Starting phenix.real_space_refine
on Tue Feb  3 13:19:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ulz_64268/02_2026/9ulz_64268.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ulz_64268/02_2026/9ulz_64268.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ulz_64268/02_2026/9ulz_64268.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ulz_64268/02_2026/9ulz_64268.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ulz_64268/02_2026/9ulz_64268.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ulz_64268/02_2026/9ulz_64268.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   1.000
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      24      5.16       5
     C    1908      2.51       5
     N     576      2.21       5
     O     660      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3168
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 264
          Classifications: {'peptide': 36}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 35}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J, K, L
  Time building chain proxies: 0.28, per 1000 atoms: 0.09
  Number of scatterers: 3168
  At special positions: 0
  Unit cell: (94.132, 56.852, 46.6, 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      24     16.00
     O     660      8.00
     N     576      7.00
     C    1908      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   2 " - pdb=" SG  CYS A   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   2 " - pdb=" SG  CYS B   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   2 " - pdb=" SG  CYS C   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   2 " - pdb=" SG  CYS D   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E   2 " - pdb=" SG  CYS E   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F   2 " - pdb=" SG  CYS F   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G   2 " - pdb=" SG  CYS G   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H   2 " - pdb=" SG  CYS H   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I   2 " - pdb=" SG  CYS I   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J   2 " - pdb=" SG  CYS J   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K   2 " - pdb=" SG  CYS K   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L   2 " - pdb=" SG  CYS L   7 " 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: 0.24
  Conformation dependent library (CDL) restraints added in 120.1 milliseconds
  

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  816

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 44.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'G' and resid 8 through 18
      removed outlier: 8.996A  pdb=" N   ALA E   8 " --> pdb=" O   THR G   9 " (cutoff:3.500A)
      removed outlier: 9.892A  pdb=" N   ARG G  11 " --> pdb=" O   ALA E   8 " (cutoff:3.500A)
      removed outlier: 8.889A  pdb=" N   GLN E  10 " --> pdb=" O   ARG G  11 " (cutoff:3.500A)
      removed outlier: 10.062A  pdb=" N   ALA G  13 " --> pdb=" O   GLN E  10 " (cutoff:3.500A)
      removed outlier: 8.910A  pdb=" N   LEU E  12 " --> pdb=" O   ALA G  13 " (cutoff:3.500A)
      removed outlier: 9.073A  pdb=" N   PHE G  15 " --> pdb=" O   LEU E  12 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ASN E  14 " --> pdb=" O   PHE G  15 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL G  17 " --> pdb=" O   ASN E  14 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   LEU E  16 " --> pdb=" O   VAL G  17 " (cutoff:3.500A)
      removed outlier: 8.994A  pdb=" N   ALA C   8 " --> pdb=" O   THR E   9 " (cutoff:3.500A)
      removed outlier: 9.896A  pdb=" N   ARG E  11 " --> pdb=" O   ALA C   8 " (cutoff:3.500A)
      removed outlier: 8.891A  pdb=" N   GLN C  10 " --> pdb=" O   ARG E  11 " (cutoff:3.500A)
      removed outlier: 10.069A  pdb=" N   ALA E  13 " --> pdb=" O   GLN C  10 " (cutoff:3.500A)
      removed outlier: 8.915A  pdb=" N   LEU C  12 " --> pdb=" O   ALA E  13 " (cutoff:3.500A)
      removed outlier: 9.084A  pdb=" N   PHE E  15 " --> pdb=" O   LEU C  12 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ASN C  14 " --> pdb=" O   PHE E  15 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   VAL E  17 " --> pdb=" O   ASN C  14 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   LEU C  16 " --> pdb=" O   VAL E  17 " (cutoff:3.500A)
      removed outlier: 9.008A  pdb=" N   ALA A   8 " --> pdb=" O   THR C   9 " (cutoff:3.500A)
      removed outlier: 9.915A  pdb=" N   ARG C  11 " --> pdb=" O   ALA A   8 " (cutoff:3.500A)
      removed outlier: 8.910A  pdb=" N   GLN A  10 " --> pdb=" O   ARG C  11 " (cutoff:3.500A)
      removed outlier: 10.090A  pdb=" N   ALA C  13 " --> pdb=" O   GLN A  10 " (cutoff:3.500A)
      removed outlier: 8.933A  pdb=" N   LEU A  12 " --> pdb=" O   ALA C  13 " (cutoff:3.500A)
      removed outlier: 9.109A  pdb=" N   PHE C  15 " --> pdb=" O   LEU A  12 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ASN A  14 " --> pdb=" O   PHE C  15 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   VAL C  17 " --> pdb=" O   ASN A  14 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   LEU A  16 " --> pdb=" O   VAL C  17 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   THR A   9 " --> pdb=" O   ALA K   8 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   GLN K  10 " --> pdb=" O   THR A   9 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   ARG A  11 " --> pdb=" O   GLN K  10 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   LEU K  12 " --> pdb=" O   ARG A  11 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   ALA A  13 " --> pdb=" O   LEU K  12 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ASN K  14 " --> pdb=" O   ALA A  13 " (cutoff:3.500A)
      removed outlier: 9.002A  pdb=" N   ALA I   8 " --> pdb=" O   THR K   9 " (cutoff:3.500A)
      removed outlier: 9.907A  pdb=" N   ARG K  11 " --> pdb=" O   ALA I   8 " (cutoff:3.500A)
      removed outlier: 8.900A  pdb=" N   GLN I  10 " --> pdb=" O   ARG K  11 " (cutoff:3.500A)
      removed outlier: 10.079A  pdb=" N   ALA K  13 " --> pdb=" O   GLN I  10 " (cutoff:3.500A)
      removed outlier: 8.922A  pdb=" N   LEU I  12 " --> pdb=" O   ALA K  13 " (cutoff:3.500A)
      removed outlier: 9.094A  pdb=" N   PHE K  15 " --> pdb=" O   LEU I  12 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ASN I  14 " --> pdb=" O   PHE K  15 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   VAL K  17 " --> pdb=" O   ASN I  14 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   LEU I  16 " --> pdb=" O   VAL K  17 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'G' and resid 21 through 22
      removed outlier: 6.633A  pdb=" N   ASN E  21 " --> pdb=" O   ASN G  22 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ASN C  21 " --> pdb=" O   ASN E  22 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ASN A  21 " --> pdb=" O   ASN C  22 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   ASN I  21 " --> pdb=" O   ASN K  22 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'G' and resid 26 through 30
      removed outlier: 6.783A  pdb=" N   LEU E  27 " --> pdb=" O   SER G  28 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   THR G  30 " --> pdb=" O   LEU E  27 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   SER E  29 " --> pdb=" O   THR G  30 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   LEU C  27 " --> pdb=" O   SER E  28 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   THR E  30 " --> pdb=" O   LEU C  27 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   SER C  29 " --> pdb=" O   THR E  30 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   LEU A  27 " --> pdb=" O   SER C  28 " (cutoff:3.500A)
      removed outlier: 8.078A  pdb=" N   THR C  30 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   SER A  29 " --> pdb=" O   THR C  30 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   LEU I  27 " --> pdb=" O   SER K  28 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   THR K  30 " --> pdb=" O   LEU I  27 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   SER I  29 " --> pdb=" O   THR K  30 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'G' and resid 35 through 36
      removed outlier: 6.603A  pdb=" N   ASN E  35 " --> pdb=" O   THR G  36 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   ASN C  35 " --> pdb=" O   THR E  36 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   ASN A  35 " --> pdb=" O   THR C  36 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ASN I  35 " --> pdb=" O   THR K  36 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 8 through 18
      removed outlier: 9.247A  pdb=" N   ALA F   8 " --> pdb=" O   THR H   9 " (cutoff:3.500A)
      removed outlier: 10.116A  pdb=" N   ARG H  11 " --> pdb=" O   ALA F   8 " (cutoff:3.500A)
      removed outlier: 9.119A  pdb=" N   GLN F  10 " --> pdb=" O   ARG H  11 " (cutoff:3.500A)
      removed outlier: 10.265A  pdb=" N   ALA H  13 " --> pdb=" O   GLN F  10 " (cutoff:3.500A)
      removed outlier: 9.123A  pdb=" N   LEU F  12 " --> pdb=" O   ALA H  13 " (cutoff:3.500A)
      removed outlier: 9.256A  pdb=" N   PHE H  15 " --> pdb=" O   LEU F  12 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   ASN F  14 " --> pdb=" O   PHE H  15 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   VAL H  17 " --> pdb=" O   ASN F  14 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   LEU F  16 " --> pdb=" O   VAL H  17 " (cutoff:3.500A)
      removed outlier: 8.961A  pdb=" N   ALA D   8 " --> pdb=" O   THR F   9 " (cutoff:3.500A)
      removed outlier: 9.883A  pdb=" N   ARG F  11 " --> pdb=" O   ALA D   8 " (cutoff:3.500A)
      removed outlier: 8.884A  pdb=" N   GLN D  10 " --> pdb=" O   ARG F  11 " (cutoff:3.500A)
      removed outlier: 10.073A  pdb=" N   ALA F  13 " --> pdb=" O   GLN D  10 " (cutoff:3.500A)
      removed outlier: 8.924A  pdb=" N   LEU D  12 " --> pdb=" O   ALA F  13 " (cutoff:3.500A)
      removed outlier: 9.072A  pdb=" N   PHE F  15 " --> pdb=" O   LEU D  12 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ASN D  14 " --> pdb=" O   PHE F  15 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   VAL F  17 " --> pdb=" O   ASN D  14 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   LEU D  16 " --> pdb=" O   VAL F  17 " (cutoff:3.500A)
      removed outlier: 9.009A  pdb=" N   ALA B   8 " --> pdb=" O   THR D   9 " (cutoff:3.500A)
      removed outlier: 9.914A  pdb=" N   ARG D  11 " --> pdb=" O   ALA B   8 " (cutoff:3.500A)
      removed outlier: 8.908A  pdb=" N   GLN B  10 " --> pdb=" O   ARG D  11 " (cutoff:3.500A)
      removed outlier: 10.090A  pdb=" N   ALA D  13 " --> pdb=" O   GLN B  10 " (cutoff:3.500A)
      removed outlier: 8.933A  pdb=" N   LEU B  12 " --> pdb=" O   ALA D  13 " (cutoff:3.500A)
      removed outlier: 9.107A  pdb=" N   PHE D  15 " --> pdb=" O   LEU B  12 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ASN B  14 " --> pdb=" O   PHE D  15 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   VAL D  17 " --> pdb=" O   ASN B  14 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   LEU B  16 " --> pdb=" O   VAL D  17 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   THR B   9 " --> pdb=" O   ALA L   8 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   GLN L  10 " --> pdb=" O   THR B   9 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   ARG B  11 " --> pdb=" O   GLN L  10 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   LEU L  12 " --> pdb=" O   ARG B  11 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   ALA B  13 " --> pdb=" O   LEU L  12 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ASN L  14 " --> pdb=" O   ALA B  13 " (cutoff:3.500A)
      removed outlier: 9.002A  pdb=" N   ALA J   8 " --> pdb=" O   THR L   9 " (cutoff:3.500A)
      removed outlier: 9.907A  pdb=" N   ARG L  11 " --> pdb=" O   ALA J   8 " (cutoff:3.500A)
      removed outlier: 8.899A  pdb=" N   GLN J  10 " --> pdb=" O   ARG L  11 " (cutoff:3.500A)
      removed outlier: 10.079A  pdb=" N   ALA L  13 " --> pdb=" O   GLN J  10 " (cutoff:3.500A)
      removed outlier: 8.922A  pdb=" N   LEU J  12 " --> pdb=" O   ALA L  13 " (cutoff:3.500A)
      removed outlier: 9.094A  pdb=" N   PHE L  15 " --> pdb=" O   LEU J  12 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ASN J  14 " --> pdb=" O   PHE L  15 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   VAL L  17 " --> pdb=" O   ASN J  14 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   LEU J  16 " --> pdb=" O   VAL L  17 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 21 through 22
      removed outlier: 6.673A  pdb=" N   ASN F  21 " --> pdb=" O   ASN H  22 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   ASN D  21 " --> pdb=" O   ASN F  22 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ASN B  21 " --> pdb=" O   ASN D  22 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   ASN J  21 " --> pdb=" O   ASN L  22 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 26 through 29
      removed outlier: 6.797A  pdb=" N   LEU B  27 " --> pdb=" O   SER D  28 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   THR D  30 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   SER B  29 " --> pdb=" O   THR D  30 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   LEU J  27 " --> pdb=" O   SER L  28 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   THR L  30 " --> pdb=" O   LEU J  27 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   SER J  29 " --> pdb=" O   THR L  30 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 35 through 36
      removed outlier: 6.637A  pdb=" N   ASN F  35 " --> pdb=" O   THR H  36 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   ASN D  35 " --> pdb=" O   THR F  36 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   ASN B  35 " --> pdb=" O   THR D  36 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ASN J  35 " --> pdb=" O   THR L  36 " (cutoff:3.500A)

    26 hydrogen bonds defined for protein.
    78 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: 0.40

  Time building geometry restraints manager: 0.34 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: 1092
        1.34 -     1.46: 723
        1.46 -     1.57: 1365
        1.57 -     1.69: 0
        1.69 -     1.80: 24
  Bond restraints: 3204
  Sorted by residual:
  bond pdb=" C   GLY I  33 "
       pdb=" O   GLY I  33 "
    ideal  model  delta    sigma   weight residual
    1.236  1.232  0.004 9.20e-03 1.18e+04 2.25e-01
  bond pdb=" C   GLY J  33 "
       pdb=" O   GLY J  33 "
    ideal  model  delta    sigma   weight residual
    1.236  1.232  0.004 9.20e-03 1.18e+04 2.25e-01
  bond pdb=" C   GLY F  33 "
       pdb=" O   GLY F  33 "
    ideal  model  delta    sigma   weight residual
    1.236  1.232  0.004 9.20e-03 1.18e+04 2.06e-01
  bond pdb=" CB  VAL E  17 "
       pdb=" CG1 VAL E  17 "
    ideal  model  delta    sigma   weight residual
    1.521  1.507  0.014 3.30e-02 9.18e+02 1.87e-01
  bond pdb=" CB  VAL A  17 "
       pdb=" CG1 VAL A  17 "
    ideal  model  delta    sigma   weight residual
    1.521  1.507  0.014 3.30e-02 9.18e+02 1.84e-01
  ... (remaining 3199 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.92: 3863
        0.92 -     1.83: 399
        1.83 -     2.75: 70
        2.75 -     3.66: 12
        3.66 -     4.58: 24
  Bond angle restraints: 4368
  Sorted by residual:
  angle pdb=" N   GLY B  24 "
        pdb=" CA  GLY B  24 "
        pdb=" C   GLY B  24 "
      ideal   model   delta    sigma   weight residual
     113.18  117.76   -4.58 2.37e+00 1.78e-01 3.73e+00
  angle pdb=" N   GLY G  24 "
        pdb=" CA  GLY G  24 "
        pdb=" C   GLY G  24 "
      ideal   model   delta    sigma   weight residual
     113.18  117.76   -4.58 2.37e+00 1.78e-01 3.73e+00
  angle pdb=" N   GLY H  24 "
        pdb=" CA  GLY H  24 "
        pdb=" C   GLY H  24 "
      ideal   model   delta    sigma   weight residual
     113.18  117.75   -4.57 2.37e+00 1.78e-01 3.72e+00
  angle pdb=" N   GLY D  24 "
        pdb=" CA  GLY D  24 "
        pdb=" C   GLY D  24 "
      ideal   model   delta    sigma   weight residual
     113.18  117.74   -4.56 2.37e+00 1.78e-01 3.71e+00
  angle pdb=" N   GLY C  24 "
        pdb=" CA  GLY C  24 "
        pdb=" C   GLY C  24 "
      ideal   model   delta    sigma   weight residual
     113.18  117.74   -4.56 2.37e+00 1.78e-01 3.71e+00
  ... (remaining 4363 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.83: 1368
        8.83 -    17.65: 312
       17.65 -    26.48: 156
       26.48 -    35.30: 24
       35.30 -    44.13: 36
  Dihedral angle restraints: 1896
    sinusoidal: 648
      harmonic: 1248
  Sorted by residual:
  dihedral pdb=" CB  CYS H   2 "
           pdb=" SG  CYS H   2 "
           pdb=" SG  CYS H   7 "
           pdb=" CB  CYS H   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -130.13   44.13     1      1.00e+01 1.00e-02 2.71e+01
  dihedral pdb=" CB  CYS D   2 "
           pdb=" SG  CYS D   2 "
           pdb=" SG  CYS D   7 "
           pdb=" CB  CYS D   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -130.12   44.12     1      1.00e+01 1.00e-02 2.71e+01
  dihedral pdb=" CB  CYS I   2 "
           pdb=" SG  CYS I   2 "
           pdb=" SG  CYS I   7 "
           pdb=" CB  CYS I   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -130.12   44.12     1      1.00e+01 1.00e-02 2.71e+01
  ... (remaining 1893 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 286
       0.024 -    0.048: 148
       0.048 -    0.072: 47
       0.072 -    0.096: 35
       0.096 -    0.120: 24
  Chirality restraints: 540
  Sorted by residual:
  chirality pdb=" CA  VAL E  17 "
            pdb=" N   VAL E  17 "
            pdb=" C   VAL E  17 "
            pdb=" CB  VAL E  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.60e-01
  chirality pdb=" CA  VAL K  17 "
            pdb=" N   VAL K  17 "
            pdb=" C   VAL K  17 "
            pdb=" CB  VAL K  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.58e-01
  chirality pdb=" CA  VAL L  17 "
            pdb=" N   VAL L  17 "
            pdb=" C   VAL L  17 "
            pdb=" CB  VAL L  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.58e-01
  ... (remaining 537 not shown)

  Planarity restraints: 576
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN F  31 "    0.002 2.00e-02 2.50e+03   4.86e-03 2.36e-01
        pdb=" C   ASN F  31 "   -0.008 2.00e-02 2.50e+03
        pdb=" O   ASN F  31 "    0.003 2.00e-02 2.50e+03
        pdb=" N   VAL F  32 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN K  31 "   -0.002 2.00e-02 2.50e+03   4.80e-03 2.31e-01
        pdb=" C   ASN K  31 "    0.008 2.00e-02 2.50e+03
        pdb=" O   ASN K  31 "   -0.003 2.00e-02 2.50e+03
        pdb=" N   VAL K  32 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN L  31 "    0.002 2.00e-02 2.50e+03   4.80e-03 2.31e-01
        pdb=" C   ASN L  31 "   -0.008 2.00e-02 2.50e+03
        pdb=" O   ASN L  31 "    0.003 2.00e-02 2.50e+03
        pdb=" N   VAL L  32 "    0.003 2.00e-02 2.50e+03
  ... (remaining 573 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 447
        2.77 -     3.30: 2912
        3.30 -     3.83: 5569
        3.83 -     4.37: 6161
        4.37 -     4.90: 12303
  Nonbonded interactions: 27392
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E  37 "
            pdb=" OG  SER G  29 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OH  TYR D  37 "
            pdb=" OG  SER F  29 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OH  TYR C  37 "
            pdb=" OG  SER E  29 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OH  TYR I  37 "
            pdb=" OG  SER K  29 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OH  TYR J  37 "
            pdb=" OG  SER L  29 "
     model   vdw
     2.250 3.040
  ... (remaining 27387 not shown)

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

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:             0.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.230
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
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      :  0.003   0.014   3216  Z= 0.140
  Angle     :  0.664   4.579   4392  Z= 0.356
  Chirality :  0.040   0.120    540
  Planarity :  0.001   0.005    576
  Dihedral  : 12.477  38.383   1044
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.76 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.33 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.22 (0.24), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.97 (0.18), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F  11 
 TYR   0.002   0.000   TYR I  37 
 PHE   0.003   0.001   PHE B  15 
 HIS   0.001   0.000   HIS F  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 3204)
  covalent geometry    : angle       0.66583 ( 4368)
  SS BOND              : bond        0.00129 (   12)
  SS BOND              : angle       0.25956 (   24)
  hydrogen bonds       : bond        0.14249 (   26)
  hydrogen bonds       : angle       6.55056 (   78)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.121 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0634
  time to fit residues: 3.1891
Evaluate side-chains
  31 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:   20.0000
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:   20.0000
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    9.9990
   chunk 25 optimal weight:    6.9990
   chunk 19 optimal weight:    0.0770
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 13 optimal weight:    6.9990
   overall best weight:    5.2146

-------------------------------------------------------------------------------
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 = 0.3949 r_free = 0.3949 target = 0.120500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.102369 restraints weight = 3819.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 2.07
r_work: 0.3611 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3514 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.1310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   3216  Z= 0.228
  Angle     :  0.620   4.782   4392  Z= 0.340
  Chirality :  0.041   0.132    540
  Planarity :  0.002   0.008    576
  Dihedral  :  8.049  30.092    456
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.27 %
    Favored  : 88.73 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 19.44 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.35 (0.22), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.07 (0.17), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  11 
 TYR   0.007   0.002   TYR I  37 
 PHE   0.005   0.001   PHE F  23 
 HIS   0.002   0.001   HIS D  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 3204)
  covalent geometry    : angle       0.62167 ( 4368)
  SS BOND              : bond        0.00130 (   12)
  SS BOND              : angle       0.29090 (   24)
  hydrogen bonds       : bond        0.01433 (   26)
  hydrogen bonds       : angle       3.96735 (   78)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.076 
Fit side-chains
  outliers start: 4
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0367
  time to fit residues: 1.6904
Evaluate side-chains
  29 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:   10.0000
   chunk 20 optimal weight:    7.9990
   chunk 9 optimal weight:   20.0000
   chunk 4 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 24 optimal weight:   20.0000
   chunk 7 optimal weight:   20.0000
   chunk 33 optimal weight:   10.0000
   chunk 17 optimal weight:    8.9990
   chunk 19 optimal weight:    8.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
B  10 GLN
C  10 GLN
D  10 GLN
E  10 GLN
F  10 GLN
G  10 GLN
H  10 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.116161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.098064 restraints weight = 3828.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 2.02
r_work: 0.3566 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3472 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   3216  Z= 0.296
  Angle     :  0.653   5.254   4392  Z= 0.362
  Chirality :  0.043   0.130    540
  Planarity :  0.002   0.012    576
  Dihedral  :  8.414  30.564    456
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.54 %
    Favored  : 89.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.50 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.42 (0.22), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.13 (0.17), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  11 
 TYR   0.010   0.002   TYR B  37 
 PHE   0.006   0.001   PHE C  23 
 HIS   0.002   0.001   HIS D  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00641 ( 3204)
  covalent geometry    : angle       0.65384 ( 4368)
  SS BOND              : bond        0.00233 (   12)
  SS BOND              : angle       0.38329 (   24)
  hydrogen bonds       : bond        0.01539 (   26)
  hydrogen bonds       : angle       3.96245 (   78)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.079 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0367
  time to fit residues: 1.4629
Evaluate side-chains
  28 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 31 optimal weight:   20.0000
   chunk 8 optimal weight:    9.9990
   chunk 3 optimal weight:   20.0000
   chunk 19 optimal weight:    0.9980
   chunk 24 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 26 optimal weight:    8.9990
   chunk 21 optimal weight:   20.0000
   chunk 34 optimal weight:   10.0000
   chunk 14 optimal weight:    6.9990
   overall best weight:    5.5986

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

Flipped N/Q/H residues before XYZ refinement:
A  10 GLN
B  10 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.118574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.100770 restraints weight = 3781.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 2.01
r_work: 0.3616 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3522 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   3216  Z= 0.237
  Angle     :  0.616   5.458   4392  Z= 0.343
  Chirality :  0.041   0.131    540
  Planarity :  0.002   0.008    576
  Dihedral  :  8.248  30.822    456
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.89 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.49 (0.21), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.18 (0.16), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  11 
 TYR   0.009   0.001   TYR A  37 
 PHE   0.004   0.001   PHE E  23 
 HIS   0.002   0.001   HIS C  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 3204)
  covalent geometry    : angle       0.61691 ( 4368)
  SS BOND              : bond        0.00176 (   12)
  SS BOND              : angle       0.35225 (   24)
  hydrogen bonds       : bond        0.01313 (   26)
  hydrogen bonds       : angle       3.80040 (   78)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.118 
Fit side-chains
REVERT: K   14 ASN cc_start: 0.8780 (m110) cc_final: 0.8562 (m110)
REVERT: L   14 ASN cc_start: 0.8790 (m110) cc_final: 0.8572 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0645
  time to fit residues: 2.8106
Evaluate side-chains
  26 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 15 optimal weight:   20.0000
   chunk 2 optimal weight:    7.9990
   chunk 1 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 28 optimal weight:    8.9990
   chunk 22 optimal weight:    0.2980
   chunk 6 optimal weight:   20.0000
   chunk 24 optimal weight:   20.0000
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:   10.0000
   overall best weight:    5.8590

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

Flipped N/Q/H residues before XYZ refinement:
B  10 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.117674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.099801 restraints weight = 3835.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 2.01
r_work: 0.3607 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3512 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   3216  Z= 0.247
  Angle     :  0.628   5.524   4392  Z= 0.351
  Chirality :  0.042   0.130    540
  Planarity :  0.002   0.008    576
  Dihedral  :  8.315  31.154    456
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 13.89 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.56 (0.21), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.23 (0.16), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  11 
 TYR   0.010   0.001   TYR B  37 
 PHE   0.004   0.001   PHE D  23 
 HIS   0.002   0.001   HIS C  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00528 ( 3204)
  covalent geometry    : angle       0.62966 ( 4368)
  SS BOND              : bond        0.00190 (   12)
  SS BOND              : angle       0.35104 (   24)
  hydrogen bonds       : bond        0.01307 (   26)
  hydrogen bonds       : angle       3.85111 (   78)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 31
  time to evaluate  : 0.123 
Fit side-chains
REVERT: K   14 ASN cc_start: 0.8754 (m110) cc_final: 0.8534 (m110)
REVERT: L   14 ASN cc_start: 0.8758 (m110) cc_final: 0.8540 (m110)
  outliers start: 2
  outliers final: 0
  residues processed: 33
  average time/residue: 0.1181
  time to fit residues: 4.5145
Evaluate side-chains
  26 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 9 optimal weight:   20.0000
   chunk 23 optimal weight:    0.0070
   chunk 31 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 16 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 28 optimal weight:   20.0000
   chunk 20 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   overall best weight:    2.7404

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

Flipped N/Q/H residues before XYZ refinement:
I  10 GLN
J  10 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.123941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.106317 restraints weight = 3748.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3813 rms_B_bonded: 2.04
r_work: 0.3710 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3617 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   3216  Z= 0.138
  Angle     :  0.581   5.363   4392  Z= 0.325
  Chirality :  0.040   0.130    540
  Planarity :  0.001   0.005    576
  Dihedral  :  7.743  28.892    456
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.56 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 14.72 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.57 (0.21), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.24 (0.16), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  11 
 TYR   0.006   0.001   TYR B  37 
 PHE   0.003   0.000   PHE I  23 
 HIS   0.002   0.001   HIS D  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3204)
  covalent geometry    : angle       0.58187 ( 4368)
  SS BOND              : bond        0.00092 (   12)
  SS BOND              : angle       0.28125 (   24)
  hydrogen bonds       : bond        0.01035 (   26)
  hydrogen bonds       : angle       3.62157 (   78)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.123 
Fit side-chains
REVERT: K   14 ASN cc_start: 0.8789 (m110) cc_final: 0.8543 (m110)
REVERT: L   14 ASN cc_start: 0.8782 (m110) cc_final: 0.8536 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.0456
  time to fit residues: 1.8803
Evaluate side-chains
  26 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 35 optimal weight:   20.0000
   chunk 5 optimal weight:    9.9990
   chunk 3 optimal weight:   20.0000
   chunk 17 optimal weight:    9.9990
   chunk 24 optimal weight:   20.0000
   chunk 28 optimal weight:   20.0000
   chunk 34 optimal weight:    0.9990
   chunk 9 optimal weight:    9.9990
   chunk 7 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 26 optimal weight:    5.9990
   overall best weight:    7.3990

-------------------------------------------------------------------------------
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 = 0.3912 r_free = 0.3912 target = 0.115998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.098035 restraints weight = 3915.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 2.02
r_work: 0.3560 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3469 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.028   3216  Z= 0.301
  Angle     :  0.649   5.507   4392  Z= 0.362
  Chirality :  0.043   0.129    540
  Planarity :  0.002   0.008    576
  Dihedral  :  8.442  32.111    456
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 14.44 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.61 (0.21), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.27 (0.16), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  11 
 TYR   0.014   0.002   TYR A  37 
 PHE   0.005   0.001   PHE I  23 
 HIS   0.002   0.001   HIS D  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00649 ( 3204)
  covalent geometry    : angle       0.64979 ( 4368)
  SS BOND              : bond        0.00233 (   12)
  SS BOND              : angle       0.38640 (   24)
  hydrogen bonds       : bond        0.01350 (   26)
  hydrogen bonds       : angle       3.48169 (   78)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 27
  time to evaluate  : 0.133 
Fit side-chains
REVERT: K   14 ASN cc_start: 0.8784 (m110) cc_final: 0.8574 (m110)
REVERT: L   14 ASN cc_start: 0.8781 (m110) cc_final: 0.8570 (m110)
  outliers start: 3
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0473
  time to fit residues: 1.9293
Evaluate side-chains
  23 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 9 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 16 optimal weight:   20.0000
   chunk 7 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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 = 0.3999 r_free = 0.3999 target = 0.121566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.103869 restraints weight = 3812.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3782 rms_B_bonded: 2.05
r_work: 0.3678 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3584 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3216  Z= 0.160
  Angle     :  0.599   5.579   4392  Z= 0.335
  Chirality :  0.040   0.130    540
  Planarity :  0.001   0.005    576
  Dihedral  :  7.963  29.894    456
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.28 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.58 (0.21), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.24 (0.16), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  11 
 TYR   0.010   0.001   TYR A  37 
 PHE   0.003   0.001   PHE I  23 
 HIS   0.002   0.001   HIS D  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 3204)
  covalent geometry    : angle       0.59976 ( 4368)
  SS BOND              : bond        0.00137 (   12)
  SS BOND              : angle       0.33658 (   24)
  hydrogen bonds       : bond        0.01015 (   26)
  hydrogen bonds       : angle       3.27447 (   78)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.118 
Fit side-chains
REVERT: K   14 ASN cc_start: 0.8748 (m110) cc_final: 0.8511 (m110)
REVERT: L   14 ASN cc_start: 0.8746 (m110) cc_final: 0.8507 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0527
  time to fit residues: 2.2567
Evaluate side-chains
  26 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 33 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 24 optimal weight:   20.0000
   chunk 11 optimal weight:    2.9990
   chunk 8 optimal weight:    9.9990
   chunk 28 optimal weight:   20.0000
   chunk 18 optimal weight:    0.4980
   chunk 20 optimal weight:    6.9990
   chunk 7 optimal weight:   20.0000
   chunk 30 optimal weight:    5.9990
   overall best weight:    4.8988

-------------------------------------------------------------------------------
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 = 0.3964 r_free = 0.3964 target = 0.119099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.101290 restraints weight = 3807.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3743 rms_B_bonded: 2.03
r_work: 0.3641 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3547 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.022   3216  Z= 0.214
  Angle     :  0.620   5.504   4392  Z= 0.348
  Chirality :  0.041   0.129    540
  Planarity :  0.002   0.005    576
  Dihedral  :  8.127  30.765    456
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.00 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.59 (0.21), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.25 (0.16), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  11 
 TYR   0.010   0.001   TYR B  37 
 PHE   0.004   0.001   PHE D  23 
 HIS   0.002   0.001   HIS C  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 3204)
  covalent geometry    : angle       0.62092 ( 4368)
  SS BOND              : bond        0.00178 (   12)
  SS BOND              : angle       0.34284 (   24)
  hydrogen bonds       : bond        0.01099 (   26)
  hydrogen bonds       : angle       3.23968 (   78)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.123 
Fit side-chains
REVERT: K   14 ASN cc_start: 0.8781 (m110) cc_final: 0.8570 (m110)
REVERT: L   14 ASN cc_start: 0.8763 (m110) cc_final: 0.8549 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.0559
  time to fit residues: 2.1948
Evaluate side-chains
  26 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 15 optimal weight:   20.0000
   chunk 25 optimal weight:   20.0000
   chunk 7 optimal weight:    9.9990
   chunk 4 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 20 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 2 optimal weight:    7.9990
   chunk 12 optimal weight:    9.9990
   overall best weight:    8.5990

-------------------------------------------------------------------------------
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 = 0.3895 r_free = 0.3895 target = 0.115098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.097336 restraints weight = 3922.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 2.03
r_work: 0.3552 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3458 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.030   3216  Z= 0.343
  Angle     :  0.669   5.686   4392  Z= 0.373
  Chirality :  0.044   0.128    540
  Planarity :  0.002   0.009    576
  Dihedral  :  8.663  32.197    456
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.25 %
    Favored  : 87.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.00 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.62 (0.21), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.28 (0.16), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  11 
 TYR   0.014   0.002   TYR B  37 
 PHE   0.006   0.001   PHE D  23 
 HIS   0.002   0.001   HIS C  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00742 ( 3204)
  covalent geometry    : angle       0.67018 ( 4368)
  SS BOND              : bond        0.00281 (   12)
  SS BOND              : angle       0.46647 (   24)
  hydrogen bonds       : bond        0.01442 (   26)
  hydrogen bonds       : angle       3.54700 (   78)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.125 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0385
  time to fit residues: 1.4284
Evaluate side-chains
  20 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 14 optimal weight:    0.2980
   chunk 26 optimal weight:    6.9990
   chunk 17 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 9 optimal weight:    7.9990
   chunk 30 optimal weight:    7.9990
   chunk 33 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   overall best weight:    5.4588

-------------------------------------------------------------------------------
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 = 0.3950 r_free = 0.3950 target = 0.117675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.099998 restraints weight = 3912.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 2.04
r_work: 0.3620 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3524 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.023   3216  Z= 0.234
  Angle     :  0.644   5.632   4392  Z= 0.362
  Chirality :  0.042   0.129    540
  Planarity :  0.002   0.006    576
  Dihedral  :  8.415  33.370    456
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.50 %
    Favored  : 87.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.00 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.62 (0.21), residues: 408
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.28 (0.16), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  11 
 TYR   0.010   0.002   TYR B  37 
 PHE   0.004   0.001   PHE E  23 
 HIS   0.002   0.001   HIS C  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 3204)
  covalent geometry    : angle       0.64536 ( 4368)
  SS BOND              : bond        0.00195 (   12)
  SS BOND              : angle       0.40757 (   24)
  hydrogen bonds       : bond        0.01242 (   26)
  hydrogen bonds       : angle       3.42408 (   78)

===============================================================================
Job complete
usr+sys time: 789.07 seconds
wall clock time: 14 minutes 41.88 seconds (881.88 seconds total)