Starting phenix.real_space_refine
on Thu Jul  2 10:42:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rk4_19259/07_2026/8rk4_19259.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rk4_19259/07_2026/8rk4_19259.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rk4_19259/07_2026/8rk4_19259.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rk4_19259/07_2026/8rk4_19259.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rk4_19259/07_2026/8rk4_19259.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rk4_19259/07_2026/8rk4_19259.map"
  }
  resolution = 4.74
  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=   0.002
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      42      5.16       5
     C    5313      2.51       5
     N    1455      2.21       5
     O    1563      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8373
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 2791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 373, 2791
          Classifications: {'peptide': 373}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 353}
  Restraints were copied for chains:
    A, C
  Time building chain proxies: 2.16, per 1000 atoms: 0.26
  Number of scatterers: 8373
  At special positions: 0
  Unit cell: (88.3616, 90.0288, 131.709, 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      42     16.00
     O    1563      8.00
     N    1455      7.00
     C    5313      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=6, symmetry=0
  Number of additional bonds: simple=6, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.68
  Conformation dependent library (CDL) restraints added in 422.3 milliseconds
  

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1968

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 21 sheets defined
      11.3% alpha, 21.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'B' and resid 17 through 19
      No H-bonds generated for 'chain 'B' and resid 17 through 19'
    Processing helix  chain 'B' and resid 20 through 35
      removed outlier: 3.644A  pdb=" N   ASP B  24 " --> pdb=" O   GLY B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 148
    Processing helix  chain 'B' and resid 217 through 228
    Processing helix  chain 'B' and resid 231 through 236
    Processing helix  chain 'A' and resid 17 through 19
      No H-bonds generated for 'chain 'A' and resid 17 through 19'
    Processing helix  chain 'A' and resid 20 through 35
      removed outlier: 3.645A  pdb=" N   ASP A  24 " --> pdb=" O   GLY A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 148
    Processing helix  chain 'A' and resid 217 through 228
    Processing helix  chain 'A' and resid 231 through 236
    Processing helix  chain 'C' and resid 17 through 19
      No H-bonds generated for 'chain 'C' and resid 17 through 19'
    Processing helix  chain 'C' and resid 20 through 35
      removed outlier: 3.645A  pdb=" N   ASP C  24 " --> pdb=" O   GLY C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 148
    Processing helix  chain 'C' and resid 217 through 228
    Processing helix  chain 'C' and resid 231 through 236
    Processing sheet with id=1, first strand: chain 'B' and resid 42 through 44
    Processing sheet with id=2, first strand: chain 'B' and resid 72 through 73
      removed outlier: 3.956A  pdb=" N   ARG B  72 " --> pdb=" O   GLU B  84 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLU B  84 " --> pdb=" O   ARG B  72 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=2
    Processing sheet with id=3, first strand: chain 'B' and resid 95 through 100
      removed outlier: 3.562A  pdb=" N   LYS B 107 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
    Processing sheet with id=4, first strand: chain 'B' and resid 133 through 136
    Processing sheet with id=5, first strand: chain 'B' and resid 189 through 190
    Processing sheet with id=6, first strand: chain 'B' and resid 195 through 202
      removed outlier: 6.077A  pdb=" N   THR B 243 " --> pdb=" O   GLY B 199 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   LYS B 201 " --> pdb=" O   PHE B 241 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   PHE B 241 " --> pdb=" O   LYS B 201 " (cutoff:3.500A)
      removed outlier: 10.304A  pdb=" N   PHE B 242 " --> pdb=" O   CYS B 357 " (cutoff:3.500A)
      removed outlier: 5.270A  pdb=" N   CYS B 357 " --> pdb=" O   PHE B 242 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA B 244 " --> pdb=" O   PHE B 355 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   PHE B 355 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   VAL B 285 " --> pdb=" O   PRO B 358 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   TRP B 360 " --> pdb=" O   THR B 283 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   THR B 283 " --> pdb=" O   TRP B 360 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   MET B 286 " --> pdb=" O   LEU B 328 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU B 328 " --> pdb=" O   MET B 286 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LEU B 288 " --> pdb=" O   VAL B 326 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   TRP B 308 " --> pdb=" O   ARG B 329 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   SER B 331 " --> pdb=" O   ARG B 306 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ARG B 306 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LEU B 307 " --> pdb=" O   ALA B 314 " (cutoff:3.500A)
    Processing sheet with id=7, first strand: chain 'B' and resid 255 through 257
      removed outlier: 3.552A  pdb=" N   TYR B 265 " --> pdb=" O   ALA B 347 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR B 346 " --> pdb=" O   HIS B 296 " (cutoff:3.500A)
    Processing sheet with id=8, first strand: chain 'A' and resid 42 through 44
    Processing sheet with id=9, first strand: chain 'A' and resid 72 through 73
      removed outlier: 3.957A  pdb=" N   ARG A  72 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLU A  84 " --> pdb=" O   ARG A  72 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=9
    Processing sheet with id=10, first strand: chain 'A' and resid 95 through 100
      removed outlier: 3.562A  pdb=" N   LYS A 107 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
    Processing sheet with id=11, first strand: chain 'A' and resid 133 through 136
    Processing sheet with id=12, first strand: chain 'A' and resid 189 through 190
    Processing sheet with id=13, first strand: chain 'A' and resid 195 through 202
      removed outlier: 6.077A  pdb=" N   THR A 243 " --> pdb=" O   GLY A 199 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   LYS A 201 " --> pdb=" O   PHE A 241 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   PHE A 241 " --> pdb=" O   LYS A 201 " (cutoff:3.500A)
      removed outlier: 10.304A  pdb=" N   PHE A 242 " --> pdb=" O   CYS A 357 " (cutoff:3.500A)
      removed outlier: 5.270A  pdb=" N   CYS A 357 " --> pdb=" O   PHE A 242 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA A 244 " --> pdb=" O   PHE A 355 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   PHE A 355 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   VAL A 285 " --> pdb=" O   PRO A 358 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   TRP A 360 " --> pdb=" O   THR A 283 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   THR A 283 " --> pdb=" O   TRP A 360 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   MET A 286 " --> pdb=" O   LEU A 328 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU A 328 " --> pdb=" O   MET A 286 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LEU A 288 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   TRP A 308 " --> pdb=" O   ARG A 329 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER A 331 " --> pdb=" O   ARG A 306 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ARG A 306 " --> pdb=" O   SER A 331 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LEU A 307 " --> pdb=" O   ALA A 314 " (cutoff:3.500A)
    Processing sheet with id=14, first strand: chain 'A' and resid 255 through 257
      removed outlier: 3.552A  pdb=" N   TYR A 265 " --> pdb=" O   ALA A 347 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR A 346 " --> pdb=" O   HIS A 296 " (cutoff:3.500A)
    Processing sheet with id=15, first strand: chain 'C' and resid 42 through 44
    Processing sheet with id=16, first strand: chain 'C' and resid 72 through 73
      removed outlier: 3.956A  pdb=" N   ARG C  72 " --> pdb=" O   GLU C  84 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLU C  84 " --> pdb=" O   ARG C  72 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=16
    Processing sheet with id=17, first strand: chain 'C' and resid 95 through 100
      removed outlier: 3.562A  pdb=" N   LYS C 107 " --> pdb=" O   VAL C  96 " (cutoff:3.500A)
    Processing sheet with id=18, first strand: chain 'C' and resid 133 through 136
    Processing sheet with id=19, first strand: chain 'C' and resid 189 through 190
    Processing sheet with id=20, first strand: chain 'C' and resid 195 through 202
      removed outlier: 6.077A  pdb=" N   THR C 243 " --> pdb=" O   GLY C 199 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   LYS C 201 " --> pdb=" O   PHE C 241 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   PHE C 241 " --> pdb=" O   LYS C 201 " (cutoff:3.500A)
      removed outlier: 10.304A  pdb=" N   PHE C 242 " --> pdb=" O   CYS C 357 " (cutoff:3.500A)
      removed outlier: 5.270A  pdb=" N   CYS C 357 " --> pdb=" O   PHE C 242 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA C 244 " --> pdb=" O   PHE C 355 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   PHE C 355 " --> pdb=" O   ALA C 244 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   VAL C 285 " --> pdb=" O   PRO C 358 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   TRP C 360 " --> pdb=" O   THR C 283 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   THR C 283 " --> pdb=" O   TRP C 360 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   MET C 286 " --> pdb=" O   LEU C 328 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU C 328 " --> pdb=" O   MET C 286 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LEU C 288 " --> pdb=" O   VAL C 326 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   TRP C 308 " --> pdb=" O   ARG C 329 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   SER C 331 " --> pdb=" O   ARG C 306 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ARG C 306 " --> pdb=" O   SER C 331 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU C 307 " --> pdb=" O   ALA C 314 " (cutoff:3.500A)
    Processing sheet with id=21, first strand: chain 'C' and resid 255 through 257
      removed outlier: 3.552A  pdb=" N   TYR C 265 " --> pdb=" O   ALA C 347 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR C 346 " --> pdb=" O   HIS C 296 " (cutoff:3.500A)

    180 hydrogen bonds defined for protein.
    468 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: 1.22

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2721
        1.34 -     1.46: 2261
        1.46 -     1.58: 3565
        1.58 -     1.70: 0
        1.70 -     1.82: 72
  Bond restraints: 8619
  Sorted by residual:
  bond pdb=" CB  TRP A  31 "
       pdb=" CG  TRP A  31 "
    ideal  model  delta    sigma   weight residual
    1.498  1.453  0.045 3.10e-02 1.04e+03 2.08e+00
  bond pdb=" CB  TRP B  31 "
       pdb=" CG  TRP B  31 "
    ideal  model  delta    sigma   weight residual
    1.498  1.453  0.045 3.10e-02 1.04e+03 2.07e+00
  bond pdb=" CB  TRP C  31 "
       pdb=" CG  TRP C  31 "
    ideal  model  delta    sigma   weight residual
    1.498  1.454  0.044 3.10e-02 1.04e+03 2.03e+00
  bond pdb=" CB  ARG A  27 "
       pdb=" CG  ARG A  27 "
    ideal  model  delta    sigma   weight residual
    1.520  1.477  0.043 3.00e-02 1.11e+03 2.01e+00
  bond pdb=" CB  ARG B  27 "
       pdb=" CG  ARG B  27 "
    ideal  model  delta    sigma   weight residual
    1.520  1.478  0.042 3.00e-02 1.11e+03 2.00e+00
  ... (remaining 8614 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 11298
        1.57 -     3.13: 389
        3.13 -     4.70: 85
        4.70 -     6.26: 15
        6.26 -     7.83: 6
  Bond angle restraints: 11793
  Sorted by residual:
  angle pdb=" C   ARG C  30 "
        pdb=" N   TRP C  31 "
        pdb=" CA  TRP C  31 "
      ideal   model   delta    sigma   weight residual
     120.44  115.23    5.21 1.36e+00 5.41e-01 1.47e+01
  angle pdb=" C   ARG A  30 "
        pdb=" N   TRP A  31 "
        pdb=" CA  TRP A  31 "
      ideal   model   delta    sigma   weight residual
     120.44  115.23    5.21 1.36e+00 5.41e-01 1.47e+01
  angle pdb=" C   ARG B  30 "
        pdb=" N   TRP B  31 "
        pdb=" CA  TRP B  31 "
      ideal   model   delta    sigma   weight residual
     120.44  115.24    5.20 1.36e+00 5.41e-01 1.46e+01
  angle pdb=" N   TRP C  31 "
        pdb=" CA  TRP C  31 "
        pdb=" C   TRP C  31 "
      ideal   model   delta    sigma   weight residual
     111.14  114.76   -3.62 1.08e+00 8.57e-01 1.12e+01
  angle pdb=" N   TRP A  31 "
        pdb=" CA  TRP A  31 "
        pdb=" C   TRP A  31 "
      ideal   model   delta    sigma   weight residual
     111.14  114.75   -3.61 1.08e+00 8.57e-01 1.11e+01
  ... (remaining 11788 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.25: 4179
       10.25 -    20.50: 459
       20.50 -    30.76: 138
       30.76 -    41.01: 54
       41.01 -    51.26: 30
  Dihedral angle restraints: 4860
    sinusoidal: 1737
      harmonic: 3123
  Sorted by residual:
  dihedral pdb=" C   ASP C  33 "
           pdb=" N   ASP C  33 "
           pdb=" CA  ASP C  33 "
           pdb=" CB  ASP C  33 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.79    9.19     0      2.50e+00 1.60e-01 1.35e+01
  dihedral pdb=" C   ASP B  33 "
           pdb=" N   ASP B  33 "
           pdb=" CA  ASP B  33 "
           pdb=" CB  ASP B  33 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.76    9.16     0      2.50e+00 1.60e-01 1.34e+01
  dihedral pdb=" C   ASP A  33 "
           pdb=" N   ASP A  33 "
           pdb=" CA  ASP A  33 "
           pdb=" CB  ASP A  33 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.72    9.12     0      2.50e+00 1.60e-01 1.33e+01
  ... (remaining 4857 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1130
       0.068 -    0.136: 130
       0.136 -    0.204: 0
       0.204 -    0.271: 2
       0.271 -    0.339: 7
  Chirality restraints: 1269
  Sorted by residual:
  chirality pdb=" CA  ASP C  33 "
            pdb=" N   ASP C  33 "
            pdb=" C   ASP C  33 "
            pdb=" CB  ASP C  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.88e+00
  chirality pdb=" CA  ASP B  33 "
            pdb=" N   ASP B  33 "
            pdb=" C   ASP B  33 "
            pdb=" CB  ASP B  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.86e+00
  chirality pdb=" CA  ASP A  33 "
            pdb=" N   ASP A  33 "
            pdb=" C   ASP A  33 "
            pdb=" CB  ASP A  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.84e+00
  ... (remaining 1266 not shown)

  Planarity restraints: 1524
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C  29 "   -0.026 2.00e-02 2.50e+03   1.70e-02 7.21e+00
        pdb=" CG  TRP C  29 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 TRP C  29 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP C  29 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP C  29 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP C  29 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP C  29 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C  29 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C  29 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP C  29 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  29 "    0.026 2.00e-02 2.50e+03   1.69e-02 7.18e+00
        pdb=" CG  TRP A  29 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  29 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  29 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  29 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  29 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  29 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  29 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  29 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  29 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  29 "   -0.026 2.00e-02 2.50e+03   1.69e-02 7.16e+00
        pdb=" CG  TRP B  29 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  29 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  29 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  29 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  29 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  29 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  29 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  29 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  29 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1521 not shown)

  Histogram of nonbonded interaction distances:
        1.00 -     1.78: 12
        1.78 -     2.56: 150
        2.56 -     3.34: 11059
        3.34 -     4.12: 21107
        4.12 -     4.90: 36858
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 69186
  Sorted by model distance:
  nonbonded pdb=" CE  MET A 157 "
            pdb=" CE  MET C 157 "
     model   vdw
     0.995 3.880
  nonbonded pdb=" CE  MET B 157 "
            pdb=" CE  MET A 157 "
     model   vdw
     0.996 3.880
  nonbonded pdb=" CE  MET B 157 "
            pdb=" CE  MET C 157 "
     model   vdw
     0.996 3.880
  nonbonded pdb=" CE  MET B 157 "
            pdb=" SD  MET A 157 "
     model   vdw
     1.248 3.820
  nonbonded pdb=" SD  MET B 157 "
            pdb=" CE  MET C 157 "
     model   vdw
     1.248 3.820
  ... (remaining 69181 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
  selection = chain 'C'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'B'
  selection = chain 'A'
  selection = chain 'C'
}
Set refine NCS operators
  NCS operators will be refined.
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 group one per residue
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:             1.080
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.130
  Find NCS groups from input model:        0.070
  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:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
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      :  0.011   0.510   8625  Z= 1.019
  Angle     :  0.721   7.831  11793  Z= 0.418
  Chirality :  0.049   0.339   1269
  Planarity :  0.005   0.048   1524
  Dihedral  : 11.118  51.261   2892
  Min Nonbonded Distance : 0.995

Molprobity Statistics.
  All-atom Clashscore : 21.26
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.04 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -1.38 (0.25), residues: 1113
  helix: -1.97 (0.43), residues: 99
  sheet: -1.23 (0.44), residues: 129
  loop : -0.77 (0.21), residues: 885

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  27 
 TYR   0.008   0.001   TYR A 109 
 PHE   0.009   0.001   PHE A 156 
 TRP   0.045   0.002   TRP A  29 
 HIS   0.006   0.002   HIS B 305 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.17 ( 8619)
  covalent geometry    : angle       0.72105 /  0.42 (11793)
  hydrogen bonds       : bond        0.28623 / 18.97 (  180)
  hydrogen bonds       : angle      11.24912 /  7.69 (  468)
  Misc. bond           : bond        0.38086 / 25.88 (    6)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  123 MET cc_start: 0.4576 (ppp) cc_final: 0.1687 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0783
  time to fit residues: 2.7487
Evaluate side-chains
  12 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 49 optimal weight:   20.0000
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0170
   chunk 5 optimal weight:    0.0970
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    0.0970
   chunk 100 optimal weight:    0.0670
   chunk 106 optimal weight:    2.9990
   overall best weight:    0.1752
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.034897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.026480 restraints weight = 59127.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.027058 restraints weight = 47197.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 16)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.027502 restraints weight = 39492.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.027802 restraints weight = 34242.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.028135 restraints weight = 30633.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6845
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8625  Z= 0.122
  Angle     :  0.668   9.777  11793  Z= 0.335
  Chirality :  0.044   0.150   1269
  Planarity :  0.006   0.099   1524
  Dihedral  :  3.863  11.552   1209
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.77 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  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: -0.95 (0.24), residues: 1113
  helix:  0.31 (0.52), residues: 81
  sheet: -1.00 (0.45), residues: 129
  loop : -0.69 (0.21), residues: 903

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  30 
 TYR   0.019   0.002   TYR A 335 
 PHE   0.009   0.002   PHE C 178 
 TRP   0.027   0.002   TRP A 281 
 HIS   0.004   0.001   HIS C 305 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.12 ( 8619)
  covalent geometry    : angle       0.66833 /  0.34 (11793)
  hydrogen bonds       : bond        0.03945 /  2.67 (  180)
  hydrogen bonds       : angle       6.98904 /  4.81 (  468)
  Misc. bond           : bond        0.00182 /  0.13 (    6)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  123 MET cc_start: 0.5078 (ppp) cc_final: 0.3865 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0744
  time to fit residues: 2.1994
Evaluate side-chains
  14 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 102 optimal weight:   10.0000
   chunk 38 optimal weight:    0.8980
   chunk 100 optimal weight:    0.8980
   chunk 18 optimal weight:   40.0000
   chunk 23 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 69 optimal weight:    0.3980
   chunk 3 optimal weight:    0.0770
   chunk 29 optimal weight:    0.0870
   overall best weight:    0.4716
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 352 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.036921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.030107 restraints weight = 53271.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.030595 restraints weight = 42976.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.030987 restraints weight = 36172.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.031294 restraints weight = 31375.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.031537 restraints weight = 27916.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.2984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   8625  Z= 0.101
  Angle     :  0.599   9.752  11793  Z= 0.293
  Chirality :  0.043   0.149   1269
  Planarity :  0.005   0.067   1524
  Dihedral  :  3.730  12.676   1209
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.77 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  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: -0.80 (0.24), residues: 1113
  helix:  1.30 (0.52), residues: 81
  sheet: -1.35 (0.43), residues: 138
  loop : -0.59 (0.21), residues: 894

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  36 
 TYR   0.016   0.001   TYR B 335 
 PHE   0.010   0.001   PHE C 361 
 TRP   0.018   0.002   TRP C  92 
 HIS   0.003   0.001   HIS C 305 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00217 /  0.10 ( 8619)
  covalent geometry    : angle       0.59941 /  0.29 (11793)
  hydrogen bonds       : bond        0.03600 /  2.45 (  180)
  hydrogen bonds       : angle       6.16921 /  4.26 (  468)
  Misc. bond           : bond        0.00118 /  0.08 (    6)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.7036 (ppp) cc_final: 0.6784 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.0557
  time to fit residues: 1.9666
Evaluate side-chains
  18 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 78 optimal weight:    5.9990
   chunk 38 optimal weight:    0.5980
   chunk 70 optimal weight:    0.4980
   chunk 37 optimal weight:   20.0000
   chunk 86 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 76 optimal weight:    8.9990
   chunk 66 optimal weight:    0.3980
   chunk 96 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    2.2984
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  21 HIS
** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 352 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.035215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.026701 restraints weight = 59327.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.027376 restraints weight = 45384.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.027887 restraints weight = 36753.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.028287 restraints weight = 31169.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.028604 restraints weight = 27339.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6847
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   8625  Z= 0.113
  Angle     :  0.588   9.415  11793  Z= 0.294
  Chirality :  0.042   0.143   1269
  Planarity :  0.006   0.095   1524
  Dihedral  :  3.837  16.786   1209
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.58 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  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: -0.83 (0.25), residues: 1113
  helix:  1.67 (0.55), residues: 81
  sheet: -2.15 (0.36), residues: 186
  loop : -0.36 (0.22), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  27 
 TYR   0.026   0.002   TYR B 109 
 PHE   0.011   0.002   PHE C 204 
 TRP   0.016   0.002   TRP C  92 
 HIS   0.006   0.002   HIS C  21 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.11 ( 8619)
  covalent geometry    : angle       0.58809 /  0.29 (11793)
  hydrogen bonds       : bond        0.03854 /  2.65 (  180)
  hydrogen bonds       : angle       5.71780 /  4.00 (  468)
  Misc. bond           : bond        0.00267 /  0.18 (    6)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  332 MET cc_start: 0.8660 (ptm) cc_final: 0.8198 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.0664
  time to fit residues: 1.9368
Evaluate side-chains
  18 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 81 optimal weight:    0.0570
   chunk 51 optimal weight:    9.9990
   chunk 9 optimal weight:    0.1980
   chunk 88 optimal weight:    9.9990
   chunk 99 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0040
   chunk 40 optimal weight:    0.0170
   chunk 75 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.2148
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.036653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.029976 restraints weight = 52562.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.030515 restraints weight = 41215.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.030914 restraints weight = 33916.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.031196 restraints weight = 29209.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.031417 restraints weight = 25962.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.4022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8625  Z= 0.101
  Angle     :  0.590   8.971  11793  Z= 0.296
  Chirality :  0.042   0.161   1269
  Planarity :  0.005   0.066   1524
  Dihedral  :  3.868  17.050   1209
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.77 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  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: -0.85 (0.25), residues: 1113
  helix:  1.47 (0.54), residues: 81
  sheet: -1.78 (0.37), residues: 201
  loop : -0.43 (0.22), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 236 
 TYR   0.019   0.001   TYR B 109 
 PHE   0.006   0.001   PHE B 166 
 TRP   0.016   0.001   TRP C  92 
 HIS   0.002   0.001   HIS C 327 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00211 /  0.10 ( 8619)
  covalent geometry    : angle       0.58973 /  0.30 (11793)
  hydrogen bonds       : bond        0.03443 /  2.32 (  180)
  hydrogen bonds       : angle       5.62582 /  3.87 (  468)
  Misc. bond           : bond        0.00267 /  0.19 (    6)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ASN cc_start: 0.8942 (t0) cc_final: 0.8719 (t0)
REVERT: A  332 MET cc_start: 0.8582 (ptm) cc_final: 0.8340 (ppp)
REVERT: A  366 ASP cc_start: 0.8380 (t0) cc_final: 0.7679 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.0578
  time to fit residues: 1.6550
Evaluate side-chains
  18 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 100 optimal weight:    0.0980
   chunk 107 optimal weight:    0.0570
   chunk 11 optimal weight:    0.2980
   chunk 73 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   chunk 52 optimal weight:    0.7980
   chunk 26 optimal weight:   30.0000
   chunk 31 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0270
   overall best weight:    0.2556
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.036945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.030121 restraints weight = 52829.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.030625 restraints weight = 42265.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.031013 restraints weight = 35436.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.031297 restraints weight = 30745.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.031543 restraints weight = 27478.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.4441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8625  Z= 0.093
  Angle     :  0.573  10.300  11793  Z= 0.285
  Chirality :  0.042   0.160   1269
  Planarity :  0.004   0.049   1524
  Dihedral  :  3.804  16.787   1209
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.31 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  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: -0.75 (0.25), residues: 1113
  helix:  2.20 (0.52), residues: 81
  sheet: -1.97 (0.40), residues: 174
  loop : -0.43 (0.21), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  93 
 TYR   0.021   0.001   TYR B 109 
 PHE   0.008   0.001   PHE B 204 
 TRP   0.016   0.001   TRP A  31 
 HIS   0.002   0.001   HIS B 296 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00200 /  0.09 ( 8619)
  covalent geometry    : angle       0.57344 /  0.28 (11793)
  hydrogen bonds       : bond        0.02940 /  2.01 (  180)
  hydrogen bonds       : angle       5.55156 /  3.82 (  468)
  Misc. bond           : bond        0.00161 /  0.11 (    6)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 MET cc_start: 0.9040 (tmm) cc_final: 0.8833 (tmm)
REVERT: A  332 MET cc_start: 0.8675 (ptm) cc_final: 0.8396 (ppp)
REVERT: A  360 TRP cc_start: 0.6705 (t60) cc_final: 0.6438 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0419
  time to fit residues: 1.2697
Evaluate side-chains
  16 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 103 optimal weight:    0.9990
   chunk 82 optimal weight:   40.0000
   chunk 74 optimal weight:   30.0000
   chunk 29 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0170
   chunk 85 optimal weight:    0.0010
   chunk 31 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0980
   chunk 63 optimal weight:    7.9990
   overall best weight:    0.3624
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.036835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.028023 restraints weight = 56382.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.028743 restraints weight = 42640.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.029281 restraints weight = 34278.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.029675 restraints weight = 28912.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.030001 restraints weight = 25302.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6800
moved from start:          0.4727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8625  Z= 0.100
  Angle     :  0.591  10.446  11793  Z= 0.292
  Chirality :  0.043   0.170   1269
  Planarity :  0.004   0.046   1524
  Dihedral  :  3.979  17.948   1209
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.58 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  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: -0.82 (0.25), residues: 1113
  helix:  1.53 (0.51), residues: 81
  sheet: -1.78 (0.36), residues: 201
  loop : -0.40 (0.22), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  93 
 TYR   0.011   0.001   TYR A 109 
 PHE   0.006   0.001   PHE A 166 
 TRP   0.010   0.001   TRP C 140 
 HIS   0.002   0.001   HIS B  21 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00216 /  0.10 ( 8619)
  covalent geometry    : angle       0.59051 /  0.29 (11793)
  hydrogen bonds       : bond        0.03578 /  2.37 (  180)
  hydrogen bonds       : angle       5.46817 /  3.75 (  468)
  Misc. bond           : bond        0.00136 /  0.09 (    6)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  332 MET cc_start: 0.8377 (ptm) cc_final: 0.7735 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0385
  time to fit residues: 1.0964
Evaluate side-chains
  15 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 20 optimal weight:    0.0470
   chunk 72 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0170
   chunk 5 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 105 optimal weight:    0.1980
   chunk 7 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0870
   chunk 26 optimal weight:   20.0000
   chunk 55 optimal weight:    5.9990
   overall best weight:    0.2696
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.036774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.028893 restraints weight = 54624.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.029657 restraints weight = 39206.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.030220 restraints weight = 30725.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.030625 restraints weight = 25463.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.030955 restraints weight = 22005.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.4920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8625  Z= 0.087
  Angle     :  0.590  11.474  11793  Z= 0.280
  Chirality :  0.041   0.160   1269
  Planarity :  0.004   0.043   1524
  Dihedral  :  3.643  16.143   1209
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.04 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -0.59 (0.25), residues: 1113
  helix:  2.43 (0.51), residues: 81
  sheet: -1.69 (0.37), residues: 201
  loop : -0.31 (0.22), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  27 
 TYR   0.009   0.001   TYR B 109 
 PHE   0.006   0.001   PHE C 166 
 TRP   0.027   0.001   TRP B  31 
 HIS   0.002   0.000   HIS C 296 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00186 /  0.09 ( 8619)
  covalent geometry    : angle       0.58982 /  0.28 (11793)
  hydrogen bonds       : bond        0.02928 /  1.96 (  180)
  hydrogen bonds       : angle       4.97884 /  3.42 (  468)
  Misc. bond           : bond        0.00132 /  0.09 (    6)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.4626 (ppp) cc_final: 0.2953 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0336
  time to fit residues: 1.0610
Evaluate side-chains
  16 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 62 optimal weight:    0.0020
   chunk 35 optimal weight:    0.2980
   chunk 23 optimal weight:    4.9990
   chunk 92 optimal weight:    6.9990
   chunk 104 optimal weight:    0.7980
   chunk 39 optimal weight:    9.9990
   chunk 60 optimal weight:    2.9990
   chunk 96 optimal weight:    0.6980
   chunk 56 optimal weight:    6.9990
   chunk 63 optimal weight:   20.0000
   chunk 110 optimal weight:    8.9990
   overall best weight:    0.9590
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.036604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.027840 restraints weight = 57457.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.028576 restraints weight = 43085.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.029130 restraints weight = 34549.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.029571 restraints weight = 28981.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.029915 restraints weight = 25199.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6843
moved from start:          0.5010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8625  Z= 0.084
  Angle     :  0.576  10.286  11793  Z= 0.268
  Chirality :  0.041   0.145   1269
  Planarity :  0.004   0.038   1524
  Dihedral  :  3.636  16.234   1209
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.31 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -0.49 (0.25), residues: 1113
  helix:  2.75 (0.52), residues: 81
  sheet: -1.81 (0.37), residues: 186
  loop : -0.25 (0.22), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 329 
 TYR   0.008   0.001   TYR C 109 
 PHE   0.006   0.001   PHE C 166 
 TRP   0.024   0.001   TRP B  31 
 HIS   0.002   0.001   HIS C 296 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00182 /  0.08 ( 8619)
  covalent geometry    : angle       0.57629 /  0.27 (11793)
  hydrogen bonds       : bond        0.02586 /  1.74 (  180)
  hydrogen bonds       : angle       4.87413 /  3.33 (  468)
  Misc. bond           : bond        0.00107 /  0.07 (    6)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.4220 (ppp) cc_final: 0.3066 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.0363
  time to fit residues: 1.1931
Evaluate side-chains
  16 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 105 optimal weight:    0.6980
   chunk 68 optimal weight:    0.0050
   chunk 84 optimal weight:    7.9990
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    8.9990
   chunk 16 optimal weight:    7.9990
   chunk 40 optimal weight:    0.0470
   chunk 71 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 80 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.6094
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.036601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.028789 restraints weight = 54226.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.029548 restraints weight = 39294.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.030110 restraints weight = 30711.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.030522 restraints weight = 25427.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.030839 restraints weight = 21934.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.5140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8625  Z= 0.080
  Angle     :  0.553  10.071  11793  Z= 0.259
  Chirality :  0.041   0.142   1269
  Planarity :  0.004   0.036   1524
  Dihedral  :  3.605  15.782   1209
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.77 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  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: -0.41 (0.25), residues: 1113
  helix:  3.06 (0.52), residues: 81
  sheet: -1.72 (0.36), residues: 186
  loop : -0.22 (0.22), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 329 
 TYR   0.007   0.001   TYR A 109 
 PHE   0.005   0.001   PHE C 166 
 TRP   0.025   0.001   TRP A  31 
 HIS   0.002   0.001   HIS C 296 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00173 /  0.08 ( 8619)
  covalent geometry    : angle       0.55268 /  0.26 (11793)
  hydrogen bonds       : bond        0.02390 /  1.60 (  180)
  hydrogen bonds       : angle       4.64561 /  3.19 (  468)
  Misc. bond           : bond        0.00128 /  0.09 (    6)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.4581 (ppp) cc_final: 0.2685 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.0311
  time to fit residues: 0.9891
Evaluate side-chains
  18 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 96 optimal weight:    0.0000
   chunk 52 optimal weight:    0.0070
   chunk 39 optimal weight:   10.0000
   chunk 22 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0020
   chunk 79 optimal weight:    8.9990
   chunk 17 optimal weight:    0.5980
   chunk 64 optimal weight:    7.9990
   chunk 27 optimal weight:   10.0000
   overall best weight:    0.2410
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.037648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.028761 restraints weight = 55371.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.029538 restraints weight = 41716.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.030097 restraints weight = 33437.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.030553 restraints weight = 28127.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.030870 restraints weight = 24413.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6830
moved from start:          0.5394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   8625  Z= 0.080
  Angle     :  0.543   9.850  11793  Z= 0.255
  Chirality :  0.041   0.148   1269
  Planarity :  0.004   0.035   1524
  Dihedral  :  3.462  14.706   1209
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.31 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  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: -0.24 (0.26), residues: 1113
  helix:  3.36 (0.51), residues: 81
  sheet: -1.08 (0.31), residues: 264
  loop : -0.15 (0.24), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 329 
 TYR   0.007   0.001   TYR C 335 
 PHE   0.006   0.001   PHE C 166 
 TRP   0.025   0.001   TRP B  31 
 HIS   0.002   0.001   HIS C 296 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00169 /  0.08 ( 8619)
  covalent geometry    : angle       0.54314 /  0.25 (11793)
  hydrogen bonds       : bond        0.02215 /  1.48 (  180)
  hydrogen bonds       : angle       4.38152 /  3.00 (  468)
  Misc. bond           : bond        0.00123 /  0.08 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1022.87 seconds
wall clock time: 18 minutes 31.19 seconds (1111.19 seconds total)