Starting phenix.real_space_refine
on Sun May  3 09:54:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/11no_75867/05_2026/11no_75867.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/11no_75867/05_2026/11no_75867.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/11no_75867/05_2026/11no_75867.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/11no_75867/05_2026/11no_75867.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/11no_75867/05_2026/11no_75867.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/11no_75867/05_2026/11no_75867.map"
  }
  resolution = 2.1
  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=   0.000 sd=   0.009
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      44      5.16       5
     C    6588      2.51       5
     N    1860      2.21       5
     O    3595      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12087
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "B"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "C"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "D"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324}
    Chain: "A"
      Number of atoms: 409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 409, 409
          Classifications: {'water': 409}
          Link IDs: {None: 408}
    Chain: "B"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 401
          Classifications: {'water': 401}
          Link IDs: {None: 400}
    Chain: "C"
      Number of atoms: 399
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 399
          Classifications: {'water': 399}
          Link IDs: {None: 398}
    Chain: "D"
      Number of atoms: 406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 406, 406
          Classifications: {'water': 406}
          Link IDs: {None: 405}
  Time building chain proxies: 3.21, per 1000 atoms: 0.27
  Number of scatterers: 12087
  At special positions: 0
  Unit cell: (100.695, 80.115, 109.515, 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      44     16.00
     O    3595      8.00
     N    1860      7.00
     C    6588      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: 1.02
  Conformation dependent library (CDL) restraints added in 307.8 milliseconds
  

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2520

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 8 sheets defined
      54.4% alpha, 12.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 23
    Processing helix  chain 'A' and resid 35 through 45
      removed outlier: 4.390A  pdb=" N   LYS A  41 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ARG A  42 " --> pdb=" O   SER A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 64
    Processing helix  chain 'A' and resid 66 through 70
    Processing helix  chain 'A' and resid 79 through 84
      removed outlier: 3.855A  pdb=" N   TYR A  84 " --> pdb=" O   HIS A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 100
    Processing helix  chain 'A' and resid 129 through 140
    Processing helix  chain 'A' and resid 159 through 180
    Processing helix  chain 'A' and resid 197 through 219
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 244 through 260
      removed outlier: 3.614A  pdb=" N   THR A 259 " --> pdb=" O   ALA A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 288
    Processing helix  chain 'A' and resid 306 through 314
    Processing helix  chain 'A' and resid 316 through 318
      No H-bonds generated for 'chain 'A' and resid 316 through 318'
    Processing helix  chain 'A' and resid 319 through 338
    Processing helix  chain 'B' and resid 8 through 23
      removed outlier: 3.548A  pdb=" N   VAL B  23 " --> pdb=" O   ALA B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 47
      removed outlier: 4.429A  pdb=" N   LYS B  41 " --> pdb=" O   GLY B  37 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ARG B  42 " --> pdb=" O   SER B  38 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ILE B  46 " --> pdb=" O   ARG B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 79 through 84
      removed outlier: 3.801A  pdb=" N   TYR B  84 " --> pdb=" O   HIS B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 100
    Processing helix  chain 'B' and resid 129 through 140
    Processing helix  chain 'B' and resid 159 through 180
    Processing helix  chain 'B' and resid 197 through 219
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 244 through 258
    Processing helix  chain 'B' and resid 275 through 288
    Processing helix  chain 'B' and resid 306 through 314
    Processing helix  chain 'B' and resid 316 through 318
      No H-bonds generated for 'chain 'B' and resid 316 through 318'
    Processing helix  chain 'B' and resid 319 through 338
    Processing helix  chain 'C' and resid 8 through 23
    Processing helix  chain 'C' and resid 35 through 47
      removed outlier: 4.374A  pdb=" N   LYS C  41 " --> pdb=" O   GLY C  37 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   ARG C  42 " --> pdb=" O   SER C  38 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ILE C  46 " --> pdb=" O   ARG C  42 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 64
    Processing helix  chain 'C' and resid 66 through 70
    Processing helix  chain 'C' and resid 81 through 85
    Processing helix  chain 'C' and resid 92 through 100
    Processing helix  chain 'C' and resid 129 through 140
    Processing helix  chain 'C' and resid 159 through 180
    Processing helix  chain 'C' and resid 197 through 219
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 244 through 260
      removed outlier: 3.596A  pdb=" N   THR C 259 " --> pdb=" O   ALA C 255 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 275 through 288
    Processing helix  chain 'C' and resid 302 through 314
      removed outlier: 3.538A  pdb=" N   GLN C 306 " --> pdb=" O   GLY C 302 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   SER C 308 " --> pdb=" O   ALA C 304 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   ALA C 309 " --> pdb=" O   LEU C 305 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 318
      No H-bonds generated for 'chain 'C' and resid 316 through 318'
    Processing helix  chain 'C' and resid 319 through 338
    Processing helix  chain 'D' and resid 8 through 23
    Processing helix  chain 'D' and resid 35 through 46
      removed outlier: 4.394A  pdb=" N   LYS D  41 " --> pdb=" O   GLY D  37 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   ARG D  42 " --> pdb=" O   SER D  38 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE D  46 " --> pdb=" O   ARG D  42 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 64
    Processing helix  chain 'D' and resid 66 through 70
    Processing helix  chain 'D' and resid 79 through 84
      removed outlier: 3.844A  pdb=" N   TYR D  84 " --> pdb=" O   HIS D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 92 through 100
    Processing helix  chain 'D' and resid 129 through 140
    Processing helix  chain 'D' and resid 159 through 180
    Processing helix  chain 'D' and resid 197 through 219
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 244 through 260
      removed outlier: 3.623A  pdb=" N   THR D 259 " --> pdb=" O   ALA D 255 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 275 through 288
    Processing helix  chain 'D' and resid 306 through 314
    Processing helix  chain 'D' and resid 316 through 318
      No H-bonds generated for 'chain 'D' and resid 316 through 318'
    Processing helix  chain 'D' and resid 319 through 338
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32
      removed outlier: 6.903A  pdb=" N   GLY A  28 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 5.961A  pdb=" N   VAL A  76 " --> pdb=" O   GLY A  28 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   LEU A  30 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 5.876A  pdb=" N   LEU A  78 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   ALA A  32 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   GLY A  74 " --> pdb=" O   VAL A 103 " (cutoff:3.500A)
      removed outlier: 7.776A  pdb=" N   GLY A 105 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   VAL A  76 " --> pdb=" O   GLY A 105 " (cutoff:3.500A)
      removed outlier: 7.894A  pdb=" N   LYS A 107 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   LEU A  78 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   VAL A 104 " --> pdb=" O   PHE A 144 " (cutoff:3.500A)
      removed outlier: 8.339A  pdb=" N   LYS A 146 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   ILE A 106 " --> pdb=" O   LYS A 146 " (cutoff:3.500A)
      removed outlier: 8.512A  pdb=" N   ARG A 148 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   LEU A 228 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114
    Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 32
      removed outlier: 6.799A  pdb=" N   GLY B  28 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   VAL B  76 " --> pdb=" O   GLY B  28 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   LEU B  30 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 5.822A  pdb=" N   LEU B  78 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   ALA B  32 " --> pdb=" O   LEU B  78 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   VAL B 104 " --> pdb=" O   PHE B 144 " (cutoff:3.500A)
      removed outlier: 8.407A  pdb=" N   LYS B 146 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   ILE B 106 " --> pdb=" O   LYS B 146 " (cutoff:3.500A)
      removed outlier: 8.707A  pdb=" N   ARG B 148 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   LEU B 228 " --> pdb=" O   THR B 268 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 114
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 32
      removed outlier: 6.884A  pdb=" N   GLY C  28 " --> pdb=" O   GLY C  74 " (cutoff:3.500A)
      removed outlier: 5.956A  pdb=" N   VAL C  76 " --> pdb=" O   GLY C  28 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   LEU C  30 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   LEU C  78 " --> pdb=" O   LEU C  30 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   ALA C  32 " --> pdb=" O   LEU C  78 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   VAL C 104 " --> pdb=" O   PHE C 144 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   LYS C 146 " --> pdb=" O   VAL C 104 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ILE C 106 " --> pdb=" O   LYS C 146 " (cutoff:3.500A)
      removed outlier: 8.492A  pdb=" N   ARG C 148 " --> pdb=" O   ILE C 106 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   TRP C 147 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLU C 187 " --> pdb=" O   TRP C 147 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   LEU C 228 " --> pdb=" O   THR C 268 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114
    Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32
      removed outlier: 6.859A  pdb=" N   GLY D  28 " --> pdb=" O   GLY D  74 " (cutoff:3.500A)
      removed outlier: 5.952A  pdb=" N   VAL D  76 " --> pdb=" O   GLY D  28 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   LEU D  30 " --> pdb=" O   VAL D  76 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   LEU D  78 " --> pdb=" O   LEU D  30 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   ALA D  32 " --> pdb=" O   LEU D  78 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   VAL D 104 " --> pdb=" O   PHE D 144 " (cutoff:3.500A)
      removed outlier: 8.261A  pdb=" N   LYS D 146 " --> pdb=" O   VAL D 104 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ILE D 106 " --> pdb=" O   LYS D 146 " (cutoff:3.500A)
      removed outlier: 8.482A  pdb=" N   ARG D 148 " --> pdb=" O   ILE D 106 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   LEU D 228 " --> pdb=" O   THR D 268 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114

    583 hydrogen bonds defined for protein.
    1686 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: 1.90

  Time building geometry restraints manager: 1.32 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2753
        1.33 -     1.45: 1780
        1.45 -     1.57: 6081
        1.57 -     1.69: 2
        1.69 -     1.81: 56
  Bond restraints: 10672
  Sorted by residual:
  bond pdb=" N   GLN A 125 "
       pdb=" CA  GLN A 125 "
    ideal  model  delta    sigma   weight residual
    1.454  1.499 -0.045 1.17e-02 7.31e+03 1.46e+01
  bond pdb=" N   ILE A 106 "
       pdb=" CA  ILE A 106 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.038 1.11e-02 8.12e+03 1.15e+01
  bond pdb=" N   ILE B 106 "
       pdb=" CA  ILE B 106 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.038 1.14e-02 7.69e+03 1.11e+01
  bond pdb=" N   ASP A 128 "
       pdb=" CA  ASP A 128 "
    ideal  model  delta    sigma   weight residual
    1.456  1.499 -0.042 1.28e-02 6.10e+03 1.09e+01
  bond pdb=" N   VAL B  76 "
       pdb=" CA  VAL B  76 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.17e-02 7.31e+03 1.04e+01
  ... (remaining 10667 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 13409
        1.53 -     3.05: 891
        3.05 -     4.58: 131
        4.58 -     6.10: 28
        6.10 -     7.63: 5
  Bond angle restraints: 14464
  Sorted by residual:
  angle pdb=" CA  PHE C 144 "
        pdb=" CB  PHE C 144 "
        pdb=" CG  PHE C 144 "
      ideal   model   delta    sigma   weight residual
     113.80  118.54   -4.74 1.00e+00 1.00e+00 2.25e+01
  angle pdb=" CA  PHE A 144 "
        pdb=" CB  PHE A 144 "
        pdb=" CG  PHE A 144 "
      ideal   model   delta    sigma   weight residual
     113.80  118.51   -4.71 1.00e+00 1.00e+00 2.22e+01
  angle pdb=" CA  PHE D 144 "
        pdb=" CB  PHE D 144 "
        pdb=" CG  PHE D 144 "
      ideal   model   delta    sigma   weight residual
     113.80  118.15   -4.35 1.00e+00 1.00e+00 1.89e+01
  angle pdb=" CA  PHE B 144 "
        pdb=" CB  PHE B 144 "
        pdb=" CG  PHE B 144 "
      ideal   model   delta    sigma   weight residual
     113.80  117.91   -4.11 1.00e+00 1.00e+00 1.69e+01
  angle pdb=" C   PRO C 262 "
        pdb=" CA  PRO C 262 "
        pdb=" CB  PRO C 262 "
      ideal   model   delta    sigma   weight residual
     111.85  106.06    5.79 1.42e+00 4.96e-01 1.66e+01
  ... (remaining 14459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 6069
       17.93 -    35.86: 296
       35.86 -    53.79: 80
       53.79 -    71.71: 37
       71.71 -    89.64: 22
  Dihedral angle restraints: 6504
    sinusoidal: 2572
      harmonic: 3932
  Sorted by residual:
  dihedral pdb=" C   PHE A 144 "
           pdb=" N   PHE A 144 "
           pdb=" CA  PHE A 144 "
           pdb=" CB  PHE A 144 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.35    8.75     0      2.50e+00 1.60e-01 1.22e+01
  dihedral pdb=" CA  HIS C   4 "
           pdb=" C   HIS C   4 "
           pdb=" N   PRO C   5 "
           pdb=" CA  PRO C   5 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.93  -17.07     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  ASP B  66 "
           pdb=" CB  ASP B  66 "
           pdb=" CG  ASP B  66 "
           pdb=" OD1 ASP B  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.77   58.77     1      2.00e+01 2.50e-03 1.16e+01
  ... (remaining 6501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1142
       0.044 -    0.088: 331
       0.088 -    0.131: 127
       0.131 -    0.175: 37
       0.175 -    0.219: 7
  Chirality restraints: 1644
  Sorted by residual:
  chirality pdb=" CA  VAL B 103 "
            pdb=" N   VAL B 103 "
            pdb=" C   VAL B 103 "
            pdb=" CB  VAL B 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  VAL B 186 "
            pdb=" N   VAL B 186 "
            pdb=" C   VAL B 186 "
            pdb=" CB  VAL B 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  PHE A 144 "
            pdb=" N   PHE A 144 "
            pdb=" C   PHE A 144 "
            pdb=" CB  PHE A 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.81e-01
  ... (remaining 1641 not shown)

  Planarity restraints: 1880
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 144 "   -0.013 2.00e-02 2.50e+03   2.64e-02 6.99e+00
        pdb=" C   PHE A 144 "    0.046 2.00e-02 2.50e+03
        pdb=" O   PHE A 144 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ALA A 145 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 147 "   -0.016 2.00e-02 2.50e+03   1.59e-02 6.32e+00
        pdb=" CG  TRP D 147 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 147 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 147 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 147 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 147 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 147 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 147 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 147 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 147 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 326 "   -0.011 2.00e-02 2.50e+03   2.14e-02 4.56e+00
        pdb=" C   GLU B 326 "    0.037 2.00e-02 2.50e+03
        pdb=" O   GLU B 326 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   TYR B 327 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1877 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 2246
        2.76 -     3.29: 12579
        3.29 -     3.83: 23772
        3.83 -     4.36: 29163
        4.36 -     4.90: 45151
  Nonbonded interactions: 112911
  Sorted by model distance:
  nonbonded pdb=" O   GLN A  60 "
            pdb=" OG1 THR A  64 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   ARG B  42 "
            pdb=" OG  SER B  45 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   HOH C 456 "
            pdb=" O   HOH C 617 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OD1 ASP B  17 "
            pdb=" O   HOH B 401 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   ALA D  32 "
            pdb=" O   HOH D 401 "
     model   vdw
     2.305 3.040
  ... (remaining 112906 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.570
  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:             0.020
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.770
  Find NCS groups from input model:        0.160
  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:5.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.071  10672  Z= 0.398
  Angle     :  0.830   7.631  14464  Z= 0.528
  Chirality :  0.051   0.219   1644
  Planarity :  0.006   0.043   1880
  Dihedral  : 13.948  89.642   3984
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  1.17 %
    Favored  : 97.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.12 (0.22), residues: 1364
  helix:  1.75 (0.19), residues: 708
  sheet: -1.46 (0.41), residues: 124
  loop :  0.04 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.003   ARG C 200 
 TYR   0.019   0.003   TYR B 213 
 PHE   0.024   0.003   PHE A 144 
 TRP   0.042   0.005   TRP D 147 
 HIS   0.009   0.002   HIS D 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00660 (10672)
  covalent geometry    : angle       0.82968 (14464)
  hydrogen bonds       : bond        0.14451 (  583)
  hydrogen bonds       : angle       5.73972 ( 1686)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 0.484 
Fit side-chains
REVERT: A   49 GLU cc_start: 0.7182 (pm20) cc_final: 0.6949 (pm20)
REVERT: A   52 GLU cc_start: 0.8261 (tt0) cc_final: 0.7528 (tm-30)
REVERT: A   66 ASP cc_start: 0.6949 (t70) cc_final: 0.6717 (m-30)
REVERT: A  242 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7833 (mmtm)
REVERT: B   42 ARG cc_start: 0.6709 (mtp180) cc_final: 0.6494 (mmp80)
REVERT: B  303 ARG cc_start: 0.7747 (mtp180) cc_final: 0.7227 (ptm160)
REVERT: C   52 GLU cc_start: 0.7923 (tt0) cc_final: 0.7487 (tm-30)
REVERT: C  341 LYS cc_start: 0.8502 (mttt) cc_final: 0.8255 (mtpt)
REVERT: D   66 ASP cc_start: 0.6829 (t70) cc_final: 0.6602 (m-30)
REVERT: D  303 ARG cc_start: 0.7648 (mtm110) cc_final: 0.7048 (ptm160)
  outliers start: 14
  outliers final: 4
  residues processed: 147
  average time/residue: 0.9177
  time to fit residues: 142.1857
Evaluate side-chains
  92 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  295 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 168 ASN
A 241 GLN
A 306 GLN
B  80 HIS
B 241 GLN
C 241 GLN
C 306 GLN
D 241 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.137732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.101868 restraints weight = 10151.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 1.26
r_work: 0.3007 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.1479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10672  Z= 0.146
  Angle     :  0.574   6.002  14464  Z= 0.307
  Chirality :  0.044   0.149   1644
  Planarity :  0.004   0.035   1880
  Dihedral  :  5.588  55.844   1480
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  6.65 %
    Favored  : 91.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.79 (0.22), residues: 1364
  helix:  2.40 (0.19), residues: 712
  sheet: -0.38 (0.37), residues: 168
  loop : -0.01 (0.25), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 330 
 TYR   0.024   0.003   TYR C 213 
 PHE   0.011   0.002   PHE B  57 
 TRP   0.021   0.003   TRP D 147 
 HIS   0.004   0.001   HIS B  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (10672)
  covalent geometry    : angle       0.57444 (14464)
  hydrogen bonds       : bond        0.06213 (  583)
  hydrogen bonds       : angle       4.65313 ( 1686)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.479 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7317 (mmtp)
REVERT: A   52 GLU cc_start: 0.8268 (tt0) cc_final: 0.7503 (tm-30)
REVERT: A  139 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8381 (ptpp)
REVERT: A  242 LYS cc_start: 0.8176 (mtmt) cc_final: 0.7824 (mmtm)
REVERT: B   41 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7278 (mmtp)
REVERT: B  303 ARG cc_start: 0.8265 (mtp180) cc_final: 0.7518 (ptm160)
REVERT: C   41 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7369 (mmtp)
REVERT: C  139 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8376 (ptpp)
REVERT: C  341 LYS cc_start: 0.8623 (mttt) cc_final: 0.8387 (mtpt)
REVERT: D  303 ARG cc_start: 0.7933 (mtm110) cc_final: 0.7263 (ptm160)
  outliers start: 20
  outliers final: 8
  residues processed: 108
  average time/residue: 0.8797
  time to fit residues: 100.8395
Evaluate side-chains
  96 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue  139 LYS
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue   41 LYS
Chi-restraints excluded: chain C residue  139 LYS
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 101 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 96 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 241 GLN
A 339 GLN
B 241 GLN
B 306 GLN
C 241 GLN
D 136 GLN
D 241 GLN
D 306 GLN
D 339 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.138443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.102763 restraints weight = 10297.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 1.27
r_work: 0.3020 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 2.91 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10672  Z= 0.120
  Angle     :  0.510   5.801  14464  Z= 0.271
  Chirality :  0.041   0.147   1644
  Planarity :  0.004   0.034   1880
  Dihedral  :  5.448  56.159   1480
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  :  7.10 %
    Favored  : 90.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.99 (0.22), residues: 1364
  helix:  2.65 (0.19), residues: 712
  sheet: -0.79 (0.34), residues: 216
  loop :  0.29 (0.27), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 330 
 TYR   0.021   0.002   TYR C 213 
 PHE   0.011   0.001   PHE C 144 
 TRP   0.014   0.002   TRP D 147 
 HIS   0.003   0.001   HIS B  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10672)
  covalent geometry    : angle       0.50966 (14464)
  hydrogen bonds       : bond        0.05458 (  583)
  hydrogen bonds       : angle       4.47686 ( 1686)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 80
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7347 (mmtp)
REVERT: A   52 GLU cc_start: 0.8251 (tt0) cc_final: 0.7465 (tm-30)
REVERT: A  242 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7797 (mmtm)
REVERT: A  303 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7301 (ptm160)
REVERT: B   41 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7261 (mmtp)
REVERT: B  303 ARG cc_start: 0.8230 (mtp180) cc_final: 0.7451 (ptm160)
REVERT: C   41 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7372 (mmtp)
REVERT: C  341 LYS cc_start: 0.8645 (mttt) cc_final: 0.8416 (mtpt)
REVERT: D  303 ARG cc_start: 0.7908 (mtm110) cc_final: 0.7410 (mmm160)
  outliers start: 24
  outliers final: 7
  residues processed: 97
  average time/residue: 0.9134
  time to fit residues: 93.6730
Evaluate side-chains
  91 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain C residue   41 LYS
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 106 optimal weight:    9.9990
   chunk 81 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 126 optimal weight:    0.9990
   chunk 128 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 136 GLN
B 241 GLN
C 241 GLN
C 319 ASN
D 241 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.138906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.103403 restraints weight = 10320.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 1.27
r_work: 0.3029 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  10672  Z= 0.114
  Angle     :  0.492   5.598  14464  Z= 0.262
  Chirality :  0.041   0.144   1644
  Planarity :  0.004   0.034   1880
  Dihedral  :  5.375  56.111   1480
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  :  7.01 %
    Favored  : 90.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  2.09 (0.23), residues: 1364
  helix:  2.75 (0.19), residues: 712
  sheet: -0.78 (0.34), residues: 216
  loop :  0.32 (0.27), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 330 
 TYR   0.021   0.002   TYR D 213 
 PHE   0.011   0.001   PHE C 144 
 TRP   0.013   0.002   TRP D 147 
 HIS   0.003   0.001   HIS B  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (10672)
  covalent geometry    : angle       0.49239 (14464)
  hydrogen bonds       : bond        0.05174 (  583)
  hydrogen bonds       : angle       4.38370 ( 1686)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.371 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7403 (mmtp)
REVERT: A   52 GLU cc_start: 0.8250 (tt0) cc_final: 0.7505 (tm-30)
REVERT: A  242 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7768 (mmtm)
REVERT: A  303 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7327 (ptm160)
REVERT: B   41 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7324 (mmtp)
REVERT: B  303 ARG cc_start: 0.8196 (mtp180) cc_final: 0.7430 (ptm160)
REVERT: C   41 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7411 (mmtp)
REVERT: C  341 LYS cc_start: 0.8674 (mttt) cc_final: 0.8462 (mtpt)
REVERT: D    2 HIS cc_start: 0.4496 (OUTLIER) cc_final: 0.3972 (m90)
REVERT: D  303 ARG cc_start: 0.7904 (mtm110) cc_final: 0.7242 (ptm160)
  outliers start: 23
  outliers final: 7
  residues processed: 98
  average time/residue: 0.8830
  time to fit residues: 91.7069
Evaluate side-chains
  92 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain C residue   41 LYS
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue    2 HIS
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 122 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9980
   chunk 48 optimal weight:    8.9990
   chunk 21 optimal weight:    4.9990
   chunk 90 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 128 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 95 optimal weight:    4.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 241 GLN
B 241 GLN
C 241 GLN
D 241 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.136010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.100397 restraints weight = 10260.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 1.26
r_work: 0.2984 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 2.87 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10672  Z= 0.146
  Angle     :  0.546   5.826  14464  Z= 0.292
  Chirality :  0.043   0.160   1644
  Planarity :  0.004   0.035   1880
  Dihedral  :  5.591  55.609   1480
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  :  6.92 %
    Favored  : 91.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.94 (0.22), residues: 1364
  helix:  2.65 (0.19), residues: 712
  sheet: -0.90 (0.34), residues: 216
  loop :  0.25 (0.27), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 172 
 TYR   0.027   0.003   TYR A 213 
 PHE   0.011   0.002   PHE C  57 
 TRP   0.018   0.002   TRP A 147 
 HIS   0.003   0.001   HIS B  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (10672)
  covalent geometry    : angle       0.54619 (14464)
  hydrogen bonds       : bond        0.06263 (  583)
  hydrogen bonds       : angle       4.57982 ( 1686)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.489 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7409 (mmtp)
REVERT: A   52 GLU cc_start: 0.8261 (tt0) cc_final: 0.7484 (tm-30)
REVERT: A  242 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7762 (mmtm)
REVERT: A  303 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7430 (ptm160)
REVERT: B   41 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7259 (mmtp)
REVERT: B  303 ARG cc_start: 0.8238 (mtp180) cc_final: 0.7474 (ptm160)
REVERT: C   41 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7425 (mmtp)
REVERT: C  341 LYS cc_start: 0.8718 (mttt) cc_final: 0.8514 (mtpt)
REVERT: D    2 HIS cc_start: 0.4539 (OUTLIER) cc_final: 0.4170 (m90)
REVERT: D  303 ARG cc_start: 0.7973 (mtm110) cc_final: 0.7364 (ptm160)
  outliers start: 23
  outliers final: 10
  residues processed: 98
  average time/residue: 0.8982
  time to fit residues: 93.1738
Evaluate side-chains
  97 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  330 ARG
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain C residue   41 LYS
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue    2 HIS
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  330 ARG
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 126 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 110 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
B 241 GLN
C 241 GLN
D 241 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.136618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.101132 restraints weight = 10224.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 1.26
r_work: 0.2994 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10672  Z= 0.135
  Angle     :  0.529   5.774  14464  Z= 0.283
  Chirality :  0.042   0.152   1644
  Planarity :  0.004   0.034   1880
  Dihedral  :  5.546  55.507   1480
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  7.73 %
    Favored  : 90.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  1.98 (0.22), residues: 1364
  helix:  2.68 (0.19), residues: 712
  sheet: -0.90 (0.34), residues: 216
  loop :  0.27 (0.27), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 172 
 TYR   0.025   0.002   TYR B 213 
 PHE   0.012   0.002   PHE C 144 
 TRP   0.015   0.002   TRP A 147 
 HIS   0.003   0.001   HIS B  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (10672)
  covalent geometry    : angle       0.52881 (14464)
  hydrogen bonds       : bond        0.05894 (  583)
  hydrogen bonds       : angle       4.53350 ( 1686)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7429 (mmtp)
REVERT: A   52 GLU cc_start: 0.8271 (tt0) cc_final: 0.7488 (tm-30)
REVERT: A  242 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7750 (mmtm)
REVERT: A  303 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7364 (ptm160)
REVERT: B   41 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7271 (mmtp)
REVERT: B  303 ARG cc_start: 0.8244 (mtp180) cc_final: 0.7466 (ptm160)
REVERT: C   41 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7414 (mmtp)
REVERT: C  341 LYS cc_start: 0.8730 (mttt) cc_final: 0.8512 (mtpt)
REVERT: D    2 HIS cc_start: 0.4503 (OUTLIER) cc_final: 0.4225 (m90)
REVERT: D  303 ARG cc_start: 0.7979 (mtm110) cc_final: 0.7357 (ptm160)
  outliers start: 18
  outliers final: 10
  residues processed: 93
  average time/residue: 0.9167
  time to fit residues: 89.9387
Evaluate side-chains
  97 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  330 ARG
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain C residue   41 LYS
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue    2 HIS
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  330 ARG
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 85 optimal weight:    7.9990
   chunk 75 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 134 optimal weight:    4.9990
   chunk 105 optimal weight:    0.0970
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 241 GLN
C 241 GLN
D 241 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.139158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.104066 restraints weight = 10283.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 1.26
r_work: 0.3038 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  10672  Z= 0.107
  Angle     :  0.480   5.595  14464  Z= 0.254
  Chirality :  0.040   0.139   1644
  Planarity :  0.003   0.034   1880
  Dihedral  :  5.321  55.556   1480
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  7.91 %
    Favored  : 90.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  2.17 (0.23), residues: 1364
  helix:  2.83 (0.19), residues: 712
  sheet: -0.83 (0.34), residues: 216
  loop :  0.36 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 330 
 TYR   0.019   0.002   TYR C 213 
 PHE   0.013   0.001   PHE C 144 
 TRP   0.009   0.001   TRP D 147 
 HIS   0.002   0.000   HIS B  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (10672)
  covalent geometry    : angle       0.47968 (14464)
  hydrogen bonds       : bond        0.04877 (  583)
  hydrogen bonds       : angle       4.33459 ( 1686)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7430 (mmtp)
REVERT: A   52 GLU cc_start: 0.8229 (tt0) cc_final: 0.7443 (tm-30)
REVERT: A  242 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7717 (mmtm)
REVERT: A  303 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7372 (ptm160)
REVERT: B   41 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7311 (mmtp)
REVERT: B  303 ARG cc_start: 0.8169 (mtp180) cc_final: 0.7360 (ptm160)
REVERT: C   41 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7422 (mmtp)
REVERT: C  341 LYS cc_start: 0.8712 (mttt) cc_final: 0.8502 (mtpt)
REVERT: D  303 ARG cc_start: 0.7920 (mtm110) cc_final: 0.7305 (ptm160)
  outliers start: 16
  outliers final: 7
  residues processed: 93
  average time/residue: 0.8813
  time to fit residues: 86.9259
Evaluate side-chains
  90 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain C residue   41 LYS
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 108 optimal weight:    5.9990
   chunk 109 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 130 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
B 241 GLN
C 241 GLN
D 241 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.138137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.102832 restraints weight = 10235.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 1.26
r_work: 0.3020 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.1903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10672  Z= 0.117
  Angle     :  0.497   5.522  14464  Z= 0.264
  Chirality :  0.041   0.148   1644
  Planarity :  0.004   0.034   1880
  Dihedral  :  5.381  55.560   1480
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  :  8.00 %
    Favored  : 90.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  2.15 (0.23), residues: 1364
  helix:  2.82 (0.19), residues: 712
  sheet: -0.85 (0.34), residues: 216
  loop :  0.34 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 330 
 TYR   0.022   0.002   TYR C 213 
 PHE   0.012   0.001   PHE C 144 
 TRP   0.014   0.002   TRP D 147 
 HIS   0.002   0.001   HIS B  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (10672)
  covalent geometry    : angle       0.49727 (14464)
  hydrogen bonds       : bond        0.05271 (  583)
  hydrogen bonds       : angle       4.37847 ( 1686)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.455 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7407 (mmtp)
REVERT: A   52 GLU cc_start: 0.8246 (tt0) cc_final: 0.7459 (tm-30)
REVERT: A  242 LYS cc_start: 0.8092 (mtmt) cc_final: 0.7706 (mmtm)
REVERT: A  303 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7373 (ptm160)
REVERT: B   41 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7321 (mmtp)
REVERT: B  303 ARG cc_start: 0.8193 (mtp180) cc_final: 0.7409 (ptm160)
REVERT: C   41 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7412 (mmtp)
REVERT: C  341 LYS cc_start: 0.8717 (mttt) cc_final: 0.8508 (mtpt)
REVERT: D  303 ARG cc_start: 0.7945 (mtm110) cc_final: 0.7342 (ptm160)
  outliers start: 17
  outliers final: 8
  residues processed: 91
  average time/residue: 0.8981
  time to fit residues: 86.5009
Evaluate side-chains
  94 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  303 ARG
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain C residue   41 LYS
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  330 ARG
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 101 optimal weight:    6.9990
   chunk 59 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   chunk 117 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0570
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 90 optimal weight:    0.6980
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
B 241 GLN
C 241 GLN
D 241 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.139313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.104915 restraints weight = 10349.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 1.25
r_work: 0.3046 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 2.87 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  10672  Z= 0.106
  Angle     :  0.477   5.707  14464  Z= 0.252
  Chirality :  0.040   0.140   1644
  Planarity :  0.003   0.034   1880
  Dihedral  :  5.270  55.680   1480
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  8.27 %
    Favored  : 90.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  2.25 (0.23), residues: 1364
  helix:  2.91 (0.19), residues: 712
  sheet: -0.81 (0.34), residues: 216
  loop :  0.39 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 330 
 TYR   0.020   0.002   TYR A 213 
 PHE   0.012   0.001   PHE C 144 
 TRP   0.011   0.001   TRP D 147 
 HIS   0.002   0.000   HIS B  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 (10672)
  covalent geometry    : angle       0.47684 (14464)
  hydrogen bonds       : bond        0.04766 (  583)
  hydrogen bonds       : angle       4.28618 ( 1686)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.482 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7434 (mmtp)
REVERT: A   52 GLU cc_start: 0.8234 (tt0) cc_final: 0.7459 (tm-30)
REVERT: A  242 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7702 (mmtm)
REVERT: B   41 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7343 (mmtp)
REVERT: B  303 ARG cc_start: 0.8143 (mtp180) cc_final: 0.7340 (ptm160)
REVERT: C   41 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7400 (mmtp)
REVERT: C  341 LYS cc_start: 0.8713 (mttt) cc_final: 0.8496 (mtpt)
REVERT: D  303 ARG cc_start: 0.7881 (mtm110) cc_final: 0.7290 (ptm160)
  outliers start: 15
  outliers final: 7
  residues processed: 90
  average time/residue: 0.9230
  time to fit residues: 87.7095
Evaluate side-chains
  90 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain C residue   41 LYS
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 118 optimal weight:    6.9990
   chunk 55 optimal weight:    0.5980
   chunk 127 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 119 optimal weight:    3.9990
   chunk 105 optimal weight:    0.1980
   chunk 74 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
B 241 GLN
C 241 GLN
D 241 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.139345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.104033 restraints weight = 10337.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 1.27
r_work: 0.3038 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 2.91 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  10672  Z= 0.107
  Angle     :  0.480   6.008  14464  Z= 0.253
  Chirality :  0.040   0.143   1644
  Planarity :  0.003   0.034   1880
  Dihedral  :  5.260  55.735   1480
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  8.63 %
    Favored  : 90.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  2.24 (0.23), residues: 1364
  helix:  2.91 (0.19), residues: 712
  sheet: -0.79 (0.34), residues: 216
  loop :  0.36 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 330 
 TYR   0.021   0.002   TYR A 213 
 PHE   0.012   0.001   PHE C 144 
 TRP   0.012   0.002   TRP D 147 
 HIS   0.002   0.000   HIS B  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (10672)
  covalent geometry    : angle       0.48002 (14464)
  hydrogen bonds       : bond        0.04850 (  583)
  hydrogen bonds       : angle       4.28254 ( 1686)

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.500 
Fit side-chains
REVERT: A   41 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7426 (mmtp)
REVERT: A   52 GLU cc_start: 0.8246 (tt0) cc_final: 0.7469 (tm-30)
REVERT: A  242 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7705 (mmtm)
REVERT: B   41 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7328 (mmtp)
REVERT: B  303 ARG cc_start: 0.8133 (mtp180) cc_final: 0.7344 (ptm160)
REVERT: C   41 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7395 (mmtp)
REVERT: C  341 LYS cc_start: 0.8711 (mttt) cc_final: 0.8498 (mtpt)
REVERT: D  303 ARG cc_start: 0.7888 (mtm110) cc_final: 0.7352 (ptm160)
  outliers start: 11
  outliers final: 8
  residues processed: 86
  average time/residue: 0.9169
  time to fit residues: 83.4742
Evaluate side-chains
  91 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  330 ARG
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   41 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain C residue   41 LYS
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  343 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 129 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 94 optimal weight:    4.9990
   chunk 133 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   chunk 109 optimal weight:    3.9990
   chunk 128 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
B 241 GLN
C 241 GLN
D 241 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 = 0.138107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.102682 restraints weight = 10305.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 1.26
r_work: 0.3017 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
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      :  0.003   0.047  10672  Z= 0.118
  Angle     :  0.500   6.179  14464  Z= 0.264
  Chirality :  0.041   0.149   1644
  Planarity :  0.004   0.033   1880
  Dihedral  :  5.357  55.586   1480
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 2.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  8.54 %
    Favored  : 90.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  2.18 (0.23), residues: 1364
  helix:  2.87 (0.19), residues: 712
  sheet: -0.83 (0.34), residues: 216
  loop :  0.33 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 330 
 TYR   0.023   0.002   TYR C 213 
 PHE   0.012   0.001   PHE C 144 
 TRP   0.013   0.002   TRP D 147 
 HIS   0.002   0.001   HIS B  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10672)
  covalent geometry    : angle       0.49978 (14464)
  hydrogen bonds       : bond        0.05293 (  583)
  hydrogen bonds       : angle       4.37392 ( 1686)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4820.20 seconds
wall clock time: 82 minutes 57.26 seconds (4977.26 seconds total)