removed outlier: 5.286A  pdb=" N   ILE B 274 " --> pdb=" O   LEU B 259 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   LEU B 259 " --> pdb=" O   ILE B 274 " (cutoff:3.500A)
      removed outlier: 5.837A  pdb=" N   TRP B 254 " --> pdb=" O   ASP B 248 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   ASP B 248 " --> pdb=" O   TRP B 254 " (cutoff:3.500A)
      removed outlier: 5.580A  pdb=" N   LYS B 256 " --> pdb=" O   ARG B 246 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   ARG B 246 " --> pdb=" O   LYS B 256 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLY B 258 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ALA B 240 " --> pdb=" O   VAL B 262 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   TYR B 280 " --> pdb=" O   PHE B 247 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   GLY B 279 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   SER B 207 " --> pdb=" O   GLY B 279 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   TRP B 281 " --> pdb=" O   ALA B 205 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   ALA B 205 " --> pdb=" O   TRP B 281 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   ALA B 283 " --> pdb=" O   VAL B 203 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96
      removed outlier: 3.933A  pdb=" N   LEU A 118 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
      removed outlier: 4.802A  pdb=" N   SER A 114 " --> pdb=" O   ALA B 123 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ALA B 123 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
      removed outlier: 5.286A  pdb=" N   ILE B 274 " --> pdb=" O   LEU B 259 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   LEU B 259 " --> pdb=" O   ILE B 274 " (cutoff:3.500A)
      removed outlier: 7.270A  pdb=" N   LEU B 187 " --> pdb=" O   LYS B 256 " (cutoff:3.500A)
      removed outlier: 8.616A  pdb=" N   GLY B 258 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 67
      removed outlier: 5.271A  pdb=" N   SER A  62 " --> pdb=" O   THR A  58 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   THR A  58 " --> pdb=" O   SER A  62 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ALA A  64 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 166 through 171
      removed outlier: 6.580A  pdb=" N   ALA A 283 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   ALA A 205 " --> pdb=" O   TRP A 281 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   TRP A 281 " --> pdb=" O   ALA A 205 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   SER A 207 " --> pdb=" O   GLY A 279 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   GLY A 279 " --> pdb=" O   SER A 207 " (cutoff:3.500A)
      removed outlier: 5.254A  pdb=" N   TYR A 280 " --> pdb=" O   PHE A 247 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ALA A 243 " --> pdb=" O   ALA A 284 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLY A 258 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   ARG A 246 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   LYS A 256 " --> pdb=" O   ARG A 246 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ASP A 248 " --> pdb=" O   TRP A 254 " (cutoff:3.500A)
      removed outlier: 5.464A  pdb=" N   TRP A 254 " --> pdb=" O   ASP A 248 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   LEU A 259 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
      removed outlier: 5.199A  pdb=" N   ILE A 274 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ALA A 123 " --> pdb=" O   SER C 114 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   SER C 114 " --> pdb=" O   ALA A 123 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   SER C 111 " --> pdb=" O   THR C  35 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 187
      removed outlier: 6.565A  pdb=" N   LEU A 259 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
      removed outlier: 5.199A  pdb=" N   ILE A 274 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ALA A 123 " --> pdb=" O   SER C 114 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   SER C 114 " --> pdb=" O   ALA A 123 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   LEU C 118 " --> pdb=" O   VAL C  96 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 155
      removed outlier: 4.203A  pdb=" N   LEU A 219 " --> pdb=" O   ARG A 155 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 73 through 78
      removed outlier: 4.993A  pdb=" N   SER B 111 " --> pdb=" O   THR B  35 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   SER B 114 " --> pdb=" O   ALA C 123 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   ALA C 123 " --> pdb=" O   SER B 114 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   ILE C 274 " --> pdb=" O   LEU C 259 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   LEU C 259 " --> pdb=" O   ILE C 274 " (cutoff:3.500A)
      removed outlier: 5.387A  pdb=" N   TRP C 254 " --> pdb=" O   ASP C 248 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   ASP C 248 " --> pdb=" O   TRP C 254 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   LYS C 256 " --> pdb=" O   ARG C 246 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   ARG C 246 " --> pdb=" O   LYS C 256 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLY C 258 " --> pdb=" O   ALA C 244 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ALA C 243 " --> pdb=" O   ALA C 284 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   TYR C 280 " --> pdb=" O   PHE C 247 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 95 through 96
      removed outlier: 4.005A  pdb=" N   LEU B 118 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   SER B 114 " --> pdb=" O   ALA C 123 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   ALA C 123 " --> pdb=" O   SER B 114 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   ILE C 274 " --> pdb=" O   LEU C 259 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   LEU C 259 " --> pdb=" O   ILE C 274 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 61 through 67
      removed outlier: 5.385A  pdb=" N   SER B  62 " --> pdb=" O   THR B  58 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   THR B  58 " --> pdb=" O   SER B  62 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ALA B  64 " --> pdb=" O   ILE B  56 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 61 through 67
      removed outlier: 5.278A  pdb=" N   SER C  62 " --> pdb=" O   THR C  58 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   THR C  58 " --> pdb=" O   SER C  62 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ALA C  64 " --> pdb=" O   ILE C  56 " (cutoff:3.500A)

    294 hydrogen bonds defined for protein.
    753 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: 1.08

  Time building geometry restraints manager: 0.57 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1621
        1.34 -     1.46: 1097
        1.46 -     1.57: 2586
        1.57 -     1.69: 0
        1.69 -     1.80: 6
  Bond restraints: 5310
  Sorted by residual:
  bond pdb=" CA  SER B 173 "
       pdb=" CB  SER B 173 "
    ideal  model  delta    sigma   weight residual
    1.536  1.496  0.040 1.42e-02 4.96e+03 7.80e+00
  bond pdb=" N   SER B 173 "
       pdb=" CA  SER B 173 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.034 1.29e-02 6.01e+03 6.77e+00
  bond pdb=" N   SER C 180 "
       pdb=" CA  SER C 180 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.033 1.33e-02 5.65e+03 6.05e+00
  bond pdb=" N   SER B 180 "
       pdb=" CA  SER B 180 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.33e-02 5.65e+03 5.89e+00
  bond pdb=" N   VAL B 220 "
       pdb=" CA  VAL B 220 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.28e-02 6.10e+03 5.48e+00
  ... (remaining 5305 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 7122
        1.96 -     3.93: 136
        3.93 -     5.89: 12
        5.89 -     7.85: 1
        7.85 -     9.82: 1
  Bond angle restraints: 7272
  Sorted by residual:
  angle pdb=" N   SER B 180 "
        pdb=" CA  SER B 180 "
        pdb=" C   SER B 180 "
      ideal   model   delta    sigma   weight residual
     112.89  108.07    4.82 1.24e+00 6.50e-01 1.51e+01
  angle pdb=" C   VAL B 220 "
        pdb=" N   ASP B 221 "
        pdb=" CA  ASP B 221 "
      ideal   model   delta    sigma   weight residual
     123.32  117.86    5.46 1.88e+00 2.83e-01 8.43e+00
  angle pdb=" N   SER B 163 "
        pdb=" CA  SER B 163 "
        pdb=" C   SER B 163 "
      ideal   model   delta    sigma   weight residual
     112.54  109.11    3.43 1.22e+00 6.72e-01 7.89e+00
  angle pdb=" CA  ASP B 221 "
        pdb=" CB  ASP B 221 "
        pdb=" CG  ASP B 221 "
      ideal   model   delta    sigma   weight residual
     112.60  115.41   -2.81 1.00e+00 1.00e+00 7.88e+00
  angle pdb=" CA  THR C 253 "
        pdb=" C   THR C 253 "
        pdb=" O   THR C 253 "
      ideal   model   delta    sigma   weight residual
     121.58  118.44    3.14 1.16e+00 7.43e-01 7.31e+00
  ... (remaining 7267 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 2737
       17.99 -    35.98: 288
       35.98 -    53.98: 34
       53.98 -    71.97: 15
       71.97 -    89.96: 8
  Dihedral angle restraints: 3082
    sinusoidal: 1097
      harmonic: 1985
  Sorted by residual:
  dihedral pdb=" CA  PHE B  57 "
           pdb=" C   PHE B  57 "
           pdb=" N   THR B  58 "
           pdb=" CA  THR B  58 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.49   16.51     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  PHE C  57 "
           pdb=" C   PHE C  57 "
           pdb=" N   THR C  58 "
           pdb=" CA  THR C  58 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.67   16.33     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CG  LYS B 250 "
           pdb=" CD  LYS B 250 "
           pdb=" CE  LYS B 250 "
           pdb=" NZ  LYS B 250 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -121.73  -58.27     3      1.50e+01 4.44e-03 9.46e+00
  ... (remaining 3079 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 601
       0.038 -    0.076: 163
       0.076 -    0.115: 84
       0.115 -    0.153: 21
       0.153 -    0.191: 3
  Chirality restraints: 872
  Sorted by residual:
  chirality pdb=" CA  VAL B 220 "
            pdb=" N   VAL B 220 "
            pdb=" C   VAL B 220 "
            pdb=" CB  VAL B 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 9.11e-01
  chirality pdb=" CB  VAL B 220 "
            pdb=" CA  VAL B 220 "
            pdb=" CG1 VAL B 220 "
            pdb=" CG2 VAL B 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.34e-01
  chirality pdb=" CA  VAL C 147 "
            pdb=" N   VAL C 147 "
            pdb=" C   VAL C 147 "
            pdb=" CB  VAL C 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.03e-01
  ... (remaining 869 not shown)

  Planarity restraints: 902
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 219 "   -0.009 2.00e-02 2.50e+03   1.84e-02 3.40e+00
        pdb=" C   LEU B 219 "    0.032 2.00e-02 2.50e+03
        pdb=" O   LEU B 219 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   VAL B 220 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 216 "   -0.027 5.00e-02 4.00e+02   4.09e-02 2.68e+00
        pdb=" N   PRO B 217 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO B 217 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 217 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 241 "    0.008 2.00e-02 2.50e+03   1.13e-02 2.58e+00
        pdb=" CG  TYR B 241 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 241 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 241 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 241 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 241 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 241 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 241 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 899 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 190
        2.72 -     3.26: 4411
        3.26 -     3.81: 8261
        3.81 -     4.35: 10688
        4.35 -     4.90: 18012
  Nonbonded interactions: 41562
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN C 214 "
            pdb=" OG1 THR C 216 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" OD1 ASN B 214 "
            pdb=" OG1 THR B 216 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" OD1 ASN A 214 "
            pdb=" OG1 THR A 216 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   ARG C 151 "
            pdb=" NH1 ARG C 151 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" O   ARG A 151 "
            pdb=" NH1 ARG A 151 "
     model   vdw
     2.294 3.120
  ... (remaining 41557 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 33 through 59 or (resid 60 through 61 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 62 through 76 or (resid 77 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 78 through 104 or (re \ 
sid 106 through 107 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 108 through 137 or resid 144 through 188 or resid 196 through 284))
  selection = (chain 'B' and (resid 33 through 59 or (resid 60 through 61 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 62 through 80 or (resid 81 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 82 through 84 or (res \ 
id 85 and (name N or name CA or name C or name O or name CB )) or resid 86 throu \ 
gh 102 or (resid 103 and (name N or name CA or name C or name O or name CB )) or \ 
 resid 104 or (resid 106 through 107 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 108 through 137 or resid 144 through 176 or (resid 177 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 178 through 188  \ 
or resid 196 through 200 or (resid 201 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 202 through 212 or (resid 213 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 214 through 284))
  selection = (chain 'C' and (resid 33 through 76 or (resid 77 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 78 through 84 or (resid 85 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 86 through 102 or (resid 103 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 104 through 176 o \ 
r (resid 177 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 
78 through 200 or (resid 201 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 202 through 212 or (resid 213 and (name N or name CA or name C or \ 
 name O or name CB )) or resid 214 through 284))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.540
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.740
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
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      :  0.004   0.054   5310  Z= 0.207
  Angle     :  0.643   9.815   7272  Z= 0.350
  Chirality :  0.047   0.191    872
  Planarity :  0.005   0.041    902
  Dihedral  : 15.410  89.960   1790
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 17.93 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.33), residues: 645
  helix:  0.81 (1.05), residues: 24
  sheet:  0.95 (0.25), residues: 389
  loop :  0.93 (0.44), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 185 
 TYR   0.028   0.002   TYR B 241 
 PHE   0.008   0.001   PHE B 247 
 TRP   0.009   0.001   TRP B 271 
 HIS   0.006   0.002   HIS C 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00406 /  0.21 ( 5310)
  covalent geometry    : angle       0.64284 /  0.35 ( 7272)
  hydrogen bonds       : bond        0.13239 / 10.25 (  222)
  hydrogen bonds       : angle       7.29514 /  5.02 (  753)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A  162 TYR cc_start: 0.8393 (m-80) cc_final: 0.7900 (m-80)
REVERT: B  126 MET cc_start: 0.8158 (mmm) cc_final: 0.7828 (mmm)
  outliers start: 3
  outliers final: 3
  residues processed: 96
  average time/residue: 0.4367
  time to fit residues: 43.9323
Evaluate side-chains
  88 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  147 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    0.0370
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0970
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    7.9990
   overall best weight:    3.6262

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  79 GLN
C  85 GLN
C 144 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.132181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.104501 restraints weight = 4685.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.55
r_work: 0.3158 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.0527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   5310  Z= 0.178
  Angle     :  0.648   9.789   7272  Z= 0.332
  Chirality :  0.049   0.152    872
  Planarity :  0.005   0.040    902
  Dihedral  :  5.123  29.536    717
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 14.31 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.34), residues: 645
  helix:  0.31 (0.98), residues: 24
  sheet:  0.87 (0.25), residues: 397
  loop :  1.15 (0.46), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 121 
 TYR   0.013   0.002   TYR C 225 
 PHE   0.008   0.002   PHE B 247 
 TRP   0.010   0.002   TRP B 271 
 HIS   0.007   0.002   HIS C 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00423 /  0.18 ( 5310)
  covalent geometry    : angle       0.64843 /  0.33 ( 7272)
  hydrogen bonds       : bond        0.03963 /  2.64 (  222)
  hydrogen bonds       : angle       5.74583 /  3.98 (  753)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.118 
Fit side-chains
REVERT: B  126 MET cc_start: 0.8114 (mmm) cc_final: 0.7750 (mmm)
REVERT: B  214 ASN cc_start: 0.8708 (p0) cc_final: 0.8491 (p0)
REVERT: C  162 TYR cc_start: 0.8284 (m-80) cc_final: 0.7764 (m-80)
  outliers start: 19
  outliers final: 13
  residues processed: 100
  average time/residue: 0.4062
  time to fit residues: 42.4253
Evaluate side-chains
  100 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ARG
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  163 SER
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  177 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 66 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 65 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 31 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 63 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 43 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   overall best weight:    4.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  79 GLN
B 144 GLN
C  85 GLN
C 144 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.131911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.104254 restraints weight = 4600.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 1.53
r_work: 0.3160 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.0625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075   5310  Z= 0.197
  Angle     :  0.664   9.982   7272  Z= 0.339
  Chirality :  0.049   0.149    872
  Planarity :  0.005   0.042    902
  Dihedral  :  5.126  28.765    715
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 14.31 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.34), residues: 645
  helix:  0.04 (0.99), residues: 24
  sheet:  0.85 (0.25), residues: 397
  loop :  1.17 (0.47), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 146 
 TYR   0.017   0.002   TYR A 241 
 PHE   0.009   0.002   PHE C 149 
 TRP   0.010   0.002   TRP B 271 
 HIS   0.007   0.002   HIS C 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00472 /  0.20 ( 5310)
  covalent geometry    : angle       0.66437 /  0.34 ( 7272)
  hydrogen bonds       : bond        0.04021 /  2.66 (  222)
  hydrogen bonds       : angle       5.75276 /  3.99 (  753)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A  162 TYR cc_start: 0.8207 (m-80) cc_final: 0.7780 (m-80)
REVERT: B  126 MET cc_start: 0.8076 (mmm) cc_final: 0.7795 (mmm)
REVERT: B  214 ASN cc_start: 0.8676 (p0) cc_final: 0.8436 (p0)
REVERT: C  154 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8743 (tp)
REVERT: C  162 TYR cc_start: 0.8169 (m-80) cc_final: 0.7664 (m-80)
  outliers start: 25
  outliers final: 15
  residues processed: 108
  average time/residue: 0.4099
  time to fit residues: 46.3372
Evaluate side-chains
  104 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  106 ARG
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  163 SER
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  166 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 31 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 42 optimal weight:    9.9990
   chunk 30 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 40 optimal weight:    8.9990
   chunk 11 optimal weight:    0.0010
   overall best weight:    5.7994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  79 GLN
B 144 GLN
C  85 GLN
C 144 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.131059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.103412 restraints weight = 4606.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 1.53
r_work: 0.3135 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.0736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.099   5310  Z= 0.257
  Angle     :  0.737  10.861   7272  Z= 0.375
  Chirality :  0.052   0.162    872
  Planarity :  0.006   0.043    902
  Dihedral  :  5.352  28.392    715
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 15.22 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.34), residues: 645
  helix: -0.17 (0.99), residues: 24
  sheet:  0.78 (0.25), residues: 397
  loop :  1.08 (0.47), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 151 
 TYR   0.020   0.003   TYR A 241 
 PHE   0.010   0.002   PHE C 149 
 TRP   0.013   0.003   TRP B 271 
 HIS   0.007   0.002   HIS B  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00618 /  0.26 ( 5310)
  covalent geometry    : angle       0.73688 /  0.38 ( 7272)
  hydrogen bonds       : bond        0.04426 /  2.93 (  222)
  hydrogen bonds       : angle       5.94209 /  4.12 (  753)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A  162 TYR cc_start: 0.8131 (m-80) cc_final: 0.7818 (m-80)
REVERT: B  126 MET cc_start: 0.8092 (mmm) cc_final: 0.7868 (mmm)
REVERT: B  214 ASN cc_start: 0.8683 (p0) cc_final: 0.8439 (p0)
REVERT: C  154 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8748 (tp)
REVERT: C  162 TYR cc_start: 0.8031 (m-80) cc_final: 0.7711 (m-80)
  outliers start: 20
  outliers final: 14
  residues processed: 98
  average time/residue: 0.3613
  time to fit residues: 37.0197
Evaluate side-chains
  101 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ARG
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  163 SER
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  180 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 3 optimal weight:   20.0000
   chunk 21 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 45 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   chunk 41 optimal weight:    6.9990
   chunk 28 optimal weight:    7.9990
   chunk 4 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    4.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  79 GLN
B 144 GLN
C  85 GLN
C 144 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.131292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.103553 restraints weight = 4705.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 1.54
r_work: 0.3143 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.0753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081   5310  Z= 0.227
  Angle     :  0.698  10.122   7272  Z= 0.355
  Chirality :  0.050   0.148    872
  Planarity :  0.006   0.043    902
  Dihedral  :  5.190  23.809    714
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 15.58 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.34), residues: 645
  helix: -0.12 (0.98), residues: 24
  sheet:  0.80 (0.25), residues: 396
  loop :  1.05 (0.46), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 121 
 TYR   0.023   0.003   TYR A 241 
 PHE   0.010   0.002   PHE C 149 
 TRP   0.011   0.002   TRP B 271 
 HIS   0.007   0.002   HIS C 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00544 /  0.23 ( 5310)
  covalent geometry    : angle       0.69763 /  0.36 ( 7272)
  hydrogen bonds       : bond        0.04167 /  2.76 (  222)
  hydrogen bonds       : angle       5.83308 /  4.04 (  753)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A  162 TYR cc_start: 0.8136 (m-80) cc_final: 0.7803 (m-80)
REVERT: B  126 MET cc_start: 0.8083 (mmm) cc_final: 0.7850 (mmm)
REVERT: B  214 ASN cc_start: 0.8691 (p0) cc_final: 0.8478 (p0)
REVERT: C  154 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8740 (tp)
REVERT: C  162 TYR cc_start: 0.8065 (m-80) cc_final: 0.7826 (m-80)
  outliers start: 24
  outliers final: 20
  residues processed: 108
  average time/residue: 0.3608
  time to fit residues: 40.9336
Evaluate side-chains
  109 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  106 ARG
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  163 SER
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  177 GLU
Chi-restraints excluded: chain C residue  180 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 64 optimal weight:   20.0000
   chunk 43 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 60 optimal weight:    7.9990
   chunk 36 optimal weight:    7.9990
   chunk 12 optimal weight:   10.0000
   chunk 19 optimal weight:    8.9990
   overall best weight:    5.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  79 GLN
A 144 GLN
B 144 GLN
C  85 GLN
C 133 GLN
C 144 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.130804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.103056 restraints weight = 4702.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 1.54
r_work: 0.3131 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.0778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.103   5310  Z= 0.267
  Angle     :  0.742  11.079   7272  Z= 0.380
  Chirality :  0.052   0.149    872
  Planarity :  0.006   0.044    902
  Dihedral  :  5.306  24.546    714
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 14.86 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.34), residues: 645
  helix: -0.21 (0.99), residues: 24
  sheet:  0.78 (0.25), residues: 393
  loop :  0.96 (0.46), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 121 
 TYR   0.024   0.003   TYR A 241 
 PHE   0.011   0.002   PHE C 149 
 TRP   0.013   0.003   TRP B 271 
 HIS   0.007   0.002   HIS B  46 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00645 /  0.27 ( 5310)
  covalent geometry    : angle       0.74193 /  0.38 ( 7272)
  hydrogen bonds       : bond        0.04450 /  2.95 (  222)
  hydrogen bonds       : angle       5.94941 /  4.12 (  753)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 87
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A  162 TYR cc_start: 0.8142 (m-80) cc_final: 0.7878 (m-80)
REVERT: B  154 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8718 (tp)
REVERT: B  214 ASN cc_start: 0.8746 (p0) cc_final: 0.8485 (p0)
REVERT: C  154 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8745 (tp)
  outliers start: 28
  outliers final: 21
  residues processed: 108
  average time/residue: 0.3409
  time to fit residues: 38.7197
Evaluate side-chains
  110 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  106 ARG
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  163 SER
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain C residue  154 LEU
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  253 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 54 optimal weight:    5.9990
   chunk 35 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 26 optimal weight:    7.9990
   overall best weight:    1.9984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  79 GLN
A 144 GLN
B 144 GLN
C  85 GLN
C 133 GLN
C 144 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.133595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.105942 restraints weight = 4676.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.54
r_work: 0.3180 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.0788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5310  Z= 0.124
  Angle     :  0.572   8.287   7272  Z= 0.295
  Chirality :  0.047   0.152    872
  Planarity :  0.005   0.039    902
  Dihedral  :  4.712  20.128    714
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 16.49 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.34), residues: 645
  helix:  0.29 (1.02), residues: 24
  sheet:  0.88 (0.25), residues: 396
  loop :  1.16 (0.47), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 151 
 TYR   0.025   0.002   TYR A 241 
 PHE   0.009   0.001   PHE C 149 
 TRP   0.009   0.001   TRP A 271 
 HIS   0.006   0.001   HIS C 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.12 ( 5310)
  covalent geometry    : angle       0.57241 /  0.29 ( 7272)
  hydrogen bonds       : bond        0.03333 /  2.19 (  222)
  hydrogen bonds       : angle       5.36120 /  3.70 (  753)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A  162 TYR cc_start: 0.8112 (m-80) cc_final: 0.7892 (m-80)
REVERT: B  126 MET cc_start: 0.8093 (mmm) cc_final: 0.7854 (mmm)
REVERT: B  214 ASN cc_start: 0.8645 (p0) cc_final: 0.8391 (p0)
  outliers start: 18
  outliers final: 16
  residues processed: 103
  average time/residue: 0.4425
  time to fit residues: 47.6406
Evaluate side-chains
  102 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  106 ARG
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  163 SER
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  180 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0670
   chunk 19 optimal weight:   10.0000
   chunk 20 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 35 optimal weight:    9.9990
   chunk 49 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 31 optimal weight:    9.9990
   chunk 56 optimal weight:    8.9990
   overall best weight:    1.9524

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  79 GLN
A 144 GLN
C  85 GLN
C 144 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.134180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.106477 restraints weight = 4687.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 1.54
r_work: 0.3185 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.0890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5310  Z= 0.119
  Angle     :  0.561   7.635   7272  Z= 0.289
  Chirality :  0.046   0.151    872
  Planarity :  0.005   0.037    902
  Dihedral  :  4.541  17.470    714
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 16.30 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.34), residues: 645
  helix:  0.56 (1.06), residues: 24
  sheet:  0.93 (0.25), residues: 396
  loop :  1.27 (0.48), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 185 
 TYR   0.028   0.002   TYR B 241 
 PHE   0.010   0.001   PHE C 149 
 TRP   0.008   0.001   TRP A 271 
 HIS   0.006   0.001   HIS C 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.12 ( 5310)
  covalent geometry    : angle       0.56105 /  0.29 ( 7272)
  hydrogen bonds       : bond        0.03233 /  2.12 (  222)
  hydrogen bonds       : angle       5.23578 /  3.61 (  753)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.142 
Fit side-chains
REVERT: B  214 ASN cc_start: 0.8609 (p0) cc_final: 0.8397 (p0)
  outliers start: 18
  outliers final: 17
  residues processed: 103
  average time/residue: 0.4152
  time to fit residues: 44.6559
Evaluate side-chains
  104 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  106 ARG
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  163 SER
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  180 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 16 optimal weight:   20.0000
   chunk 7 optimal weight:    5.9990
   chunk 25 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 31 optimal weight:    9.9990
   chunk 55 optimal weight:   10.0000
   chunk 43 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   overall best weight:    1.5784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  79 GLN
A 144 GLN
C  85 GLN
C 144 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.136388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.108397 restraints weight = 4691.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 1.56
r_work: 0.3194 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.1049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5310  Z= 0.107
  Angle     :  0.541   6.901   7272  Z= 0.279
  Chirality :  0.045   0.152    872
  Planarity :  0.005   0.035    902
  Dihedral  :  4.381  15.571    713
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.67 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.34), residues: 645
  helix:  0.61 (1.06), residues: 24
  sheet:  0.99 (0.25), residues: 396
  loop :  1.26 (0.47), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 151 
 TYR   0.028   0.002   TYR B 241 
 PHE   0.007   0.001   PHE C 149 
 TRP   0.008   0.001   TRP A 271 
 HIS   0.006   0.001   HIS C 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.11 ( 5310)
  covalent geometry    : angle       0.54116 /  0.28 ( 7272)
  hydrogen bonds       : bond        0.03062 /  2.00 (  222)
  hydrogen bonds       : angle       5.08123 /  3.50 (  753)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  162 TYR cc_start: 0.8162 (m-80) cc_final: 0.7942 (m-80)
  outliers start: 17
  outliers final: 16
  residues processed: 101
  average time/residue: 0.4310
  time to fit residues: 45.5405
Evaluate side-chains
  102 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  163 SER
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  180 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 61 optimal weight:    9.9990
   chunk 12 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 48 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   chunk 18 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 20 optimal weight:    8.9990
   chunk 59 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    2.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  79 GLN
A 144 GLN
C  85 GLN
C 144 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.133763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.105814 restraints weight = 4684.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 1.55
r_work: 0.3175 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.0936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5310  Z= 0.141
  Angle     :  0.596   8.410   7272  Z= 0.304
  Chirality :  0.047   0.148    872
  Planarity :  0.005   0.039    902
  Dihedral  :  4.616  16.270    713
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.67 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.34), residues: 645
  helix:  0.53 (1.04), residues: 24
  sheet:  0.97 (0.25), residues: 396
  loop :  1.19 (0.47), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 151 
 TYR   0.029   0.002   TYR B 241 
 PHE   0.009   0.001   PHE C 149 
 TRP   0.008   0.001   TRP A 271 
 HIS   0.007   0.002   HIS C 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.14 ( 5310)
  covalent geometry    : angle       0.59551 /  0.30 ( 7272)
  hydrogen bonds       : bond        0.03429 /  2.24 (  222)
  hydrogen bonds       : angle       5.31494 /  3.66 (  753)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A  162 TYR cc_start: 0.8121 (m-80) cc_final: 0.7913 (m-80)
  outliers start: 17
  outliers final: 16
  residues processed: 99
  average time/residue: 0.4039
  time to fit residues: 41.9321
Evaluate side-chains
  103 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  180 SER
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  163 SER
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  180 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   chunk 58 optimal weight:   10.0000
   chunk 63 optimal weight:    9.9990
   chunk 2 optimal weight:    9.9990
   chunk 6 optimal weight:    0.6980
   chunk 19 optimal weight:   10.0000
   chunk 65 optimal weight:    8.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    4.7388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  79 GLN
A 144 GLN
C  85 GLN
C 144 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.131728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.103711 restraints weight = 4744.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 1.56
r_work: 0.3146 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.0893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078   5310  Z= 0.221
  Angle     :  0.699  10.148   7272  Z= 0.355
  Chirality :  0.050   0.149    872
  Planarity :  0.006   0.038    902
  Dihedral  :  5.013  17.386    713
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 16.30 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.33), residues: 645
  helix:  0.13 (1.00), residues: 24
  sheet:  0.84 (0.25), residues: 396
  loop :  1.06 (0.46), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 151 
 TYR   0.026   0.003   TYR B 241 
 PHE   0.011   0.002   PHE C 149 
 TRP   0.010   0.002   TRP B 271 
 HIS   0.009   0.002   HIS C 148 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00529 /  0.22 ( 5310)
  covalent geometry    : angle       0.69899 /  0.35 ( 7272)
  hydrogen bonds       : bond        0.04081 /  2.68 (  222)
  hydrogen bonds       : angle       5.70710 /  3.94 (  753)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3148.12 seconds
wall clock time: 53 minutes 54.85 seconds (3234.85 seconds total)