Starting phenix.real_space_refine
on Wed Mar 12 07:43:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7oag_12776/03_2025/7oag_12776.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7oag_12776/03_2025/7oag_12776.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7oag_12776/03_2025/7oag_12776.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7oag_12776/03_2025/7oag_12776.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7oag_12776/03_2025/7oag_12776.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7oag_12776/03_2025/7oag_12776.cif"
  }
  resolution = 3.4
  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=   0.001
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     175      5.16       5
     C    4750      2.51       5
     N    1325      2.21       5
     O    1350      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7600
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 304
          Classifications: {'peptide': 40}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 38}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V,
    Y, X
  Time building chain proxies: 3.05, per 1000 atoms: 0.40
  Number of scatterers: 7600
  At special positions: 0
  Unit cell: (76.911, 76.911, 124.877, 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     175     16.00
     O    1350      8.00
     N    1325      7.00
     C    4750      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=75, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   4 " - pdb=" SG  CYS A  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  19 " - pdb=" SG  CYS A  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   4 " - pdb=" SG  CYS C  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   4 " - pdb=" SG  CYS B  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E   4 " - pdb=" SG  CYS E  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   4 " - pdb=" SG  CYS D  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G   4 " - pdb=" SG  CYS G  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F   4 " - pdb=" SG  CYS F  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I   4 " - pdb=" SG  CYS I  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H   4 " - pdb=" SG  CYS H  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K   4 " - pdb=" SG  CYS K  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J   4 " - pdb=" SG  CYS J  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M   4 " - pdb=" SG  CYS M  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L   4 " - pdb=" SG  CYS L  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O   4 " - pdb=" SG  CYS O  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N   4 " - pdb=" SG  CYS N  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS Q   4 " - pdb=" SG  CYS Q  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P   4 " - pdb=" SG  CYS P  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S   4 " - pdb=" SG  CYS S  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R   4 " - pdb=" SG  CYS R  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS U   4 " - pdb=" SG  CYS U  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS T   4 " - pdb=" SG  CYS T  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS W   4 " - pdb=" SG  CYS W  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS V   4 " - pdb=" SG  CYS V  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS Y   4 " - pdb=" SG  CYS Y  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X   4 " - pdb=" SG  CYS X  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  15 " - pdb=" SG  CYS C  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  15 " - pdb=" SG  CYS B  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  15 " - pdb=" SG  CYS E  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  15 " - pdb=" SG  CYS D  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  15 " - pdb=" SG  CYS G  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  15 " - pdb=" SG  CYS F  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  15 " - pdb=" SG  CYS I  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  15 " - pdb=" SG  CYS H  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  15 " - pdb=" SG  CYS K  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  15 " - pdb=" SG  CYS J  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  15 " - pdb=" SG  CYS M  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  15 " - pdb=" SG  CYS L  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O  15 " - pdb=" SG  CYS O  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  15 " - pdb=" SG  CYS N  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS Q  15 " - pdb=" SG  CYS Q  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P  15 " - pdb=" SG  CYS P  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  15 " - pdb=" SG  CYS S  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  15 " - pdb=" SG  CYS R  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS U  15 " - pdb=" SG  CYS U  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS T  15 " - pdb=" SG  CYS T  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS W  15 " - pdb=" SG  CYS W  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS V  15 " - pdb=" SG  CYS V  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS Y  15 " - pdb=" SG  CYS Y  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X  15 " - pdb=" SG  CYS X  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  19 " - pdb=" SG  CYS C  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  19 " - pdb=" SG  CYS B  39 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  19 " - pdb=" SG  CYS E  39 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  19 " - pdb=" SG  CYS D  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  19 " - pdb=" SG  CYS G  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  19 " - pdb=" SG  CYS F  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  19 " - pdb=" SG  CYS I  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  19 " - pdb=" SG  CYS H  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  19 " - pdb=" SG  CYS K  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  19 " - pdb=" SG  CYS J  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  19 " - pdb=" SG  CYS M  39 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  19 " - pdb=" SG  CYS L  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O  19 " - pdb=" SG  CYS O  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  19 " - pdb=" SG  CYS N  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS Q  19 " - pdb=" SG  CYS Q  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P  19 " - pdb=" SG  CYS P  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  19 " - pdb=" SG  CYS S  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  19 " - pdb=" SG  CYS R  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS U  19 " - pdb=" SG  CYS U  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS T  19 " - pdb=" SG  CYS T  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS W  19 " - pdb=" SG  CYS W  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS V  19 " - pdb=" SG  CYS V  39 " distance=2.03
    Simple disulfide: pdb=" SG  CYS Y  19 " - pdb=" SG  CYS Y  39 " distance=2.02
    Simple disulfide: pdb=" SG  CYS X  19 " - pdb=" SG  CYS X  39 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.96
  Conformation dependent library (CDL) restraints added in 995.6 milliseconds
  

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1600

  Finding SS restraints...
    Secondary structure from input PDB file:
      75 helices and 25 sheets defined
      47.5% alpha, 12.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 9
    Processing helix  chain 'A' and resid 13 through 21
    Processing helix  chain 'A' and resid 31 through 35
    Processing helix  chain 'B' and resid 5 through 9
    Processing helix  chain 'B' and resid 13 through 21
    Processing helix  chain 'B' and resid 31 through 35
    Processing helix  chain 'C' and resid 5 through 9
    Processing helix  chain 'C' and resid 13 through 21
    Processing helix  chain 'C' and resid 31 through 35
    Processing helix  chain 'D' and resid 5 through 9
    Processing helix  chain 'D' and resid 13 through 21
    Processing helix  chain 'D' and resid 31 through 35
    Processing helix  chain 'E' and resid 5 through 9
    Processing helix  chain 'E' and resid 13 through 21
    Processing helix  chain 'E' and resid 31 through 35
    Processing helix  chain 'F' and resid 5 through 9
    Processing helix  chain 'F' and resid 13 through 21
    Processing helix  chain 'F' and resid 31 through 35
    Processing helix  chain 'G' and resid 5 through 9
    Processing helix  chain 'G' and resid 13 through 21
    Processing helix  chain 'G' and resid 31 through 35
    Processing helix  chain 'H' and resid 5 through 9
    Processing helix  chain 'H' and resid 13 through 21
    Processing helix  chain 'H' and resid 31 through 35
    Processing helix  chain 'I' and resid 5 through 9
    Processing helix  chain 'I' and resid 13 through 21
    Processing helix  chain 'I' and resid 31 through 35
    Processing helix  chain 'J' and resid 5 through 9
    Processing helix  chain 'J' and resid 13 through 21
    Processing helix  chain 'J' and resid 31 through 35
    Processing helix  chain 'K' and resid 5 through 9
    Processing helix  chain 'K' and resid 13 through 21
    Processing helix  chain 'K' and resid 31 through 35
    Processing helix  chain 'L' and resid 5 through 9
    Processing helix  chain 'L' and resid 13 through 21
    Processing helix  chain 'L' and resid 31 through 35
    Processing helix  chain 'M' and resid 5 through 9
    Processing helix  chain 'M' and resid 13 through 21
    Processing helix  chain 'M' and resid 31 through 35
    Processing helix  chain 'N' and resid 5 through 9
    Processing helix  chain 'N' and resid 13 through 21
    Processing helix  chain 'N' and resid 31 through 35
    Processing helix  chain 'O' and resid 5 through 9
    Processing helix  chain 'O' and resid 13 through 21
    Processing helix  chain 'O' and resid 31 through 35
    Processing helix  chain 'P' and resid 5 through 9
    Processing helix  chain 'P' and resid 13 through 21
    Processing helix  chain 'P' and resid 31 through 35
    Processing helix  chain 'Q' and resid 5 through 9
    Processing helix  chain 'Q' and resid 13 through 21
    Processing helix  chain 'Q' and resid 31 through 35
    Processing helix  chain 'R' and resid 5 through 9
    Processing helix  chain 'R' and resid 13 through 21
    Processing helix  chain 'R' and resid 31 through 35
    Processing helix  chain 'S' and resid 5 through 9
    Processing helix  chain 'S' and resid 13 through 21
    Processing helix  chain 'S' and resid 31 through 35
    Processing helix  chain 'T' and resid 5 through 9
    Processing helix  chain 'T' and resid 13 through 21
    Processing helix  chain 'T' and resid 31 through 35
    Processing helix  chain 'U' and resid 5 through 9
    Processing helix  chain 'U' and resid 13 through 21
    Processing helix  chain 'U' and resid 31 through 35
    Processing helix  chain 'V' and resid 5 through 9
    Processing helix  chain 'V' and resid 13 through 21
    Processing helix  chain 'V' and resid 31 through 35
    Processing helix  chain 'W' and resid 5 through 9
    Processing helix  chain 'W' and resid 13 through 21
    Processing helix  chain 'W' and resid 31 through 35
    Processing helix  chain 'X' and resid 5 through 9
    Processing helix  chain 'X' and resid 13 through 21
    Processing helix  chain 'X' and resid 31 through 35
    Processing helix  chain 'Y' and resid 5 through 9
    Processing helix  chain 'Y' and resid 13 through 21
    Processing helix  chain 'Y' and resid 31 through 35
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30
    Processing sheet with id=AA2, first strand: chain 'B' and resid 28 through 30
    Processing sheet with id=AA3, first strand: chain 'C' and resid 28 through 30
    Processing sheet with id=AA4, first strand: chain 'D' and resid 28 through 30
    Processing sheet with id=AA5, first strand: chain 'E' and resid 28 through 30
    Processing sheet with id=AA6, first strand: chain 'F' and resid 28 through 30
    Processing sheet with id=AA7, first strand: chain 'G' and resid 28 through 30
    Processing sheet with id=AA8, first strand: chain 'H' and resid 28 through 30
    Processing sheet with id=AA9, first strand: chain 'I' and resid 28 through 30
    Processing sheet with id=AB1, first strand: chain 'J' and resid 28 through 30
    Processing sheet with id=AB2, first strand: chain 'K' and resid 28 through 30
    Processing sheet with id=AB3, first strand: chain 'L' and resid 28 through 30
    Processing sheet with id=AB4, first strand: chain 'M' and resid 28 through 30
    Processing sheet with id=AB5, first strand: chain 'N' and resid 28 through 30
    Processing sheet with id=AB6, first strand: chain 'O' and resid 28 through 30
    Processing sheet with id=AB7, first strand: chain 'P' and resid 28 through 30
    Processing sheet with id=AB8, first strand: chain 'Q' and resid 28 through 30
    Processing sheet with id=AB9, first strand: chain 'R' and resid 28 through 30
    Processing sheet with id=AC1, first strand: chain 'S' and resid 28 through 30
    Processing sheet with id=AC2, first strand: chain 'T' and resid 28 through 30
    Processing sheet with id=AC3, first strand: chain 'U' and resid 28 through 30
    Processing sheet with id=AC4, first strand: chain 'V' and resid 28 through 30
    Processing sheet with id=AC5, first strand: chain 'W' and resid 28 through 30
    Processing sheet with id=AC6, first strand: chain 'X' and resid 28 through 30
    Processing sheet with id=AC7, first strand: chain 'Y' and resid 28 through 30

    250 hydrogen bonds defined for protein.
    600 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: 2.05

  Time building geometry restraints manager: 2.40 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2350
        1.34 -     1.46: 2020
        1.46 -     1.57: 3255
        1.57 -     1.69: 0
        1.69 -     1.80: 200
  Bond restraints: 7825
  Sorted by residual:
  bond pdb=" CB  TRP V   8 "
       pdb=" CG  TRP V   8 "
    ideal  model  delta    sigma   weight residual
    1.498  1.460  0.038 3.10e-02 1.04e+03 1.50e+00
  bond pdb=" CB  TRP P   8 "
       pdb=" CG  TRP P   8 "
    ideal  model  delta    sigma   weight residual
    1.498  1.460  0.038 3.10e-02 1.04e+03 1.50e+00
  bond pdb=" CB  TRP M   8 "
       pdb=" CG  TRP M   8 "
    ideal  model  delta    sigma   weight residual
    1.498  1.460  0.038 3.10e-02 1.04e+03 1.49e+00
  bond pdb=" CB  TRP R   8 "
       pdb=" CG  TRP R   8 "
    ideal  model  delta    sigma   weight residual
    1.498  1.460  0.038 3.10e-02 1.04e+03 1.49e+00
  bond pdb=" CB  TRP J   8 "
       pdb=" CG  TRP J   8 "
    ideal  model  delta    sigma   weight residual
    1.498  1.460  0.038 3.10e-02 1.04e+03 1.49e+00
  ... (remaining 7820 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.74: 8591
        0.74 -     1.48: 1283
        1.48 -     2.22: 351
        2.22 -     2.97: 100
        2.97 -     3.71: 50
  Bond angle restraints: 10375
  Sorted by residual:
  angle pdb=" CA  LYS U  26 "
        pdb=" CB  LYS U  26 "
        pdb=" CG  LYS U  26 "
      ideal   model   delta    sigma   weight residual
     114.10  117.63   -3.53 2.00e+00 2.50e-01 3.11e+00
  angle pdb=" C   LEU Q  36 "
        pdb=" N   CYS Q  37 "
        pdb=" CA  CYS Q  37 "
      ideal   model   delta    sigma   weight residual
     122.17  119.31    2.86 1.62e+00 3.81e-01 3.11e+00
  angle pdb=" CA  LYS B  26 "
        pdb=" CB  LYS B  26 "
        pdb=" CG  LYS B  26 "
      ideal   model   delta    sigma   weight residual
     114.10  117.62   -3.52 2.00e+00 2.50e-01 3.10e+00
  angle pdb=" CA  LYS F  26 "
        pdb=" CB  LYS F  26 "
        pdb=" CG  LYS F  26 "
      ideal   model   delta    sigma   weight residual
     114.10  117.62   -3.52 2.00e+00 2.50e-01 3.09e+00
  angle pdb=" CA  LYS G  26 "
        pdb=" CB  LYS G  26 "
        pdb=" CG  LYS G  26 "
      ideal   model   delta    sigma   weight residual
     114.10  117.62   -3.52 2.00e+00 2.50e-01 3.09e+00
  ... (remaining 10370 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.37: 3548
        8.37 -    16.74: 702
       16.74 -    25.11: 175
       25.11 -    33.48: 100
       33.48 -    41.84: 100
  Dihedral angle restraints: 4625
    sinusoidal: 1975
      harmonic: 2650
  Sorted by residual:
  dihedral pdb=" CA  ILE N  22 "
           pdb=" CB  ILE N  22 "
           pdb=" CG1 ILE N  22 "
           pdb=" CD1 ILE N  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   98.05  -38.05     3      1.50e+01 4.44e-03 6.68e+00
  dihedral pdb=" CA  ILE W  22 "
           pdb=" CB  ILE W  22 "
           pdb=" CG1 ILE W  22 "
           pdb=" CD1 ILE W  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   98.04  -38.04     3      1.50e+01 4.44e-03 6.68e+00
  dihedral pdb=" CA  ILE U  22 "
           pdb=" CB  ILE U  22 "
           pdb=" CG1 ILE U  22 "
           pdb=" CD1 ILE U  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   98.03  -38.03     3      1.50e+01 4.44e-03 6.68e+00
  ... (remaining 4622 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 463
       0.025 -    0.049: 148
       0.049 -    0.074: 89
       0.074 -    0.098: 95
       0.098 -    0.123: 55
  Chirality restraints: 850
  Sorted by residual:
  chirality pdb=" CA  LYS K  26 "
            pdb=" N   LYS K  26 "
            pdb=" C   LYS K  26 "
            pdb=" CB  LYS K  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.75e-01
  chirality pdb=" CA  LYS N  26 "
            pdb=" N   LYS N  26 "
            pdb=" C   LYS N  26 "
            pdb=" CB  LYS N  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.72e-01
  chirality pdb=" CA  LYS L  26 "
            pdb=" N   LYS L  26 "
            pdb=" C   LYS L  26 "
            pdb=" CB  LYS L  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.67e-01
  ... (remaining 847 not shown)

  Planarity restraints: 1350
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C   6 "    0.015 5.00e-02 4.00e+02   2.30e-02 8.49e-01
        pdb=" N   PRO C   7 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO C   7 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO C   7 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY Q   6 "    0.015 5.00e-02 4.00e+02   2.30e-02 8.49e-01
        pdb=" N   PRO Q   7 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO Q   7 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO Q   7 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY H   6 "    0.015 5.00e-02 4.00e+02   2.30e-02 8.48e-01
        pdb=" N   PRO H   7 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO H   7 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO H   7 "    0.013 5.00e-02 4.00e+02
  ... (remaining 1347 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 2997
        2.84 -     3.35: 7691
        3.35 -     3.87: 13985
        3.87 -     4.38: 16356
        4.38 -     4.90: 25243
  Nonbonded interactions: 66272
  Sorted by model distance:
  nonbonded pdb=" N   PHE L   2 "
            pdb=" OD2 ASP P  11 "
     model   vdw
     2.321 3.120
  nonbonded pdb=" OD2 ASP Q  11 "
            pdb=" N   PHE U   2 "
     model   vdw
     2.358 3.120
  nonbonded pdb=" O   HIS K  18 "
            pdb=" OG  SER K  21 "
     model   vdw
     2.401 3.040
  nonbonded pdb=" O   HIS E  18 "
            pdb=" OG  SER E  21 "
     model   vdw
     2.402 3.040
  nonbonded pdb=" O   HIS M  18 "
            pdb=" OG  SER M  21 "
     model   vdw
     2.402 3.040
  ... (remaining 66267 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'L'
  selection = chain 'O'
  selection = chain 'N'
  selection = chain 'Q'
  selection = chain 'P'
  selection = chain 'S'
  selection = chain 'R'
  selection = chain 'U'
  selection = chain 'T'
  selection = chain 'W'
  selection = chain 'V'
  selection = chain 'Y'
  selection = chain 'X'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.750
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     20.590
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.040
  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:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8702
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.038   7825  Z= 0.447
  Angle     :  0.673   3.707  10375  Z= 0.381
  Chirality :  0.049   0.123    850
  Planarity :  0.004   0.023   1350
  Dihedral  : 10.390  38.045   2800
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  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: -0.35 (0.28), residues: 950
  helix:  1.41 (0.37), residues: 200
  sheet:  None (None), residues: 0
  loop : -0.74 (0.23), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP R   8 
 HIS   0.002   0.001   HIS U  16 
 PHE   0.008   0.001   PHE W   2 
 TYR   0.005   0.001   TYR F  40 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.912 
Fit side-chains
REVERT: L   23 LYS cc_start: 0.9235 (mppt) cc_final: 0.9034 (mmtm)
REVERT: L   25 TYR cc_start: 0.9451 (m-80) cc_final: 0.9073 (m-80)
REVERT: V    5 ASN cc_start: 0.9346 (t0) cc_final: 0.9021 (t0)
REVERT: V   32 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8150 (ttpt)
REVERT: X    5 ASN cc_start: 0.9226 (t0) cc_final: 0.8941 (t0)
REVERT: X   32 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8137 (mtpt)
REVERT: Y    5 ASN cc_start: 0.8722 (t0) cc_final: 0.8509 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.3957
  time to fit residues: 56.4645
Evaluate side-chains
  104 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0980
   chunk 42 optimal weight:    0.9980
   chunk 25 optimal weight:    7.9990
   chunk 51 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 78 optimal weight:    7.9990
   chunk 30 optimal weight:   20.0000
   chunk 47 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 90 optimal weight:    7.9990
   overall best weight:    2.6186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.038521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2401 r_free = 0.2401 target = 0.023671 restraints weight = 38613.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.2357 rms_B_bonded: 5.22
r_work: 0.2207 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.2207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8989
moved from start:          0.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7825  Z= 0.224
  Angle     :  0.571   5.037  10375  Z= 0.292
  Chirality :  0.044   0.109    850
  Planarity :  0.004   0.028   1350
  Dihedral  :  3.940  20.858   1075
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  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:  0.23 (0.27), residues: 950
  helix:  1.90 (0.36), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.43 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP W   8 
 HIS   0.002   0.000   HIS W  16 
 PHE   0.011   0.001   PHE Y  35 
 TYR   0.005   0.001   TYR J  25 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.808 
Fit side-chains
REVERT: C   26 LYS cc_start: 0.9379 (ptmm) cc_final: 0.9082 (ptmm)
REVERT: I   13 MET cc_start: 0.8623 (mpp) cc_final: 0.8136 (mpp)
REVERT: K    5 ASN cc_start: 0.9368 (t0) cc_final: 0.8736 (t0)
REVERT: P   20 LYS cc_start: 0.9632 (mmmt) cc_final: 0.9310 (mmmm)
REVERT: T    5 ASN cc_start: 0.9449 (t0) cc_final: 0.8965 (t0)
REVERT: V    5 ASN cc_start: 0.9494 (t0) cc_final: 0.8896 (t0)
REVERT: V   32 LYS cc_start: 0.9652 (mmtt) cc_final: 0.8737 (ttpt)
REVERT: W   25 TYR cc_start: 0.9358 (m-80) cc_final: 0.9010 (m-80)
REVERT: W   26 LYS cc_start: 0.9119 (ptmm) cc_final: 0.8841 (ptmm)
REVERT: X    5 ASN cc_start: 0.9337 (t0) cc_final: 0.8865 (t0)
REVERT: X   32 LYS cc_start: 0.9626 (mmtt) cc_final: 0.8920 (mtpt)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.3913
  time to fit residues: 57.1154
Evaluate side-chains
  114 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 86 optimal weight:    6.9990
   chunk 10 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 61 optimal weight:    6.9990
   chunk 80 optimal weight:    1.9990
   chunk 66 optimal weight:    8.9990
   chunk 29 optimal weight:    6.9990
   chunk 3 optimal weight:    9.9990
   chunk 1 optimal weight:   20.0000
   chunk 84 optimal weight:    7.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    5.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.037132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2336 r_free = 0.2336 target = 0.022648 restraints weight = 38864.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.2285 rms_B_bonded: 5.13
r_work: 0.2132 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.2132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9007
moved from start:          0.3714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042   7825  Z= 0.461
  Angle     :  0.681   6.511  10375  Z= 0.344
  Chirality :  0.047   0.121    850
  Planarity :  0.004   0.029   1350
  Dihedral  :  4.366  20.859   1075
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  9.42 %
    Favored  : 90.32 %
  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:  0.15 (0.28), residues: 950
  helix:  2.25 (0.37), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.65 (0.24), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP Y   8 
 HIS   0.003   0.001   HIS B  16 
 PHE   0.007   0.001   PHE Y   2 
 TYR   0.011   0.001   TYR D  25 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 116
  time to evaluate  : 0.972 
Fit side-chains
REVERT: C   26 LYS cc_start: 0.9399 (ptmm) cc_final: 0.9151 (ptmm)
REVERT: G   11 ASP cc_start: 0.8194 (t0) cc_final: 0.7807 (t0)
REVERT: I   13 MET cc_start: 0.8782 (mpp) cc_final: 0.8290 (mpp)
REVERT: K   11 ASP cc_start: 0.8061 (t0) cc_final: 0.7860 (t0)
REVERT: M   10 GLU cc_start: 0.9090 (pm20) cc_final: 0.8828 (pm20)
REVERT: M   26 LYS cc_start: 0.9352 (ptmt) cc_final: 0.8987 (ptmm)
REVERT: O   10 GLU cc_start: 0.9092 (pm20) cc_final: 0.8763 (pm20)
REVERT: T   11 ASP cc_start: 0.8333 (t0) cc_final: 0.8118 (t0)
REVERT: V   32 LYS cc_start: 0.9682 (mmtt) cc_final: 0.8979 (mtpt)
REVERT: X    5 ASN cc_start: 0.9575 (t0) cc_final: 0.9147 (t0)
REVERT: X   32 LYS cc_start: 0.9699 (mmtt) cc_final: 0.8940 (ttpt)
REVERT: Y   13 MET cc_start: 0.8576 (mmt) cc_final: 0.8259 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 117
  average time/residue: 0.3879
  time to fit residues: 53.8241
Evaluate side-chains
  111 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    0.2980
   chunk 96 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 50 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 73 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 99 optimal weight:    4.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    1.2184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.037908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2366 r_free = 0.2366 target = 0.023163 restraints weight = 37505.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.2333 rms_B_bonded: 5.21
r_work: 0.2179 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.2179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8944
moved from start:          0.4025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   7825  Z= 0.149
  Angle     :  0.506   5.066  10375  Z= 0.256
  Chirality :  0.041   0.107    850
  Planarity :  0.003   0.025   1350
  Dihedral  :  3.724  19.025   1075
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.10 %
    Favored  : 88.90 %
  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:  0.17 (0.28), residues: 950
  helix:  2.17 (0.37), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.60 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP K   8 
 HIS   0.001   0.000   HIS Y  18 
 PHE   0.004   0.001   PHE Y  35 
 TYR   0.012   0.001   TYR F  25 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.907 
Fit side-chains
REVERT: C   26 LYS cc_start: 0.9348 (ptmm) cc_final: 0.8944 (ptmm)
REVERT: D   10 GLU cc_start: 0.8992 (pm20) cc_final: 0.8651 (pm20)
REVERT: D   20 LYS cc_start: 0.9619 (mmmt) cc_final: 0.9387 (mmmm)
REVERT: D   25 TYR cc_start: 0.9537 (m-80) cc_final: 0.9269 (m-80)
REVERT: G   11 ASP cc_start: 0.8195 (t0) cc_final: 0.7846 (t0)
REVERT: I    5 ASN cc_start: 0.9329 (t0) cc_final: 0.8606 (t0)
REVERT: I   13 MET cc_start: 0.8719 (mpp) cc_final: 0.8267 (mpp)
REVERT: I   20 LYS cc_start: 0.9582 (mmmt) cc_final: 0.9370 (mmmm)
REVERT: J   20 LYS cc_start: 0.9613 (mmmt) cc_final: 0.9344 (mmmm)
REVERT: K    5 ASN cc_start: 0.9323 (t0) cc_final: 0.8632 (t0)
REVERT: K   20 LYS cc_start: 0.9617 (mmmt) cc_final: 0.9409 (mmmm)
REVERT: M    5 ASN cc_start: 0.9365 (t0) cc_final: 0.8714 (t0)
REVERT: M   10 GLU cc_start: 0.9078 (pm20) cc_final: 0.8854 (pm20)
REVERT: M   26 LYS cc_start: 0.9331 (ptmt) cc_final: 0.8961 (ptmm)
REVERT: N   20 LYS cc_start: 0.9641 (mmmt) cc_final: 0.9420 (mmmm)
REVERT: O    5 ASN cc_start: 0.9319 (t0) cc_final: 0.8684 (t0)
REVERT: O   10 GLU cc_start: 0.9045 (pm20) cc_final: 0.8789 (pm20)
REVERT: P   20 LYS cc_start: 0.9640 (mmmt) cc_final: 0.9272 (mmmm)
REVERT: T    5 ASN cc_start: 0.9428 (t0) cc_final: 0.8819 (t0)
REVERT: T   20 LYS cc_start: 0.9627 (mmmt) cc_final: 0.9323 (mmmm)
REVERT: V    5 ASN cc_start: 0.9500 (t0) cc_final: 0.8863 (t0)
REVERT: V   10 GLU cc_start: 0.8859 (pm20) cc_final: 0.8473 (pm20)
REVERT: V   20 LYS cc_start: 0.9643 (mmmt) cc_final: 0.9417 (mmmm)
REVERT: V   32 LYS cc_start: 0.9596 (mmtt) cc_final: 0.8835 (mtpt)
REVERT: W   25 TYR cc_start: 0.9483 (m-80) cc_final: 0.9192 (m-80)
REVERT: X    5 ASN cc_start: 0.9350 (t0) cc_final: 0.8751 (t0)
REVERT: X   20 LYS cc_start: 0.9664 (mmmt) cc_final: 0.9463 (mmmm)
REVERT: X   26 LYS cc_start: 0.9444 (pttm) cc_final: 0.9071 (ptpp)
REVERT: X   32 LYS cc_start: 0.9625 (mmtt) cc_final: 0.8771 (ttpt)
REVERT: Y   25 TYR cc_start: 0.9600 (m-80) cc_final: 0.9200 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.3953
  time to fit residues: 62.7095
Evaluate side-chains
  129 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 91 optimal weight:    8.9990
   chunk 57 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 20 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 76 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 42 optimal weight:    9.9990
   chunk 49 optimal weight:    7.9990
   chunk 81 optimal weight:    6.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    3.1586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.037179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2349 r_free = 0.2349 target = 0.022735 restraints weight = 36991.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.2320 rms_B_bonded: 5.11
r_work: 0.2163 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.2163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8940
moved from start:          0.4078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   7825  Z= 0.252
  Angle     :  0.560   6.489  10375  Z= 0.282
  Chirality :  0.042   0.108    850
  Planarity :  0.003   0.025   1350
  Dihedral  :  3.638  18.622   1075
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 10.97 %
    Favored  : 88.90 %
  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:  0.22 (0.28), residues: 950
  helix:  2.32 (0.37), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.60 (0.24), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP U   8 
 HIS   0.002   0.000   HIS Y  16 
 PHE   0.003   0.001   PHE U   2 
 TYR   0.012   0.001   TYR H  25 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.802 
Fit side-chains
REVERT: D   20 LYS cc_start: 0.9622 (mmmt) cc_final: 0.9376 (mmmm)
REVERT: G   11 ASP cc_start: 0.8213 (t0) cc_final: 0.7855 (t0)
REVERT: I   13 MET cc_start: 0.8784 (mpp) cc_final: 0.8332 (mpp)
REVERT: I   20 LYS cc_start: 0.9602 (mmmt) cc_final: 0.9368 (mmmm)
REVERT: J   20 LYS cc_start: 0.9640 (mmmt) cc_final: 0.9367 (mmmm)
REVERT: K    5 ASN cc_start: 0.9397 (t0) cc_final: 0.8735 (t0)
REVERT: K   20 LYS cc_start: 0.9622 (mmmt) cc_final: 0.9391 (mmmm)
REVERT: M   10 GLU cc_start: 0.9130 (pm20) cc_final: 0.8898 (pm20)
REVERT: M   26 LYS cc_start: 0.9327 (ptmt) cc_final: 0.8929 (ptmm)
REVERT: N   20 LYS cc_start: 0.9644 (mmmt) cc_final: 0.9399 (mmmm)
REVERT: O    5 ASN cc_start: 0.9381 (t0) cc_final: 0.8748 (t0)
REVERT: O   10 GLU cc_start: 0.9083 (pm20) cc_final: 0.8841 (pm20)
REVERT: P   20 LYS cc_start: 0.9650 (mmmt) cc_final: 0.9286 (mmmm)
REVERT: T    5 ASN cc_start: 0.9499 (t0) cc_final: 0.8967 (t0)
REVERT: T   20 LYS cc_start: 0.9647 (mmmt) cc_final: 0.9338 (mmmm)
REVERT: V    5 ASN cc_start: 0.9541 (t0) cc_final: 0.8906 (t0)
REVERT: V   20 LYS cc_start: 0.9653 (mmmt) cc_final: 0.9417 (mmmm)
REVERT: V   32 LYS cc_start: 0.9622 (mmtt) cc_final: 0.8878 (mtpt)
REVERT: X    5 ASN cc_start: 0.9441 (t0) cc_final: 0.8944 (t0)
REVERT: X   20 LYS cc_start: 0.9683 (mmmt) cc_final: 0.9475 (mmmm)
REVERT: X   26 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9103 (ptpp)
REVERT: X   32 LYS cc_start: 0.9635 (mmtt) cc_final: 0.8831 (ttpt)
REVERT: Y   13 MET cc_start: 0.8453 (mmt) cc_final: 0.8162 (mmm)
REVERT: Y   25 TYR cc_start: 0.9584 (m-80) cc_final: 0.9075 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 127
  average time/residue: 0.3845
  time to fit residues: 57.5122
Evaluate side-chains
  127 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   26 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 78 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 34 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0020
   chunk 32 optimal weight:    2.9990
   chunk 17 optimal weight:    8.9990
   chunk 97 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    2.3996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.037900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2363 r_free = 0.2363 target = 0.022934 restraints weight = 37196.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.2314 rms_B_bonded: 5.22
r_work: 0.2151 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.2151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8945
moved from start:          0.4196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   7825  Z= 0.203
  Angle     :  0.538   6.376  10375  Z= 0.271
  Chirality :  0.041   0.109    850
  Planarity :  0.003   0.026   1350
  Dihedral  :  3.577  20.755   1075
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 11.61 %
    Favored  : 88.13 %
  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:  0.27 (0.28), residues: 950
  helix:  2.35 (0.37), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.56 (0.24), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP Y   8 
 HIS   0.001   0.000   HIS S  18 
 PHE   0.005   0.001   PHE S   2 
 TYR   0.014   0.001   TYR W  25 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 131
  time to evaluate  : 0.909 
Fit side-chains
REVERT: D   20 LYS cc_start: 0.9615 (mmmt) cc_final: 0.9353 (mmmm)
REVERT: D   25 TYR cc_start: 0.9549 (m-80) cc_final: 0.9327 (m-80)
REVERT: G   11 ASP cc_start: 0.8234 (t0) cc_final: 0.7971 (t0)
REVERT: I    5 ASN cc_start: 0.9361 (t0) cc_final: 0.8653 (t0)
REVERT: I   20 LYS cc_start: 0.9600 (mmmt) cc_final: 0.9361 (mmmm)
REVERT: J   20 LYS cc_start: 0.9640 (mmmt) cc_final: 0.9348 (mmmm)
REVERT: K    5 ASN cc_start: 0.9347 (t0) cc_final: 0.8640 (t0)
REVERT: K   10 GLU cc_start: 0.9008 (pm20) cc_final: 0.8787 (pm20)
REVERT: K   20 LYS cc_start: 0.9624 (mmmt) cc_final: 0.9395 (mmmm)
REVERT: M    5 ASN cc_start: 0.9400 (t0) cc_final: 0.8723 (t0)
REVERT: M   10 GLU cc_start: 0.9143 (pm20) cc_final: 0.8922 (pm20)
REVERT: M   26 LYS cc_start: 0.9343 (ptmt) cc_final: 0.8957 (ptmm)
REVERT: N   20 LYS cc_start: 0.9631 (mmmt) cc_final: 0.9381 (mmmm)
REVERT: O    5 ASN cc_start: 0.9302 (t0) cc_final: 0.8650 (t0)
REVERT: O   10 GLU cc_start: 0.9083 (pm20) cc_final: 0.8852 (pm20)
REVERT: P   20 LYS cc_start: 0.9657 (mmmt) cc_final: 0.9312 (mmmm)
REVERT: S   20 LYS cc_start: 0.9628 (mmmt) cc_final: 0.9412 (mmmm)
REVERT: T    5 ASN cc_start: 0.9451 (t0) cc_final: 0.8829 (t0)
REVERT: T   20 LYS cc_start: 0.9645 (mmmt) cc_final: 0.9328 (mmmm)
REVERT: V    5 ASN cc_start: 0.9509 (t0) cc_final: 0.8874 (t0)
REVERT: V   20 LYS cc_start: 0.9653 (mmmt) cc_final: 0.9412 (mmmm)
REVERT: V   32 LYS cc_start: 0.9603 (mmtt) cc_final: 0.8847 (mtpt)
REVERT: X    5 ASN cc_start: 0.9369 (t0) cc_final: 0.8764 (t0)
REVERT: X   20 LYS cc_start: 0.9665 (mmmt) cc_final: 0.9447 (mmmm)
REVERT: X   26 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9120 (ptpp)
REVERT: X   32 LYS cc_start: 0.9635 (mmtt) cc_final: 0.8820 (ttpt)
REVERT: Y   13 MET cc_start: 0.8366 (mmt) cc_final: 0.8055 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 131
  average time/residue: 0.3815
  time to fit residues: 58.9647
Evaluate side-chains
  130 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   26 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 70 optimal weight:    4.9990
   chunk 30 optimal weight:    7.9990
   chunk 42 optimal weight:   10.0000
   chunk 15 optimal weight:    6.9990
   chunk 32 optimal weight:    0.0980
   chunk 50 optimal weight:   10.0000
   chunk 90 optimal weight:    0.7980
   chunk 98 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.7786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.037786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2377 r_free = 0.2377 target = 0.023122 restraints weight = 36266.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.2346 rms_B_bonded: 5.14
r_work: 0.2178 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.2178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8932
moved from start:          0.4334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7825  Z= 0.171
  Angle     :  0.539   6.830  10375  Z= 0.270
  Chirality :  0.041   0.115    850
  Planarity :  0.003   0.025   1350
  Dihedral  :  3.423  21.130   1075
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 11.87 %
    Favored  : 88.00 %
  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:  0.28 (0.28), residues: 950
  helix:  2.35 (0.37), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.56 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP T   8 
 HIS   0.001   0.000   HIS O  18 
 PHE   0.002   0.001   PHE Y  35 
 TYR   0.014   0.001   TYR W  25 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 1.280 
Fit side-chains
REVERT: A   20 LYS cc_start: 0.9643 (mmmt) cc_final: 0.9419 (mmmm)
REVERT: D   20 LYS cc_start: 0.9629 (mmmt) cc_final: 0.9366 (mmmm)
REVERT: G    5 ASN cc_start: 0.9249 (t0) cc_final: 0.8507 (t0)
REVERT: G   11 ASP cc_start: 0.8221 (t0) cc_final: 0.7796 (t0)
REVERT: G   20 LYS cc_start: 0.9586 (mmmt) cc_final: 0.9382 (mmmm)
REVERT: I    5 ASN cc_start: 0.9294 (t0) cc_final: 0.8497 (t0)
REVERT: I   20 LYS cc_start: 0.9600 (mmmt) cc_final: 0.9362 (mmmm)
REVERT: J   20 LYS cc_start: 0.9646 (mmmt) cc_final: 0.9351 (mmmm)
REVERT: K    5 ASN cc_start: 0.9305 (t0) cc_final: 0.8594 (t0)
REVERT: K   10 GLU cc_start: 0.9030 (pm20) cc_final: 0.8810 (pm20)
REVERT: K   20 LYS cc_start: 0.9630 (mmmt) cc_final: 0.9404 (mmmm)
REVERT: L   20 LYS cc_start: 0.9646 (mmmt) cc_final: 0.9400 (mmmm)
REVERT: M    5 ASN cc_start: 0.9366 (t0) cc_final: 0.8675 (t0)
REVERT: M   26 LYS cc_start: 0.9315 (ptmt) cc_final: 0.8918 (ptmm)
REVERT: N   20 LYS cc_start: 0.9650 (mmmt) cc_final: 0.9406 (mmmm)
REVERT: O    5 ASN cc_start: 0.9272 (t0) cc_final: 0.8587 (t0)
REVERT: P   20 LYS cc_start: 0.9622 (mmmt) cc_final: 0.9290 (mmmm)
REVERT: Q   20 LYS cc_start: 0.9666 (mmmt) cc_final: 0.9451 (mmmm)
REVERT: R    5 ASN cc_start: 0.9378 (t0) cc_final: 0.8894 (t0)
REVERT: S   20 LYS cc_start: 0.9644 (mmmt) cc_final: 0.9414 (mmmm)
REVERT: T    5 ASN cc_start: 0.9402 (t0) cc_final: 0.8976 (t0)
REVERT: T   10 GLU cc_start: 0.8802 (pm20) cc_final: 0.8541 (pm20)
REVERT: T   20 LYS cc_start: 0.9638 (mmmt) cc_final: 0.9309 (mmmm)
REVERT: T   25 TYR cc_start: 0.9498 (m-80) cc_final: 0.9175 (m-80)
REVERT: U   20 LYS cc_start: 0.9673 (mmmt) cc_final: 0.9431 (mmmm)
REVERT: V    5 ASN cc_start: 0.9424 (t0) cc_final: 0.8741 (t0)
REVERT: V   10 GLU cc_start: 0.8771 (pm20) cc_final: 0.8420 (pm20)
REVERT: V   20 LYS cc_start: 0.9656 (mmmt) cc_final: 0.9413 (mmmm)
REVERT: V   32 LYS cc_start: 0.9604 (mmtt) cc_final: 0.8885 (mtpt)
REVERT: X    5 ASN cc_start: 0.9348 (t0) cc_final: 0.8711 (t0)
REVERT: X   20 LYS cc_start: 0.9660 (mmmt) cc_final: 0.9451 (mmmm)
REVERT: X   26 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.9119 (ptpp)
REVERT: X   32 LYS cc_start: 0.9622 (mmtt) cc_final: 0.8790 (ttpt)
REVERT: Y   13 MET cc_start: 0.8367 (mmt) cc_final: 0.8055 (mmm)
REVERT: Y   25 TYR cc_start: 0.9596 (m-80) cc_final: 0.9098 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 140
  average time/residue: 0.4050
  time to fit residues: 66.5135
Evaluate side-chains
  137 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   26 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 51 optimal weight:    9.9990
   chunk 88 optimal weight:    0.6980
   chunk 90 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 97 optimal weight:    0.3980
   chunk 28 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 47 optimal weight:    0.3980
   overall best weight:    1.2984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.038004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2381 r_free = 0.2381 target = 0.023233 restraints weight = 36727.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.2352 rms_B_bonded: 5.20
r_work: 0.2187 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.2187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8923
moved from start:          0.4424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7825  Z= 0.158
  Angle     :  0.561   7.636  10375  Z= 0.278
  Chirality :  0.040   0.112    850
  Planarity :  0.003   0.025   1350
  Dihedral  :  3.290  20.560   1075
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 11.87 %
    Favored  : 88.00 %
  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:  0.26 (0.28), residues: 950
  helix:  2.29 (0.37), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.55 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP M   8 
 HIS   0.001   0.000   HIS Y  18 
 PHE   0.003   0.000   PHE A   2 
 TYR   0.014   0.001   TYR W  25 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 0.817 
Fit side-chains
REVERT: A    5 ASN cc_start: 0.9223 (t0) cc_final: 0.8536 (t0)
REVERT: A   20 LYS cc_start: 0.9648 (mmmt) cc_final: 0.9429 (mmmm)
REVERT: D   20 LYS cc_start: 0.9615 (mmmt) cc_final: 0.9348 (mmmm)
REVERT: E   20 LYS cc_start: 0.9594 (mmmt) cc_final: 0.9387 (mmmm)
REVERT: G    5 ASN cc_start: 0.9231 (t0) cc_final: 0.8457 (t0)
REVERT: G   11 ASP cc_start: 0.8191 (t0) cc_final: 0.7913 (t0)
REVERT: G   20 LYS cc_start: 0.9583 (mmmt) cc_final: 0.9288 (mmmm)
REVERT: I    5 ASN cc_start: 0.9250 (t0) cc_final: 0.8441 (t0)
REVERT: I   20 LYS cc_start: 0.9613 (mmmt) cc_final: 0.9396 (mmmm)
REVERT: J   20 LYS cc_start: 0.9655 (mmmt) cc_final: 0.9355 (mmmm)
REVERT: K    5 ASN cc_start: 0.9268 (t0) cc_final: 0.8514 (t0)
REVERT: K   20 LYS cc_start: 0.9627 (mmmt) cc_final: 0.9404 (mmmm)
REVERT: L   20 LYS cc_start: 0.9659 (mmmt) cc_final: 0.9411 (mmmm)
REVERT: M    5 ASN cc_start: 0.9305 (t0) cc_final: 0.8565 (t0)
REVERT: M   10 GLU cc_start: 0.9034 (pm20) cc_final: 0.8719 (pm20)
REVERT: M   26 LYS cc_start: 0.9312 (ptmt) cc_final: 0.8897 (ptmm)
REVERT: N   20 LYS cc_start: 0.9645 (mmmt) cc_final: 0.9399 (mmmm)
REVERT: O    5 ASN cc_start: 0.9227 (t0) cc_final: 0.8501 (t0)
REVERT: O   10 GLU cc_start: 0.8991 (pm20) cc_final: 0.8697 (pm20)
REVERT: P    5 ASN cc_start: 0.9370 (t0) cc_final: 0.8974 (t0)
REVERT: P   20 LYS cc_start: 0.9625 (mmmt) cc_final: 0.9276 (mmmm)
REVERT: Q   20 LYS cc_start: 0.9679 (mmmt) cc_final: 0.9469 (mmmm)
REVERT: R    5 ASN cc_start: 0.9348 (t0) cc_final: 0.8858 (t0)
REVERT: S   20 LYS cc_start: 0.9644 (mmmt) cc_final: 0.9424 (mmmm)
REVERT: T    5 ASN cc_start: 0.9359 (t0) cc_final: 0.8914 (t0)
REVERT: T   20 LYS cc_start: 0.9629 (mmmt) cc_final: 0.9294 (mmmm)
REVERT: T   25 TYR cc_start: 0.9484 (m-80) cc_final: 0.9170 (m-80)
REVERT: U   20 LYS cc_start: 0.9682 (mmmt) cc_final: 0.9442 (mmmm)
REVERT: V    5 ASN cc_start: 0.9388 (t0) cc_final: 0.8699 (t0)
REVERT: V   10 GLU cc_start: 0.8808 (pm20) cc_final: 0.8460 (pm20)
REVERT: V   20 LYS cc_start: 0.9666 (mmmt) cc_final: 0.9430 (mmmm)
REVERT: V   25 TYR cc_start: 0.9518 (m-80) cc_final: 0.9238 (m-80)
REVERT: V   32 LYS cc_start: 0.9596 (mmtt) cc_final: 0.8876 (mtpt)
REVERT: X    5 ASN cc_start: 0.9301 (t0) cc_final: 0.8652 (t0)
REVERT: X   20 LYS cc_start: 0.9663 (mmmt) cc_final: 0.9448 (mmmm)
REVERT: X   26 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9094 (ptpp)
REVERT: X   32 LYS cc_start: 0.9617 (mmtt) cc_final: 0.8786 (ttpt)
REVERT: Y   13 MET cc_start: 0.8394 (mmt) cc_final: 0.8076 (mmm)
REVERT: Y   25 TYR cc_start: 0.9592 (m-80) cc_final: 0.9083 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 148
  average time/residue: 0.3795
  time to fit residues: 66.1185
Evaluate side-chains
  143 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   26 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0070
   chunk 18 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   chunk 77 optimal weight:    8.9990
   chunk 17 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   overall best weight:    1.4004

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.037910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2385 r_free = 0.2385 target = 0.023243 restraints weight = 36930.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.2353 rms_B_bonded: 5.19
r_work: 0.2187 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.2187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8918
moved from start:          0.4481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7825  Z= 0.175
  Angle     :  0.598   8.031  10375  Z= 0.295
  Chirality :  0.040   0.113    850
  Planarity :  0.003   0.025   1350
  Dihedral  :  3.201  20.700   1075
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 12.26 %
    Favored  : 87.61 %
  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:  0.29 (0.28), residues: 950
  helix:  2.34 (0.37), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.54 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP K   8 
 HIS   0.001   0.000   HIS Y  18 
 PHE   0.003   0.000   PHE J   2 
 TYR   0.014   0.001   TYR W  25 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 149
  time to evaluate  : 0.848 
Fit side-chains
REVERT: A    5 ASN cc_start: 0.9218 (t0) cc_final: 0.8499 (t0)
REVERT: A   20 LYS cc_start: 0.9642 (mmmt) cc_final: 0.9417 (mmmm)
REVERT: C   10 GLU cc_start: 0.8905 (pm20) cc_final: 0.8559 (pm20)
REVERT: D   20 LYS cc_start: 0.9620 (mmmt) cc_final: 0.9355 (mmmm)
REVERT: D   25 TYR cc_start: 0.9540 (m-80) cc_final: 0.9285 (m-80)
REVERT: E   20 LYS cc_start: 0.9619 (mmmt) cc_final: 0.9406 (mmmm)
REVERT: F   20 LYS cc_start: 0.9615 (mmmt) cc_final: 0.9334 (mmmm)
REVERT: G    5 ASN cc_start: 0.9219 (t0) cc_final: 0.8435 (t0)
REVERT: G   11 ASP cc_start: 0.8177 (t0) cc_final: 0.7892 (t0)
REVERT: G   20 LYS cc_start: 0.9588 (mmmt) cc_final: 0.9298 (mmmm)
REVERT: I    5 ASN cc_start: 0.9238 (t0) cc_final: 0.8409 (t0)
REVERT: I   10 GLU cc_start: 0.8837 (pm20) cc_final: 0.8582 (pm20)
REVERT: I   20 LYS cc_start: 0.9616 (mmmt) cc_final: 0.9404 (mmmm)
REVERT: J   20 LYS cc_start: 0.9657 (mmmt) cc_final: 0.9358 (mmmm)
REVERT: K    5 ASN cc_start: 0.9260 (t0) cc_final: 0.8488 (t0)
REVERT: K   20 LYS cc_start: 0.9630 (mmmt) cc_final: 0.9409 (mmmm)
REVERT: L   20 LYS cc_start: 0.9675 (mmmt) cc_final: 0.9434 (mmmm)
REVERT: M    5 ASN cc_start: 0.9298 (t0) cc_final: 0.8559 (t0)
REVERT: M   10 GLU cc_start: 0.9060 (pm20) cc_final: 0.8753 (pm20)
REVERT: M   26 LYS cc_start: 0.9301 (ptmt) cc_final: 0.8884 (ptmm)
REVERT: N   20 LYS cc_start: 0.9646 (mmmt) cc_final: 0.9398 (mmmm)
REVERT: O    5 ASN cc_start: 0.9230 (t0) cc_final: 0.8521 (t0)
REVERT: O   10 GLU cc_start: 0.9071 (pm20) cc_final: 0.8801 (pm20)
REVERT: P    5 ASN cc_start: 0.9372 (t0) cc_final: 0.8961 (t0)
REVERT: P   20 LYS cc_start: 0.9632 (mmmt) cc_final: 0.9281 (mmmm)
REVERT: Q   20 LYS cc_start: 0.9688 (mmmt) cc_final: 0.9477 (mmmm)
REVERT: R    5 ASN cc_start: 0.9343 (t0) cc_final: 0.8867 (t0)
REVERT: S   20 LYS cc_start: 0.9656 (mmmt) cc_final: 0.9437 (mmmm)
REVERT: T    5 ASN cc_start: 0.9352 (t0) cc_final: 0.8884 (t0)
REVERT: T   10 GLU cc_start: 0.8809 (pm20) cc_final: 0.8526 (pm20)
REVERT: T   20 LYS cc_start: 0.9648 (mmmt) cc_final: 0.9326 (mmmm)
REVERT: T   25 TYR cc_start: 0.9481 (m-80) cc_final: 0.9122 (m-80)
REVERT: U   20 LYS cc_start: 0.9660 (mmmt) cc_final: 0.9423 (mmmm)
REVERT: V    5 ASN cc_start: 0.9386 (t0) cc_final: 0.8693 (t0)
REVERT: V   10 GLU cc_start: 0.8845 (pm20) cc_final: 0.8490 (pm20)
REVERT: V   20 LYS cc_start: 0.9665 (mmmt) cc_final: 0.9437 (mmmm)
REVERT: V   25 TYR cc_start: 0.9500 (m-80) cc_final: 0.9261 (m-80)
REVERT: V   32 LYS cc_start: 0.9597 (mmtt) cc_final: 0.8881 (mtpt)
REVERT: W    5 ASN cc_start: 0.9249 (t0) cc_final: 0.8600 (t0)
REVERT: X    5 ASN cc_start: 0.9296 (t0) cc_final: 0.8624 (t0)
REVERT: X   20 LYS cc_start: 0.9660 (mmmt) cc_final: 0.9443 (mmmm)
REVERT: X   26 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.9099 (ptpp)
REVERT: X   32 LYS cc_start: 0.9617 (mmtt) cc_final: 0.8799 (ttpt)
REVERT: Y   13 MET cc_start: 0.8388 (mmt) cc_final: 0.8069 (mmm)
REVERT: Y   25 TYR cc_start: 0.9582 (m-80) cc_final: 0.9072 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 149
  average time/residue: 0.3641
  time to fit residues: 64.1856
Evaluate side-chains
  148 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 147
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   26 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 91 optimal weight:    0.0570
   chunk 45 optimal weight:    6.9990
   chunk 58 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   chunk 41 optimal weight:    0.0370
   chunk 19 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 83 optimal weight:    0.0970
   chunk 63 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.4378

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.038114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2379 r_free = 0.2379 target = 0.023243 restraints weight = 37723.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.2342 rms_B_bonded: 5.25
r_work: 0.2181 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.2181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8931
moved from start:          0.4511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7825  Z= 0.180
  Angle     :  0.615   8.551  10375  Z= 0.304
  Chirality :  0.040   0.112    850
  Planarity :  0.003   0.025   1350
  Dihedral  :  3.187  20.307   1075
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 12.52 %
    Favored  : 87.35 %
  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:  0.28 (0.28), residues: 950
  helix:  2.37 (0.37), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.56 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP K   8 
 HIS   0.001   0.000   HIS T  18 
 PHE   0.003   0.000   PHE P   2 
 TYR   0.014   0.001   TYR W  25 

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.846 
Fit side-chains
REVERT: A    5 ASN cc_start: 0.9216 (t0) cc_final: 0.8508 (t0)
REVERT: A   20 LYS cc_start: 0.9645 (mmmt) cc_final: 0.9426 (mmmm)
REVERT: C   10 GLU cc_start: 0.8930 (pm20) cc_final: 0.8596 (pm20)
REVERT: D   20 LYS cc_start: 0.9629 (mmmt) cc_final: 0.9366 (mmmm)
REVERT: E   20 LYS cc_start: 0.9611 (mmmt) cc_final: 0.9398 (mmmm)
REVERT: F   20 LYS cc_start: 0.9619 (mmmt) cc_final: 0.9345 (mmmm)
REVERT: G    5 ASN cc_start: 0.9215 (t0) cc_final: 0.8445 (t0)
REVERT: G   11 ASP cc_start: 0.8181 (t0) cc_final: 0.7895 (t0)
REVERT: G   20 LYS cc_start: 0.9599 (mmmt) cc_final: 0.9315 (mmmm)
REVERT: H   20 LYS cc_start: 0.9610 (mmmt) cc_final: 0.9393 (mmmm)
REVERT: I    5 ASN cc_start: 0.9226 (t0) cc_final: 0.8413 (t0)
REVERT: I   10 GLU cc_start: 0.8865 (pm20) cc_final: 0.8637 (pm20)
REVERT: I   20 LYS cc_start: 0.9616 (mmmt) cc_final: 0.9409 (mmmm)
REVERT: J   20 LYS cc_start: 0.9657 (mmmt) cc_final: 0.9360 (mmmm)
REVERT: K    5 ASN cc_start: 0.9260 (t0) cc_final: 0.8511 (t0)
REVERT: K   20 LYS cc_start: 0.9635 (mmmt) cc_final: 0.9417 (mmmm)
REVERT: L   20 LYS cc_start: 0.9676 (mmmt) cc_final: 0.9437 (mmmm)
REVERT: M    5 ASN cc_start: 0.9309 (t0) cc_final: 0.8579 (t0)
REVERT: M   10 GLU cc_start: 0.9064 (pm20) cc_final: 0.8756 (pm20)
REVERT: M   26 LYS cc_start: 0.9303 (ptmt) cc_final: 0.8899 (ptmm)
REVERT: N   20 LYS cc_start: 0.9647 (mmmt) cc_final: 0.9396 (mmmm)
REVERT: O    5 ASN cc_start: 0.9224 (t0) cc_final: 0.8520 (t0)
REVERT: O   10 GLU cc_start: 0.9130 (pm20) cc_final: 0.8876 (pm20)
REVERT: P    5 ASN cc_start: 0.9363 (t0) cc_final: 0.8958 (t0)
REVERT: P   20 LYS cc_start: 0.9634 (mmmt) cc_final: 0.9280 (mmmm)
REVERT: Q   10 GLU cc_start: 0.9048 (pm20) cc_final: 0.8760 (pm20)
REVERT: Q   20 LYS cc_start: 0.9688 (mmmt) cc_final: 0.9481 (mmmm)
REVERT: R    5 ASN cc_start: 0.9346 (t0) cc_final: 0.8880 (t0)
REVERT: S   20 LYS cc_start: 0.9651 (mmmt) cc_final: 0.9435 (mmmm)
REVERT: T    5 ASN cc_start: 0.9351 (t0) cc_final: 0.8894 (t0)
REVERT: T   10 GLU cc_start: 0.8828 (pm20) cc_final: 0.8548 (pm20)
REVERT: T   20 LYS cc_start: 0.9648 (mmmt) cc_final: 0.9326 (mmmm)
REVERT: T   25 TYR cc_start: 0.9485 (m-80) cc_final: 0.9137 (m-80)
REVERT: U   13 MET cc_start: 0.8511 (mmp) cc_final: 0.8245 (mmp)
REVERT: U   20 LYS cc_start: 0.9661 (mmmt) cc_final: 0.9424 (mmmm)
REVERT: V    5 ASN cc_start: 0.9386 (t0) cc_final: 0.8697 (t0)
REVERT: V   10 GLU cc_start: 0.8837 (pm20) cc_final: 0.8497 (pm20)
REVERT: V   20 LYS cc_start: 0.9662 (mmmt) cc_final: 0.9433 (mmmm)
REVERT: V   32 LYS cc_start: 0.9606 (mmtt) cc_final: 0.8885 (mtpt)
REVERT: W    5 ASN cc_start: 0.9251 (t0) cc_final: 0.8609 (t0)
REVERT: X    5 ASN cc_start: 0.9302 (t0) cc_final: 0.8640 (t0)
REVERT: X   20 LYS cc_start: 0.9662 (mmmt) cc_final: 0.9451 (mmmm)
REVERT: X   26 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.9152 (ptpp)
REVERT: X   32 LYS cc_start: 0.9621 (mmtt) cc_final: 0.8804 (ttpt)
REVERT: Y    5 ASN cc_start: 0.9220 (t0) cc_final: 0.8606 (t0)
REVERT: Y   13 MET cc_start: 0.8395 (mmt) cc_final: 0.8070 (mmm)
REVERT: Y   25 TYR cc_start: 0.9591 (m-80) cc_final: 0.9128 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 151
  average time/residue: 0.3684
  time to fit residues: 65.6662
Evaluate side-chains
  152 residues out of total 775 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain X residue   26 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 4 optimal weight:    7.9990
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.038332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2396 r_free = 0.2396 target = 0.023504 restraints weight = 36380.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.2366 rms_B_bonded: 5.21
r_work: 0.2201 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.2201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8896
moved from start:          0.4613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7825  Z= 0.170
  Angle     :  0.612   8.389  10375  Z= 0.301
  Chirality :  0.040   0.114    850
  Planarity :  0.003   0.024   1350
  Dihedral  :  3.099  19.273   1075
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  : 12.52 %
    Favored  : 87.35 %
  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:  0.26 (0.27), residues: 950
  helix:  2.35 (0.37), residues: 225
  sheet:  None (None), residues: 0
  loop : -0.57 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP G   8 
 HIS   0.001   0.000   HIS L  18 
 PHE   0.003   0.000   PHE Y  35 
 TYR   0.015   0.001   TYR W  25 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3502.12 seconds
wall clock time: 61 minutes 11.11 seconds (3671.11 seconds total)