Starting phenix.real_space_refine
on Tue Apr 29 05:26:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rk4_19259/04_2025/8rk4_19259.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rk4_19259/04_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rk4_19259/04_2025/8rk4_19259.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rk4_19259/04_2025/8rk4_19259.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rk4_19259/04_2025/8rk4_19259.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rk4_19259/04_2025/8rk4_19259.cif"
  }
  resolution = 4.74
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8373
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      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:
    C, B
  Time building chain proxies: 5.36, per 1000 atoms: 0.64
  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: 2.36
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.09
  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: 2.24

  Time building geometry restraints manager: 2.65 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}
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:             1.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.680
  Find NCS groups from input model:        0.150
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.590
-------------------------------------------------------------------------------
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 : 21.20
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.045   0.002   TRP A  29 
 HIS   0.006   0.002   HIS B 305 
 PHE   0.009   0.001   PHE A 156 
 TYR   0.008   0.001   TYR A 109 
 ARG   0.010   0.001   ARG B  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.28623 (  180)
  hydrogen bonds       : angle      11.24912 (  468)
  covalent geometry    : bond        0.00321 ( 8619)
  covalent geometry    : angle       0.72105 (11793)
  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
  23 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.6529 (ppp) cc_final: 0.6020 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.2309
  time to fit residues: 6.3783
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  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    9.9990
   chunk 84 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9990
   chunk 28 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 44 optimal weight:    0.0770
   chunk 87 optimal weight:    0.4980
   chunk 33 optimal weight:   10.0000
   chunk 52 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0770
   chunk 100 optimal weight:   20.0000
   overall best weight:    0.9300
-------------------------------------------------------------------------------
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 = 0.3215 r_free = 0.3215 target = 0.037045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.028288 restraints weight = 54855.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.028974 restraints weight = 43424.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.029517 restraints weight = 35937.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6586
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8625  Z= 0.119
  Angle     :  0.637   9.860  11793  Z= 0.324
  Chirality :  0.044   0.143   1269
  Planarity :  0.006   0.103   1524
  Dihedral  :  3.815  11.647   1209
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.04 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  3.24 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.25), residues: 1113
  helix:  0.16 (0.52), residues: 81
  sheet: -0.78 (0.46), residues: 129
  loop : -0.69 (0.21), residues: 903

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP C  92 
 HIS   0.004   0.001   HIS C 305 
 PHE   0.009   0.002   PHE C 156 
 TYR   0.014   0.001   TYR A 344 
 ARG   0.005   0.001   ARG B  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04368 (  180)
  hydrogen bonds       : angle       7.32496 (  468)
  covalent geometry    : bond        0.00263 ( 8619)
  covalent geometry    : angle       0.63665 (11793)
  Misc. bond           : bond        0.00187 (    6)

*********************** REFINEMENT MACRO_CYCLE 2 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
  30 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 29
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  342 CYS cc_start: 0.7237 (t) cc_final: 0.3232 (t)
REVERT: C  374 ILE cc_start: 0.6625 (mm) cc_final: 0.6423 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 30
  average time/residue: 0.1301
  time to fit residues: 5.1028
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  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 62 optimal weight:    0.0670
   chunk 88 optimal weight:    7.9990
   chunk 8 optimal weight:   20.0000
   chunk 7 optimal weight:    0.3980
   chunk 86 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 91 optimal weight:    0.0470
   chunk 103 optimal weight:    0.9980
   chunk 48 optimal weight:    9.9990
   chunk 79 optimal weight:    0.0870
   chunk 49 optimal weight:    9.9990
   overall best weight:    0.3194
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3305 r_free = 0.3305 target = 0.041059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.030574 restraints weight = 48621.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.031230 restraints weight = 38879.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.031746 restraints weight = 32689.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6908
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8625  Z= 0.111
  Angle     :  0.575   9.796  11793  Z= 0.295
  Chirality :  0.042   0.140   1269
  Planarity :  0.005   0.074   1524
  Dihedral  :  3.678  13.157   1209
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.31 %
    Favored  : 95.42 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.24), residues: 1113
  helix:  0.90 (0.55), residues: 81
  sheet: -1.24 (0.43), residues: 138
  loop : -0.76 (0.21), residues: 894

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C  92 
 HIS   0.002   0.001   HIS C 327 
 PHE   0.006   0.001   PHE A 166 
 TYR   0.010   0.001   TYR C 344 
 ARG   0.002   0.000   ARG B  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03796 (  180)
  hydrogen bonds       : angle       6.13287 (  468)
  covalent geometry    : bond        0.00232 ( 8619)
  covalent geometry    : angle       0.57503 (11793)
  Misc. bond           : bond        0.00141 (    6)

*********************** REFINEMENT MACRO_CYCLE 3 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  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  374 ILE cc_start: 0.5237 (mm) cc_final: 0.4930 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.1380
  time to fit residues: 4.1464
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  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   chunk 2 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0770
   chunk 66 optimal weight:    0.9990
   chunk 37 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 87 optimal weight:    2.9990
   chunk 62 optimal weight:   30.0000
   chunk 35 optimal weight:    0.4980
   overall best weight:    1.1144
-------------------------------------------------------------------------------
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 = 0.3212 r_free = 0.3212 target = 0.036809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.028221 restraints weight = 57092.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.028924 restraints weight = 43268.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.029472 restraints weight = 34993.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.3551

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= 0.091
  Angle     :  0.520   9.083  11793  Z= 0.260
  Chirality :  0.041   0.125   1269
  Planarity :  0.004   0.039   1524
  Dihedral  :  3.420  12.369   1209
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  7.55 %
    Favored  : 92.18 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.24), residues: 1113
  helix:  1.19 (0.50), residues: 81
  sheet: -2.06 (0.36), residues: 192
  loop : -0.99 (0.21), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  92 
 HIS   0.002   0.001   HIS C 327 
 PHE   0.006   0.001   PHE A 166 
 TYR   0.007   0.001   TYR C 133 
 ARG   0.002   0.000   ARG B  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02927 (  180)
  hydrogen bonds       : angle       5.53477 (  468)
  covalent geometry    : bond        0.00201 ( 8619)
  covalent geometry    : angle       0.52045 (11793)
  Misc. bond           : bond        0.00115 (    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
  20 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  332 MET cc_start: 0.8822 (ppp) cc_final: 0.8504 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.1583
  time to fit residues: 4.1512
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  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 25 optimal weight:    0.0570
   chunk 43 optimal weight:   10.0000
   chunk 13 optimal weight:    7.9990
   chunk 90 optimal weight:    5.9990
   chunk 94 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 107 optimal weight:    0.3980
   chunk 69 optimal weight:    0.3980
   chunk 103 optimal weight:    0.0980
   chunk 89 optimal weight:   10.0000
   chunk 99 optimal weight:    0.0570
   overall best weight:    0.2016
-------------------------------------------------------------------------------
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 = 0.037272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.028471 restraints weight = 55494.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.029196 restraints weight = 41880.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.029759 restraints weight = 33658.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6998
moved from start:          0.3954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8625  Z= 0.097
  Angle     :  0.545   9.071  11793  Z= 0.275
  Chirality :  0.042   0.129   1269
  Planarity :  0.006   0.088   1524
  Dihedral  :  3.611  12.877   1209
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  7.55 %
    Favored  : 92.18 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.24), residues: 1113
  helix:  0.47 (0.50), residues: 81
  sheet: -1.78 (0.39), residues: 174
  loop : -1.20 (0.20), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A  31 
 HIS   0.006   0.001   HIS A 305 
 PHE   0.012   0.001   PHE C 204 
 TYR   0.013   0.001   TYR A 344 
 ARG   0.004   0.001   ARG B  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02960 (  180)
  hydrogen bonds       : angle       5.85094 (  468)
  covalent geometry    : bond        0.00209 ( 8619)
  covalent geometry    : angle       0.54504 (11793)
  Misc. bond           : bond        0.00304 (    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
  20 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  332 MET cc_start: 0.8613 (ppp) cc_final: 0.8400 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.1610
  time to fit residues: 4.2151
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  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 41 optimal weight:    0.3980
   chunk 34 optimal weight:    9.9990
   chunk 12 optimal weight:    9.9990
   chunk 86 optimal weight:    9.9990
   chunk 84 optimal weight:    6.9990
   chunk 110 optimal weight:    0.0570
   chunk 47 optimal weight:    6.9990
   chunk 43 optimal weight:   10.0000
   chunk 55 optimal weight:    0.0570
   chunk 73 optimal weight:    0.0570
   chunk 100 optimal weight:   20.0000
   overall best weight:    1.5136
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  21 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 = 0.3214 r_free = 0.3214 target = 0.036920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.028158 restraints weight = 58220.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.028863 restraints weight = 44061.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.029407 restraints weight = 35616.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7007
moved from start:          0.4286

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= 0.096
  Angle     :  0.521  10.411  11793  Z= 0.263
  Chirality :  0.041   0.174   1269
  Planarity :  0.005   0.056   1524
  Dihedral  :  3.854  15.603   1209
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  7.55 %
    Favored  : 92.18 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.24), residues: 1113
  helix:  1.16 (0.53), residues: 81
  sheet: -2.43 (0.34), residues: 171
  loop : -1.11 (0.20), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  31 
 HIS   0.007   0.002   HIS C 305 
 PHE   0.010   0.001   PHE C 204 
 TYR   0.005   0.001   TYR B 335 
 ARG   0.003   0.000   ARG B 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03027 (  180)
  hydrogen bonds       : angle       5.85355 (  468)
  covalent geometry    : bond        0.00208 ( 8619)
  covalent geometry    : angle       0.52081 (11793)
  Misc. bond           : bond        0.00195 (    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
  19 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 19
  average time/residue: 0.1575
  time to fit residues: 3.9247
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  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   chunk 92 optimal weight:    0.0980
   chunk 32 optimal weight:    0.9990
   chunk 109 optimal weight:    4.9990
   chunk 97 optimal weight:    0.0470
   chunk 5 optimal weight:    0.1980
   chunk 26 optimal weight:   20.0000
   chunk 68 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0570
   overall best weight:    0.2798
-------------------------------------------------------------------------------
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 = 0.3249 r_free = 0.3249 target = 0.037896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.028933 restraints weight = 56241.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.029665 restraints weight = 42535.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.030263 restraints weight = 34293.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6972
moved from start:          0.4514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   8625  Z= 0.085
  Angle     :  0.527   9.868  11793  Z= 0.257
  Chirality :  0.041   0.133   1269
  Planarity :  0.004   0.045   1524
  Dihedral  :  3.408  12.382   1209
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  8.09 %
    Favored  : 91.64 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.24), residues: 1113
  helix:  2.16 (0.50), residues: 84
  sheet: -2.24 (0.34), residues: 198
  loop : -1.06 (0.21), residues: 831

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 360 
 HIS   0.005   0.001   HIS C 305 
 PHE   0.007   0.001   PHE C 330 
 TYR   0.013   0.001   TYR B 344 
 ARG   0.003   0.000   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02455 (  180)
  hydrogen bonds       : angle       5.11601 (  468)
  covalent geometry    : bond        0.00180 ( 8619)
  covalent geometry    : angle       0.52687 (11793)
  Misc. bond           : bond        0.00211 (    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  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  332 MET cc_start: 0.8944 (ppp) cc_final: 0.8726 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.1449
  time to fit residues: 4.3904
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  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 52 optimal weight:    0.0270
   chunk 45 optimal weight:    7.9990
   chunk 19 optimal weight:    0.3980
   chunk 99 optimal weight:   20.0000
   chunk 110 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0270
   chunk 55 optimal weight:    0.0570
   chunk 89 optimal weight:    0.0270
   chunk 68 optimal weight:    0.0370
   chunk 24 optimal weight:    0.6980
   chunk 90 optimal weight:    5.9990
   overall best weight:    0.0350
-------------------------------------------------------------------------------
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 = 0.3254 r_free = 0.3254 target = 0.037832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.031147 restraints weight = 52118.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.031728 restraints weight = 40301.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.032158 restraints weight = 32785.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.4655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8625  Z= 0.087
  Angle     :  0.542   9.860  11793  Z= 0.268
  Chirality :  0.041   0.169   1269
  Planarity :  0.004   0.044   1524
  Dihedral  :  3.345  13.200   1209
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  7.28 %
    Favored  : 92.45 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.24), residues: 1113
  helix:  0.37 (0.47), residues: 81
  sheet: -2.04 (0.34), residues: 213
  loop : -1.06 (0.21), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP C  31 
 HIS   0.004   0.001   HIS C 305 
 PHE   0.005   0.001   PHE C 166 
 TYR   0.011   0.001   TYR A 109 
 ARG   0.001   0.000   ARG C  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02886 (  180)
  hydrogen bonds       : angle       5.06600 (  468)
  covalent geometry    : bond        0.00185 ( 8619)
  covalent geometry    : angle       0.54181 (11793)
  Misc. bond           : bond        0.00157 (    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
  25 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1344
  time to fit residues: 4.4267
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  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 49 optimal weight:    0.0050
   chunk 7 optimal weight:    8.9990
   chunk 19 optimal weight:    0.0870
   chunk 47 optimal weight:    8.9990
   chunk 5 optimal weight:    0.0370
   chunk 31 optimal weight:    0.0000
   chunk 72 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9980
   chunk 75 optimal weight:    0.0370
   chunk 28 optimal weight:   20.0000
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.0332
-------------------------------------------------------------------------------
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 = 0.3261 r_free = 0.3261 target = 0.038356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.031518 restraints weight = 51402.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.032078 restraints weight = 40332.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.032506 restraints weight = 33305.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.4859

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= 0.091
  Angle     :  0.536   9.720  11793  Z= 0.266
  Chirality :  0.041   0.138   1269
  Planarity :  0.004   0.039   1524
  Dihedral  :  3.270  13.050   1209
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.88
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.23), residues: 1113
  helix:  0.06 (0.40), residues: 81
  sheet: -2.13 (0.33), residues: 231
  loop : -1.02 (0.21), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.001   TRP A  31 
 HIS   0.003   0.001   HIS C 305 
 PHE   0.005   0.001   PHE B 330 
 TYR   0.010   0.001   TYR A 109 
 ARG   0.002   0.000   ARG C  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02876 (  180)
  hydrogen bonds       : angle       5.20685 (  468)
  covalent geometry    : bond        0.00187 ( 8619)
  covalent geometry    : angle       0.53574 (11793)
  Misc. bond           : bond        0.00156 (    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
  25 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 MET cc_start: 0.9141 (mmp) cc_final: 0.8935 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1353
  time to fit residues: 4.4473
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  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 59 optimal weight:    0.2980
   chunk 31 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 85 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   chunk 2 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.6980
-------------------------------------------------------------------------------
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 = 0.3241 r_free = 0.3241 target = 0.037873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.029029 restraints weight = 55063.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.029759 restraints weight = 41729.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.030302 restraints weight = 33602.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7022
moved from start:          0.4986

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= 0.082
  Angle     :  0.506   9.500  11793  Z= 0.249
  Chirality :  0.040   0.122   1269
  Planarity :  0.004   0.038   1524
  Dihedral  :  3.126  14.668   1209
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.31
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.24), residues: 1113
  helix:  0.59 (0.43), residues: 81
  sheet: -1.94 (0.34), residues: 213
  loop : -1.00 (0.21), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP B  31 
 HIS   0.003   0.001   HIS C 305 
 PHE   0.006   0.001   PHE A 166 
 TYR   0.009   0.001   TYR A 109 
 ARG   0.001   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02773 (  180)
  hydrogen bonds       : angle       4.91282 (  468)
  covalent geometry    : bond        0.00175 ( 8619)
  covalent geometry    : angle       0.50572 (11793)
  Misc. bond           : bond        0.00135 (    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
  25 residues out of total 278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1291
  time to fit residues: 4.3170
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  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 61 optimal weight:    0.0670
   chunk 100 optimal weight:    9.9990
   chunk 18 optimal weight:   30.0000
   chunk 25 optimal weight:    0.0470
   chunk 30 optimal weight:    0.9990
   chunk 105 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 45 optimal weight:   20.0000
   chunk 94 optimal weight:    0.0020
   overall best weight:    0.4026
-------------------------------------------------------------------------------
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 = 0.3251 r_free = 0.3251 target = 0.038122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.030496 restraints weight = 51520.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.031223 restraints weight = 37958.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.031751 restraints weight = 30099.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.5149

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= 0.080
  Angle     :  0.507   9.497  11793  Z= 0.248
  Chirality :  0.041   0.125   1269
  Planarity :  0.004   0.037   1524
  Dihedral  :  3.070  12.354   1209
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  7.01 %
    Favored  : 92.72 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.24), residues: 1113
  helix:  0.85 (0.44), residues: 81
  sheet: -1.88 (0.36), residues: 213
  loop : -1.00 (0.21), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP B  31 
 HIS   0.003   0.001   HIS C 305 
 PHE   0.006   0.001   PHE A 166 
 TYR   0.008   0.001   TYR A 109 
 ARG   0.001   0.000   ARG C  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02595 (  180)
  hydrogen bonds       : angle       4.65070 (  468)
  covalent geometry    : bond        0.00168 ( 8619)
  covalent geometry    : angle       0.50717 (11793)
  Misc. bond           : bond        0.00138 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2084.75 seconds
wall clock time: 37 minutes 5.72 seconds (2225.72 seconds total)