Starting phenix.real_space_refine
on Fri Aug 22 22:42:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rk4_19259/08_2025/8rk4_19259.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rk4_19259/08_2025/8rk4_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_19259/08_2025/8rk4_19259.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rk4_19259/08_2025/8rk4_19259.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rk4_19259/08_2025/8rk4_19259.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rk4_19259/08_2025/8rk4_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-2.0-5787/lib/python3.9/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: 2.25, per 1000 atoms: 0.27
  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: 0.78
  Conformation dependent library (CDL) restraints added in 496.6 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.34
  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: 1.32

  Time building geometry restraints manager: 1.01 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:                  0.010
  Normalize map: mean=0, sd=1:             1.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.870
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.000
  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:1.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
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 aren 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
  covalent geometry    : bond        0.00321 ( 8619)
  covalent geometry    : angle       0.72105 (11793)
  hydrogen bonds       : bond        0.28623 (  180)
  hydrogen bonds       : angle      11.24912 (  468)
  Misc. bond           : bond        0.38086 (    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  : 0.108 
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: 0.0861
  time to fit residues: 2.9909
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  : 0.106 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
** 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: 0.7021
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 aren 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
  covalent geometry    : bond        0.00259 ( 8619)
  covalent geometry    : angle       0.66833 (11793)
  hydrogen bonds       : bond        0.03945 (  180)
  hydrogen bonds       : angle       6.98904 (  468)
  Misc. bond           : bond        0.00182 (    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  : 0.082 
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: 0.0798
  time to fit residues: 2.3481
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  : 0.105 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
A 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 = 43)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.030104 restraints weight = 53279.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.030596 restraints weight = 42953.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.030983 restraints weight = 36137.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.031298 restraints weight = 31398.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.031543 restraints weight = 27845.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.2998

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 : 10.26
  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 aren 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
  covalent geometry    : bond        0.00217 ( 8619)
  covalent geometry    : angle       0.59941 (11793)
  hydrogen bonds       : bond        0.03600 (  180)
  hydrogen bonds       : angle       6.16921 (  468)
  Misc. bond           : bond        0.00118 (    6)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 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  : 0.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.7034 (ppp) cc_final: 0.6783 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.0664
  time to fit residues: 2.3333
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  : 0.105 
-------------------------------------------------------------------------------
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:    0.0970
   chunk 70 optimal weight:    0.9980
   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:    0.0070
   chunk 96 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    2.0200
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C  21 HIS
** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.036011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.027588 restraints weight = 55918.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.028220 restraints weight = 43798.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.028727 restraints weight = 36159.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.029149 restraints weight = 30976.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.029419 restraints weight = 27277.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          0.3527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   8625  Z= 0.106
  Angle     :  0.579   9.563  11793  Z= 0.289
  Chirality :  0.041   0.143   1269
  Planarity :  0.006   0.089   1524
  Dihedral  :  3.757  16.779   1209
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.12 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  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 aren not related in a simple way.
  whole: -0.97 (0.25), residues: 1113
  helix:  1.25 (0.55), residues: 81
  sheet: -2.00 (0.38), residues: 168
  loop : -0.54 (0.21), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 306 
 TYR   0.026   0.002   TYR B 109 
 PHE   0.012   0.001   PHE C 204 
 TRP   0.016   0.002   TRP C  92 
 HIS   0.004   0.002   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 8619)
  covalent geometry    : angle       0.57940 (11793)
  hydrogen bonds       : bond        0.03743 (  180)
  hydrogen bonds       : angle       5.73736 (  468)
  Misc. bond           : bond        0.00148 (    6)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  342 CYS cc_start: 0.8316 (t) cc_final: 0.5399 (t)
REVERT: C  374 ILE cc_start: 0.7277 (mm) cc_final: 0.6994 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0534
  time to fit residues: 2.3559
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  : 0.100 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 81 optimal weight:    4.9990
   chunk 51 optimal weight:    9.9990
   chunk 9 optimal weight:    0.0370
   chunk 88 optimal weight:    9.9990
   chunk 99 optimal weight:    0.5980
   chunk 62 optimal weight:    0.5980
   chunk 79 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0060
   chunk 75 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    0.3874
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 305 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.036423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.027568 restraints weight = 56109.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.028222 restraints weight = 43157.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.028717 restraints weight = 35448.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.029106 restraints weight = 30374.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.029414 restraints weight = 26903.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.4414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8625  Z= 0.114
  Angle     :  0.599   8.762  11793  Z= 0.302
  Chirality :  0.043   0.142   1269
  Planarity :  0.005   0.071   1524
  Dihedral  :  3.848  14.345   1209
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  6.74 %
    Favored  : 92.99 %
  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 aren not related in a simple way.
  whole: -1.40 (0.24), residues: 1113
  helix:  0.19 (0.54), residues: 81
  sheet: -1.29 (0.43), residues: 153
  loop : -1.04 (0.20), residues: 879

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B  30 
 TYR   0.015   0.002   TYR C 109 
 PHE   0.012   0.001   PHE A 156 
 TRP   0.016   0.002   TRP B 281 
 HIS   0.002   0.001   HIS B 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 8619)
  covalent geometry    : angle       0.59902 (11793)
  hydrogen bonds       : bond        0.03550 (  180)
  hydrogen bonds       : angle       5.79645 (  468)
  Misc. bond           : bond        0.00268 (    6)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 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  : 0.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  332 MET cc_start: 0.8762 (ppp) cc_final: 0.8492 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0428
  time to fit residues: 1.3025
Evaluate side-chains
  17 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 12 optimal weight:    8.9990
   chunk 100 optimal weight:    0.0010
   chunk 107 optimal weight:    9.9990
   chunk 11 optimal weight:    0.6980
   chunk 73 optimal weight:    8.9990
   chunk 6 optimal weight:    9.9990
   chunk 52 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0010
   chunk 31 optimal weight:    0.0050
   chunk 30 optimal weight:    0.0670
   overall best weight:    0.1344
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.037131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.028122 restraints weight = 55589.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.028800 restraints weight = 43174.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.029330 restraints weight = 35363.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.029756 restraints weight = 30219.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.030082 restraints weight = 26573.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7013
moved from start:          0.4796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8625  Z= 0.101
  Angle     :  0.551   9.894  11793  Z= 0.269
  Chirality :  0.041   0.126   1269
  Planarity :  0.004   0.044   1524
  Dihedral  :  3.509  11.431   1209
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  6.74 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  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 aren not related in a simple way.
  whole: -1.36 (0.23), residues: 1113
  helix:  1.01 (0.54), residues: 81
  sheet: -1.14 (0.46), residues: 144
  loop : -1.13 (0.19), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  30 
 TYR   0.012   0.001   TYR C 344 
 PHE   0.005   0.001   PHE A 166 
 TRP   0.011   0.001   TRP C  92 
 HIS   0.004   0.001   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 8619)
  covalent geometry    : angle       0.55109 (11793)
  hydrogen bonds       : bond        0.02971 (  180)
  hydrogen bonds       : angle       5.20385 (  468)
  Misc. bond           : bond        0.00139 (    6)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 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  332 MET cc_start: 0.8614 (ppp) cc_final: 0.8370 (ppp)
REVERT: A  360 TRP cc_start: 0.3931 (t60) cc_final: 0.3303 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.0664
  time to fit residues: 1.8671
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  : 0.108 
-------------------------------------------------------------------------------
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:    0.0470
   chunk 22 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   chunk 82 optimal weight:    8.9990
   chunk 74 optimal weight:    9.9990
   chunk 29 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 85 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 63 optimal weight:    8.9990
   overall best weight:    0.8680
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.036549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.027712 restraints weight = 56662.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.028352 restraints weight = 43893.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.028863 restraints weight = 36194.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.029267 restraints weight = 31047.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.029578 restraints weight = 27483.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7020
moved from start:          0.5050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8625  Z= 0.096
  Angle     :  0.559   9.801  11793  Z= 0.279
  Chirality :  0.041   0.160   1269
  Planarity :  0.004   0.038   1524
  Dihedral  :  3.683  16.428   1209
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  7.28 %
    Favored  : 92.45 %
  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 aren not related in a simple way.
  whole: -1.46 (0.24), residues: 1113
  helix:  0.49 (0.52), residues: 81
  sheet: -1.62 (0.41), residues: 177
  loop : -1.02 (0.20), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  30 
 TYR   0.008   0.001   TYR C 335 
 PHE   0.009   0.001   PHE C 204 
 TRP   0.016   0.001   TRP C  31 
 HIS   0.004   0.001   HIS A 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 8619)
  covalent geometry    : angle       0.55912 (11793)
  hydrogen bonds       : bond        0.03463 (  180)
  hydrogen bonds       : angle       5.28060 (  468)
  Misc. bond           : bond        0.00147 (    6)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 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  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  332 MET cc_start: 0.8452 (ppp) cc_final: 0.8229 (ppp)
REVERT: A  360 TRP cc_start: 0.4525 (t60) cc_final: 0.3808 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.0478
  time to fit residues: 1.5383
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  : 0.103 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 72 optimal weight:    0.2980
   chunk 48 optimal weight:    0.0030
   chunk 5 optimal weight:    0.3980
   chunk 36 optimal weight:    9.9990
   chunk 105 optimal weight:    0.0010
   chunk 7 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0970
   chunk 42 optimal weight:    0.3980
   chunk 26 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.1594
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.037270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.028211 restraints weight = 56905.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.028885 restraints weight = 44063.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.029417 restraints weight = 36156.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.029826 restraints weight = 30844.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.030144 restraints weight = 27181.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7017
moved from start:          0.5345

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= 0.085
  Angle     :  0.537   9.716  11793  Z= 0.262
  Chirality :  0.041   0.123   1269
  Planarity :  0.004   0.036   1524
  Dihedral  :  3.499  15.775   1209
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  7.28 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  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 aren not related in a simple way.
  whole: -1.35 (0.24), residues: 1113
  helix:  0.89 (0.50), residues: 81
  sheet: -1.54 (0.39), residues: 186
  loop : -0.96 (0.21), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  30 
 TYR   0.011   0.001   TYR B 344 
 PHE   0.006   0.001   PHE C 156 
 TRP   0.009   0.001   TRP A  92 
 HIS   0.004   0.001   HIS C 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00180 ( 8619)
  covalent geometry    : angle       0.53672 (11793)
  hydrogen bonds       : bond        0.02962 (  180)
  hydrogen bonds       : angle       4.93818 (  468)
  Misc. bond           : bond        0.00159 (    6)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 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  : 0.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  332 MET cc_start: 0.8344 (ppp) cc_final: 0.8117 (ppp)
REVERT: A  360 TRP cc_start: 0.4444 (t60) cc_final: 0.3617 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.0424
  time to fit residues: 1.4070
Evaluate side-chains
  19 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
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:    0.0370
   chunk 35 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 92 optimal weight:    0.8980
   chunk 104 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 60 optimal weight:    0.6980
   chunk 96 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 63 optimal weight:   10.0000
   chunk 110 optimal weight:    8.9990
   overall best weight:    0.5458
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.036953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.028944 restraints weight = 54388.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.029694 restraints weight = 39984.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.030232 restraints weight = 31585.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.030629 restraints weight = 26453.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.030938 restraints weight = 23023.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.5471

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= 0.081
  Angle     :  0.522   9.378  11793  Z= 0.253
  Chirality :  0.040   0.120   1269
  Planarity :  0.004   0.034   1524
  Dihedral  :  3.490  15.876   1209
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  6.47 %
    Favored  : 93.26 %
  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 aren not related in a simple way.
  whole: -1.21 (0.24), residues: 1113
  helix:  1.33 (0.53), residues: 81
  sheet: -1.55 (0.39), residues: 186
  loop : -0.88 (0.21), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  30 
 TYR   0.007   0.001   TYR C 335 
 PHE   0.006   0.001   PHE C 166 
 TRP   0.010   0.001   TRP C  31 
 HIS   0.003   0.001   HIS B 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00172 ( 8619)
  covalent geometry    : angle       0.52173 (11793)
  hydrogen bonds       : bond        0.02818 (  180)
  hydrogen bonds       : angle       4.70840 (  468)
  Misc. bond           : bond        0.00136 (    6)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 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  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.0362
  time to fit residues: 1.1884
Evaluate side-chains
  17 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
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:    0.0270
   chunk 68 optimal weight:    0.0270
   chunk 84 optimal weight:    8.9990
   chunk 33 optimal weight:    0.0030
   chunk 65 optimal weight:    8.9990
   chunk 16 optimal weight:    0.1980
   chunk 40 optimal weight:    9.9990
   chunk 71 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 80 optimal weight:    9.9990
   chunk 29 optimal weight:    0.0970
   overall best weight:    0.0704
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.037071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.028249 restraints weight = 57865.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.028908 restraints weight = 44278.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.029438 restraints weight = 36115.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.029836 restraints weight = 30642.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.030139 restraints weight = 26893.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.5559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   8625  Z= 0.089
  Angle     :  0.554   9.299  11793  Z= 0.276
  Chirality :  0.042   0.207   1269
  Planarity :  0.004   0.032   1524
  Dihedral  :  3.458  15.772   1209
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  7.28 %
    Favored  : 92.45 %
  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 aren not related in a simple way.
  whole: -1.38 (0.24), residues: 1113
  helix:  0.39 (0.50), residues: 81
  sheet: -1.62 (0.36), residues: 198
  loop : -0.90 (0.21), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  30 
 TYR   0.006   0.001   TYR B 335 
 PHE   0.007   0.001   PHE C 330 
 TRP   0.045   0.002   TRP B  31 
 HIS   0.003   0.001   HIS C 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00186 ( 8619)
  covalent geometry    : angle       0.55391 (11793)
  hydrogen bonds       : bond        0.03557 (  180)
  hydrogen bonds       : angle       4.82005 (  468)
  Misc. bond           : bond        0.00163 (    6)

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

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

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  742 Ramachandran restraints generated.
    371 Oldfield, 0 Emsley, 371 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  : 0.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.0410
  time to fit residues: 1.3708
Evaluate side-chains
  17 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 60 optimal weight:    0.0270
   chunk 96 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 46 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0370
   chunk 17 optimal weight:    0.0670
   chunk 64 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   overall best weight:    0.3054
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.037033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.029338 restraints weight = 54275.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.029991 restraints weight = 40639.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.030482 restraints weight = 32789.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.030850 restraints weight = 27780.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.031131 restraints weight = 24353.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.5791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   8625  Z= 0.083
  Angle     :  0.529   9.165  11793  Z= 0.261
  Chirality :  0.041   0.137   1269
  Planarity :  0.004   0.037   1524
  Dihedral  :  3.423  15.851   1209
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  6.74 %
    Favored  : 92.99 %
  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 aren not related in a simple way.
  whole: -1.26 (0.24), residues: 1113
  helix:  1.09 (0.50), residues: 81
  sheet: -1.58 (0.37), residues: 198
  loop : -0.87 (0.21), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  30 
 TYR   0.007   0.001   TYR C 335 
 PHE   0.005   0.001   PHE C 166 
 TRP   0.063   0.002   TRP B  31 
 HIS   0.002   0.001   HIS B 305 

Details of bonding type rmsd
  covalent geometry    : bond        0.00171 ( 8619)
  covalent geometry    : angle       0.52907 (11793)
  hydrogen bonds       : bond        0.03248 (  180)
  hydrogen bonds       : angle       4.67009 (  468)
  Misc. bond           : bond        0.00144 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1088.73 seconds
wall clock time: 19 minutes 41.87 seconds (1181.87 seconds total)