Starting phenix.real_space_refine
on Thu Mar 13 06:52:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zzy_15041/03_2025/7zzy_15041.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zzy_15041/03_2025/7zzy_15041.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zzy_15041/03_2025/7zzy_15041.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zzy_15041/03_2025/7zzy_15041.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zzy_15041/03_2025/7zzy_15041.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zzy_15041/03_2025/7zzy_15041.cif"
  }
  resolution = 3.3
  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=   0.013
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      48      5.16       5
     C    5600      2.51       5
     N    1488      2.21       5
     O    1648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8784
  Number of models: 1
  Model: ""
    Number of chains: 16
    Chain: "A"
      Number of atoms: 1095
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 138, 1087
          Classifications: {'peptide': 138}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 138, 1087
          Classifications: {'peptide': 138}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 1098
    Chain: "G"
      Number of atoms: 1095
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 138, 1087
          Classifications: {'peptide': 138}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 138, 1087
          Classifications: {'peptide': 138}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 1098
    Chain: "E"
      Number of atoms: 1095
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 138, 1087
          Classifications: {'peptide': 138}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 138, 1087
          Classifications: {'peptide': 138}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 1098
    Chain: "C"
      Number of atoms: 1095
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 138, 1087
          Classifications: {'peptide': 138}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 138, 1087
          Classifications: {'peptide': 138}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 1098
    Chain: "H"
      Number of atoms: 1095
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 138, 1087
          Classifications: {'peptide': 138}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 138, 1087
          Classifications: {'peptide': 138}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 1098
    Chain: "B"
      Number of atoms: 1095
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 138, 1087
          Classifications: {'peptide': 138}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 138, 1087
          Classifications: {'peptide': 138}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 1098
    Chain: "D"
      Number of atoms: 1095
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 138, 1087
          Classifications: {'peptide': 138}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 138, 1087
          Classifications: {'peptide': 138}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 1098
    Chain: "F"
      Number of atoms: 1095
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 138, 1087
          Classifications: {'peptide': 138}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 138, 1087
          Classifications: {'peptide': 138}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 1098
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "G"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "E"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "H"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "F"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Residues with excluded nonbonded symmetry interactions: 8
    residue:
      pdb=" N  AMET A  46 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CE BMET A  46 " occ=0.50
    residue:
      pdb=" N  AMET G  46 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CE BMET G  46 " occ=0.50
    residue:
      pdb=" N  AMET E  46 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CE BMET E  46 " occ=0.50
    residue:
      pdb=" N  AMET C  46 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CE BMET C  46 " occ=0.50
    residue:
      pdb=" N  AMET H  46 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CE BMET H  46 " occ=0.50
    residue:
      pdb=" N  AMET B  46 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CE BMET B  46 " occ=0.50
    residue:
      pdb=" N  AMET D  46 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CE BMET D  46 " occ=0.50
    residue:
      pdb=" N  AMET F  46 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CE BMET F  46 " occ=0.50
  Time building chain proxies: 8.65, per 1000 atoms: 0.98
  Number of scatterers: 8784
  At special positions: 0
  Unit cell: (97.65, 97.65, 80.91, 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      48     16.00
     O    1648      8.00
     N    1488      7.00
     C    5600      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.00
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2032

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 8 sheets defined
      48.6% alpha, 14.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 25
    Processing helix  chain 'A' and resid 28 through 45
      removed outlier: 3.584A  pdb=" N   GLU A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   THR A  43 " --> pdb=" O   ARG A  39 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ARG A  44 " --> pdb=" O   GLY A  40 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ILE A  45 " --> pdb=" O   MET A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 68
      removed outlier: 3.712A  pdb=" N   ILE A  67 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 119
      removed outlier: 3.989A  pdb=" N   GLN A 119 " --> pdb=" O   TRP A 115 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 25
    Processing helix  chain 'G' and resid 28 through 45
      removed outlier: 3.577A  pdb=" N   GLU G  32 " --> pdb=" O   GLU G  28 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   THR G  43 " --> pdb=" O   ARG G  39 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ARG G  44 " --> pdb=" O   GLY G  40 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ILE G  45 " --> pdb=" O   MET G  41 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 52 through 68
      removed outlier: 3.740A  pdb=" N   ILE G  67 " --> pdb=" O   LEU G  63 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 104 through 119
      removed outlier: 3.515A  pdb=" N   LEU G 108 " --> pdb=" O   LEU G 104 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   GLN G 119 " --> pdb=" O   TRP G 115 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 10 through 25
    Processing helix  chain 'E' and resid 28 through 45
      removed outlier: 3.594A  pdb=" N   GLU E  32 " --> pdb=" O   GLU E  28 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   THR E  43 " --> pdb=" O   ARG E  39 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ARG E  44 " --> pdb=" O   GLY E  40 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ILE E  45 " --> pdb=" O   MET E  41 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 52 through 68
      removed outlier: 3.742A  pdb=" N   ILE E  67 " --> pdb=" O   LEU E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 104 through 119
      removed outlier: 3.533A  pdb=" N   LEU E 108 " --> pdb=" O   LEU E 104 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   GLN E 119 " --> pdb=" O   TRP E 115 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 25
    Processing helix  chain 'C' and resid 28 through 45
      removed outlier: 3.598A  pdb=" N   GLU C  32 " --> pdb=" O   GLU C  28 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   THR C  43 " --> pdb=" O   ARG C  39 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ARG C  44 " --> pdb=" O   GLY C  40 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ILE C  45 " --> pdb=" O   MET C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 68
      removed outlier: 3.724A  pdb=" N   ILE C  67 " --> pdb=" O   LEU C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 119
      removed outlier: 3.954A  pdb=" N   GLN C 119 " --> pdb=" O   TRP C 115 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 10 through 25
    Processing helix  chain 'H' and resid 28 through 45
      removed outlier: 3.599A  pdb=" N   GLU H  32 " --> pdb=" O   GLU H  28 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   THR H  43 " --> pdb=" O   ARG H  39 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ARG H  44 " --> pdb=" O   GLY H  40 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE H  45 " --> pdb=" O   MET H  41 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 52 through 68
      removed outlier: 3.718A  pdb=" N   ILE H  67 " --> pdb=" O   LEU H  63 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 104 through 119
      removed outlier: 3.536A  pdb=" N   LEU H 108 " --> pdb=" O   LEU H 104 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   GLN H 119 " --> pdb=" O   TRP H 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 25
    Processing helix  chain 'B' and resid 28 through 45
      removed outlier: 3.593A  pdb=" N   GLU B  32 " --> pdb=" O   GLU B  28 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   THR B  43 " --> pdb=" O   ARG B  39 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ARG B  44 " --> pdb=" O   GLY B  40 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE B  45 " --> pdb=" O   MET B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 68
      removed outlier: 3.838A  pdb=" N   ILE B  67 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 119
      removed outlier: 3.537A  pdb=" N   LEU B 108 " --> pdb=" O   LEU B 104 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   GLN B 119 " --> pdb=" O   TRP B 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 10 through 25
    Processing helix  chain 'D' and resid 28 through 45
      removed outlier: 3.603A  pdb=" N   GLU D  32 " --> pdb=" O   GLU D  28 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR D  43 " --> pdb=" O   ARG D  39 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ARG D  44 " --> pdb=" O   GLY D  40 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ILE D  45 " --> pdb=" O   MET D  41 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 52 through 68
      removed outlier: 3.720A  pdb=" N   ILE D  67 " --> pdb=" O   LEU D  63 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 119
      removed outlier: 3.536A  pdb=" N   LEU D 108 " --> pdb=" O   LEU D 104 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   GLN D 119 " --> pdb=" O   TRP D 115 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 10 through 25
    Processing helix  chain 'F' and resid 28 through 45
      removed outlier: 3.577A  pdb=" N   GLU F  32 " --> pdb=" O   GLU F  28 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   THR F  43 " --> pdb=" O   ARG F  39 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ARG F  44 " --> pdb=" O   GLY F  40 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ILE F  45 " --> pdb=" O   MET F  41 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 52 through 68
      removed outlier: 3.740A  pdb=" N   ILE F  67 " --> pdb=" O   LEU F  63 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 104 through 119
      removed outlier: 3.551A  pdb=" N   LEU F 108 " --> pdb=" O   LEU F 104 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   GLN F 119 " --> pdb=" O   TRP F 115 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 77
    Processing sheet with id=AA2, first strand: chain 'G' and resid 71 through 77
      removed outlier: 3.503A  pdb=" N   ARG G 150 " --> pdb=" O   VAL G 127 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 71 through 77
    Processing sheet with id=AA4, first strand: chain 'C' and resid 71 through 77
    Processing sheet with id=AA5, first strand: chain 'H' and resid 71 through 77
    Processing sheet with id=AA6, first strand: chain 'B' and resid 71 through 77
    Processing sheet with id=AA7, first strand: chain 'D' and resid 71 through 77
    Processing sheet with id=AA8, first strand: chain 'F' and resid 71 through 77

    497 hydrogen bonds defined for protein.
    1395 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: 2.11

  Time building geometry restraints manager: 2.39 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: 2881
        1.34 -     1.46: 1496
        1.46 -     1.58: 4463
        1.58 -     1.69: 0
        1.69 -     1.81: 88
  Bond restraints: 8928
  Sorted by residual:
  bond pdb=" CB  PRO F  99 "
       pdb=" CG  PRO F  99 "
    ideal  model  delta    sigma   weight residual
    1.506  1.481  0.025 3.90e-02 6.57e+02 4.23e-01
  bond pdb=" CB  PRO B  99 "
       pdb=" CG  PRO B  99 "
    ideal  model  delta    sigma   weight residual
    1.506  1.481  0.025 3.90e-02 6.57e+02 4.19e-01
  bond pdb=" CB  PRO E  99 "
       pdb=" CG  PRO E  99 "
    ideal  model  delta    sigma   weight residual
    1.506  1.481  0.025 3.90e-02 6.57e+02 4.19e-01
  bond pdb=" CB  PRO H  99 "
       pdb=" CG  PRO H  99 "
    ideal  model  delta    sigma   weight residual
    1.506  1.481  0.025 3.90e-02 6.57e+02 4.10e-01
  bond pdb=" CB  PRO D  99 "
       pdb=" CG  PRO D  99 "
    ideal  model  delta    sigma   weight residual
    1.506  1.481  0.025 3.90e-02 6.57e+02 4.04e-01
  ... (remaining 8923 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.36: 11944
        1.36 -     2.72: 126
        2.72 -     4.08: 68
        4.08 -     5.44: 12
        5.44 -     6.80: 2
  Bond angle restraints: 12152
  Sorted by residual:
  angle pdb=" N   GLY C  70 "
        pdb=" CA  GLY C  70 "
        pdb=" C   GLY C  70 "
      ideal   model   delta    sigma   weight residual
     111.56  114.39   -2.83 1.01e+00 9.80e-01 7.83e+00
  angle pdb=" N   GLY G  70 "
        pdb=" CA  GLY G  70 "
        pdb=" C   GLY G  70 "
      ideal   model   delta    sigma   weight residual
     111.56  114.32   -2.76 1.01e+00 9.80e-01 7.44e+00
  angle pdb=" N   GLY F  70 "
        pdb=" CA  GLY F  70 "
        pdb=" C   GLY F  70 "
      ideal   model   delta    sigma   weight residual
     111.56  114.31   -2.75 1.01e+00 9.80e-01 7.43e+00
  angle pdb=" N   GLY D  70 "
        pdb=" CA  GLY D  70 "
        pdb=" C   GLY D  70 "
      ideal   model   delta    sigma   weight residual
     110.60  114.27   -3.67 1.46e+00 4.69e-01 6.34e+00
  angle pdb=" CA  LEU E  76 "
        pdb=" CB  LEU E  76 "
        pdb=" CG  LEU E  76 "
      ideal   model   delta    sigma   weight residual
     116.30  123.10   -6.80 3.50e+00 8.16e-02 3.77e+00
  ... (remaining 12147 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.37: 4697
       17.37 -    34.75: 484
       34.75 -    52.12: 117
       52.12 -    69.50: 25
       69.50 -    86.87: 29
  Dihedral angle restraints: 5352
    sinusoidal: 2200
      harmonic: 3152
  Sorted by residual:
  dihedral pdb=" CA BMET G  46 "
           pdb=" CB BMET G  46 "
           pdb=" CG BMET G  46 "
           pdb=" SD BMET G  46 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  130.53   49.47     3      1.50e+01 4.44e-03 8.78e+00
  dihedral pdb=" CA BMET F  46 "
           pdb=" CB BMET F  46 "
           pdb=" CG BMET F  46 "
           pdb=" SD BMET F  46 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  130.60   49.40     3      1.50e+01 4.44e-03 8.77e+00
  dihedral pdb=" CB  ARG D  35 "
           pdb=" CG  ARG D  35 "
           pdb=" CD  ARG D  35 "
           pdb=" NE  ARG D  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -109.12   49.12     3      1.50e+01 4.44e-03 8.73e+00
  ... (remaining 5349 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 921
       0.028 -    0.057: 344
       0.057 -    0.085: 78
       0.085 -    0.114: 61
       0.114 -    0.142: 12
  Chirality restraints: 1416
  Sorted by residual:
  chirality pdb=" CG  LEU A  63 "
            pdb=" CB  LEU A  63 "
            pdb=" CD1 LEU A  63 "
            pdb=" CD2 LEU A  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 5.05e-01
  chirality pdb=" CG  LEU H  63 "
            pdb=" CB  LEU H  63 "
            pdb=" CD1 LEU H  63 "
            pdb=" CD2 LEU H  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.92e-01
  chirality pdb=" CA  ILE E  85 "
            pdb=" N   ILE E  85 "
            pdb=" C   ILE E  85 "
            pdb=" CB  ILE E  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.74e-01
  ... (remaining 1413 not shown)

  Planarity restraints: 1552
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL F 140 "   -0.020 5.00e-02 4.00e+02   2.98e-02 1.42e+00
        pdb=" N   PRO F 141 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO F 141 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO F 141 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL H 140 "    0.020 5.00e-02 4.00e+02   2.98e-02 1.42e+00
        pdb=" N   PRO H 141 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO H 141 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO H 141 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL G 140 "    0.020 5.00e-02 4.00e+02   2.97e-02 1.41e+00
        pdb=" N   PRO G 141 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO G 141 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO G 141 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1549 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1250
        2.77 -     3.30: 7733
        3.30 -     3.84: 13861
        3.84 -     4.37: 15448
        4.37 -     4.90: 28821
  Nonbonded interactions: 67113
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP F  80 "
            pdb=" OG  SER F  82 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OD2 ASP H  80 "
            pdb=" OG  SER H  82 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OD2 ASP B  80 "
            pdb=" OG  SER B  82 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OD2 ASP D  80 "
            pdb=" OG  SER D  82 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OD2 ASP E  80 "
            pdb=" OG  SER E  82 "
     model   vdw
     2.248 3.040
  ... (remaining 67108 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' and (resid 6 through 45 or resid 47 through 151))
  selection = (chain 'B' and (resid 6 through 45 or resid 47 through 151))
  selection = (chain 'C' and (resid 6 through 45 or resid 47 through 151))
  selection = (chain 'D' and (resid 6 through 45 or resid 47 through 151))
  selection = (chain 'E' and (resid 6 through 45 or resid 47 through 151))
  selection = (chain 'F' and (resid 6 through 45 or resid 47 through 151))
  selection = (chain 'G' and (resid 6 through 45 or resid 47 through 151))
  selection = (chain 'H' and (resid 6 through 45 or resid 47 through 151))
}

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=0.50 max=1.00 mean=0.99
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:             2.290
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.980
  Find NCS groups from input model:        0.390
  Set up NCS constraints:                  0.050
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
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      :  0.002   0.025   8928  Z= 0.130
  Angle     :  0.470   6.800  12152  Z= 0.240
  Chirality :  0.036   0.142   1416
  Planarity :  0.004   0.030   1552
  Dihedral  : 16.507  86.874   3320
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  0.62 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.25), residues: 1080
  helix:  1.91 (0.23), residues: 488
  sheet:  0.90 (0.31), residues: 232
  loop : -1.09 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 103 
 HIS   0.001   0.000   HIS C  87 
 PHE   0.002   0.000   PHE G  10 
 TYR   0.004   0.001   TYR A 112 
 ARG   0.002   0.000   ARG G 114 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 222
  average time/residue: 0.2677
  time to fit residues: 81.0373
Evaluate side-chains
  162 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 78 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 94 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3223 r_free = 0.3223 target = 0.059285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.044497 restraints weight = 162890.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.2796 rms_B_bonded: 9.64
r_work: 0.2528 rms_B_bonded: 8.63 restraints_weight: 2.0000
r_work: 0.2694 rms_B_bonded: 5.41 restraints_weight: 4.0000
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2659
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2659 r_free = 0.2659    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2657 r_free = 0.2657    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2657
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8928  Z= 0.216
  Angle     :  0.644   7.290  12152  Z= 0.334
  Chirality :  0.040   0.140   1416
  Planarity :  0.004   0.030   1552
  Dihedral  :  3.377  13.533   1192
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 11.57 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.25), residues: 1080
  helix:  2.19 (0.22), residues: 488
  sheet:  1.07 (0.31), residues: 232
  loop : -1.09 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  69 
 HIS   0.001   0.001   HIS C  87 
 PHE   0.003   0.001   PHE B  10 
 TYR   0.006   0.001   TYR G 112 
 ARG   0.002   0.000   ARG G  35 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 180
  time to evaluate  : 0.926 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8300 (mmtt)
REVERT: A   20 GLU cc_start: 0.9189 (tp30) cc_final: 0.8986 (tp30)
REVERT: A   59 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9107 (mm-30)
REVERT: A  149 MET cc_start: 0.9387 (tpp) cc_final: 0.8806 (tpt)
REVERT: G    7 LYS cc_start: 0.8497 (mmmt) cc_final: 0.7980 (mmtm)
REVERT: G   20 GLU cc_start: 0.9244 (tp30) cc_final: 0.9035 (tp30)
REVERT: G   55 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8774 (mmtp)
REVERT: G   59 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8951 (mm-30)
REVERT: G  149 MET cc_start: 0.9544 (mmm) cc_final: 0.8858 (mmm)
REVERT: E   20 GLU cc_start: 0.9184 (tp30) cc_final: 0.8978 (tp30)
REVERT: E  149 MET cc_start: 0.9426 (tpp) cc_final: 0.8931 (tpt)
REVERT: C    7 LYS cc_start: 0.8624 (mmmt) cc_final: 0.8286 (mmtt)
REVERT: C   20 GLU cc_start: 0.9178 (tp30) cc_final: 0.8964 (tp30)
REVERT: C   59 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8965 (mm-30)
REVERT: C  149 MET cc_start: 0.9413 (tpp) cc_final: 0.8919 (tpt)
REVERT: H    7 LYS cc_start: 0.8485 (mmmt) cc_final: 0.7997 (mmtm)
REVERT: H   20 GLU cc_start: 0.9190 (tp30) cc_final: 0.8980 (tp30)
REVERT: H   59 GLU cc_start: 0.9296 (mm-30) cc_final: 0.9066 (mm-30)
REVERT: H  149 MET cc_start: 0.9422 (tpp) cc_final: 0.9179 (mmm)
REVERT: B    7 LYS cc_start: 0.8636 (mmmt) cc_final: 0.8300 (mmtt)
REVERT: B   20 GLU cc_start: 0.9206 (tp30) cc_final: 0.8974 (tp30)
REVERT: B   59 GLU cc_start: 0.9320 (mm-30) cc_final: 0.9093 (mm-30)
REVERT: B  149 MET cc_start: 0.9440 (tpp) cc_final: 0.8941 (tpt)
REVERT: D   36 GLU cc_start: 0.9301 (mm-30) cc_final: 0.9062 (mm-30)
REVERT: D  149 MET cc_start: 0.9453 (tpp) cc_final: 0.8959 (tpt)
REVERT: F    7 LYS cc_start: 0.8510 (mmmt) cc_final: 0.8019 (mmtm)
REVERT: F   20 GLU cc_start: 0.9234 (tp30) cc_final: 0.9022 (tp30)
REVERT: F   59 GLU cc_start: 0.9323 (mm-30) cc_final: 0.9091 (mm-30)
  outliers start: 9
  outliers final: 0
  residues processed: 181
  average time/residue: 0.2073
  time to fit residues: 51.4153
Evaluate side-chains
  149 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   55 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 99 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 84 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 100 optimal weight:    0.0010
   chunk 8 optimal weight:    0.9980
   chunk 76 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   overall best weight:    1.1992

-------------------------------------------------------------------------------
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 = 0.3204 r_free = 0.3204 target = 0.057758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.043227 restraints weight = 147832.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.2766 rms_B_bonded: 9.24
r_work: 0.2506 rms_B_bonded: 8.29 restraints_weight: 2.0000
r_work: 0.2680 rms_B_bonded: 5.11 restraints_weight: 4.0000
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2641
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2641 r_free = 0.2641    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2641 r_free = 0.2641    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2641
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   8928  Z= 0.244
  Angle     :  0.658   5.126  12152  Z= 0.343
  Chirality :  0.039   0.115   1416
  Planarity :  0.004   0.028   1552
  Dihedral  :  3.737  17.654   1192
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 15.60 %
    Favored  : 83.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.25), residues: 1080
  helix:  2.24 (0.23), residues: 488
  sheet:  1.22 (0.30), residues: 232
  loop : -1.06 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  69 
 HIS   0.002   0.001   HIS D  87 
 PHE   0.020   0.003   PHE F 123 
 TYR   0.011   0.002   TYR A 126 
 ARG   0.002   0.000   ARG A  35 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 168
  time to evaluate  : 1.132 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8783 (mmmt) cc_final: 0.8358 (mmtt)
REVERT: A   20 GLU cc_start: 0.9234 (tp30) cc_final: 0.9003 (tp30)
REVERT: A   59 GLU cc_start: 0.9352 (mm-30) cc_final: 0.9108 (mm-30)
REVERT: A  109 GLU cc_start: 0.8782 (tt0) cc_final: 0.8475 (tm-30)
REVERT: A  149 MET cc_start: 0.9391 (tpp) cc_final: 0.8865 (tpt)
REVERT: G    7 LYS cc_start: 0.8574 (mmmt) cc_final: 0.8128 (mmtt)
REVERT: G   20 GLU cc_start: 0.9242 (tp30) cc_final: 0.8996 (tp30)
REVERT: G   59 GLU cc_start: 0.9341 (mm-30) cc_final: 0.9113 (mm-30)
REVERT: G  149 MET cc_start: 0.9486 (mmm) cc_final: 0.8837 (mmm)
REVERT: E   20 GLU cc_start: 0.9253 (tp30) cc_final: 0.9012 (tp30)
REVERT: E  149 MET cc_start: 0.9403 (tpp) cc_final: 0.8856 (tpt)
REVERT: C    7 LYS cc_start: 0.8797 (mmmt) cc_final: 0.8370 (mmtt)
REVERT: C   20 GLU cc_start: 0.9236 (tp30) cc_final: 0.8997 (tp30)
REVERT: C   59 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9072 (mm-30)
REVERT: C  149 MET cc_start: 0.9393 (tpp) cc_final: 0.8845 (tpt)
REVERT: H    7 LYS cc_start: 0.8525 (mmmt) cc_final: 0.8099 (mmtt)
REVERT: H   20 GLU cc_start: 0.9238 (tp30) cc_final: 0.8994 (tp30)
REVERT: H   59 GLU cc_start: 0.9339 (mm-30) cc_final: 0.9089 (mm-30)
REVERT: H  149 MET cc_start: 0.9378 (tpp) cc_final: 0.8833 (tpt)
REVERT: B    7 LYS cc_start: 0.8793 (mmmt) cc_final: 0.8359 (mmtt)
REVERT: B   20 GLU cc_start: 0.9241 (tp30) cc_final: 0.8993 (tp30)
REVERT: B   59 GLU cc_start: 0.9365 (mm-30) cc_final: 0.9128 (mm-30)
REVERT: B  149 MET cc_start: 0.9393 (tpp) cc_final: 0.8839 (tpt)
REVERT: D   36 GLU cc_start: 0.9341 (mm-30) cc_final: 0.9094 (mm-30)
REVERT: D  149 MET cc_start: 0.9416 (tpp) cc_final: 0.8862 (tpt)
REVERT: F    7 LYS cc_start: 0.8566 (mmmt) cc_final: 0.8104 (mmtt)
REVERT: F   20 GLU cc_start: 0.9266 (tp30) cc_final: 0.9029 (tp30)
REVERT: F   59 GLU cc_start: 0.9327 (mm-30) cc_final: 0.9097 (mm-30)
REVERT: F  109 GLU cc_start: 0.8719 (tt0) cc_final: 0.8463 (tm-30)
REVERT: F  149 MET cc_start: 0.9475 (mmm) cc_final: 0.8944 (tpt)
  outliers start: 8
  outliers final: 0
  residues processed: 168
  average time/residue: 0.2560
  time to fit residues: 59.6309
Evaluate side-chains
  156 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.5986

-------------------------------------------------------------------------------
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 = 0.3158 r_free = 0.3158 target = 0.055546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.041109 restraints weight = 166982.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.2709 rms_B_bonded: 9.40
r_work: 0.2439 rms_B_bonded: 8.48 restraints_weight: 2.0000
r_work: 0.2604 rms_B_bonded: 5.32 restraints_weight: 4.0000
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2568
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2568 r_free = 0.2568    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2568 r_free = 0.2568    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2568
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   8928  Z= 0.268
  Angle     :  0.654   5.820  12152  Z= 0.340
  Chirality :  0.040   0.127   1416
  Planarity :  0.004   0.026   1552
  Dihedral  :  3.566  13.150   1192
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 14.05 %
    Favored  : 85.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.25), residues: 1080
  helix:  2.21 (0.23), residues: 488
  sheet:  1.43 (0.29), residues: 232
  loop : -1.22 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  19 
 HIS   0.002   0.001   HIS D  87 
 PHE   0.023   0.003   PHE E 123 
 TYR   0.006   0.001   TYR B 112 
 ARG   0.001   0.000   ARG A 114 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 168
  time to evaluate  : 1.021 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8860 (mmmt) cc_final: 0.8423 (mmtt)
REVERT: A   20 GLU cc_start: 0.9224 (tp30) cc_final: 0.9000 (tp30)
REVERT: A   59 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9127 (mm-30)
REVERT: A  109 GLU cc_start: 0.8867 (tt0) cc_final: 0.8541 (tm-30)
REVERT: A  149 MET cc_start: 0.9384 (tpp) cc_final: 0.8854 (tpt)
REVERT: G    7 LYS cc_start: 0.8733 (mmmt) cc_final: 0.8246 (mmtt)
REVERT: G   20 GLU cc_start: 0.9291 (tp30) cc_final: 0.9002 (tp30)
REVERT: G   59 GLU cc_start: 0.9402 (mm-30) cc_final: 0.9139 (mm-30)
REVERT: G  109 GLU cc_start: 0.8788 (tt0) cc_final: 0.8452 (tm-30)
REVERT: G  149 MET cc_start: 0.9480 (mmm) cc_final: 0.9278 (mmm)
REVERT: E   20 GLU cc_start: 0.9267 (tp30) cc_final: 0.9014 (tp30)
REVERT: E   59 GLU cc_start: 0.9349 (mm-30) cc_final: 0.9095 (mm-30)
REVERT: C    7 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8412 (mmtt)
REVERT: C   20 GLU cc_start: 0.9271 (tp30) cc_final: 0.9019 (tp30)
REVERT: C   59 GLU cc_start: 0.9417 (mm-30) cc_final: 0.9156 (mm-30)
REVERT: H    7 LYS cc_start: 0.8711 (mmmt) cc_final: 0.8234 (mmtt)
REVERT: H   20 GLU cc_start: 0.9285 (tp30) cc_final: 0.9040 (tp30)
REVERT: H   59 GLU cc_start: 0.9378 (mm-30) cc_final: 0.9110 (mm-30)
REVERT: H  149 MET cc_start: 0.9377 (tpp) cc_final: 0.8842 (tpt)
REVERT: B   20 GLU cc_start: 0.9289 (tp30) cc_final: 0.9041 (tp30)
REVERT: B   59 GLU cc_start: 0.9393 (mm-30) cc_final: 0.9156 (mm-30)
REVERT: D  109 GLU cc_start: 0.8842 (tt0) cc_final: 0.8497 (tm-30)
REVERT: F    7 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8245 (mmtt)
REVERT: F   20 GLU cc_start: 0.9281 (tp30) cc_final: 0.9015 (tp30)
REVERT: F   59 GLU cc_start: 0.9387 (mm-30) cc_final: 0.9137 (mm-30)
REVERT: F  109 GLU cc_start: 0.8833 (tt0) cc_final: 0.8510 (tm-30)
REVERT: F  149 MET cc_start: 0.9501 (mmm) cc_final: 0.9033 (tpt)
  outliers start: 2
  outliers final: 2
  residues processed: 170
  average time/residue: 0.2038
  time to fit residues: 48.1608
Evaluate side-chains
  159 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 157
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  118 SER
Chi-restraints excluded: chain F residue  118 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   chunk 83 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9980
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.3150 r_free = 0.3150 target = 0.055507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.041014 restraints weight = 168027.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.2725 rms_B_bonded: 9.44
r_work: 0.2454 rms_B_bonded: 8.47 restraints_weight: 2.0000
r_work: 0.2616 rms_B_bonded: 5.39 restraints_weight: 4.0000
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2581
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2581 r_free = 0.2581    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2581 r_free = 0.2581    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2581
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8928  Z= 0.250
  Angle     :  0.656   7.300  12152  Z= 0.341
  Chirality :  0.041   0.122   1416
  Planarity :  0.004   0.026   1552
  Dihedral  :  3.682  12.696   1192
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 15.70 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.25), residues: 1080
  helix:  2.22 (0.23), residues: 488
  sheet:  1.43 (0.29), residues: 232
  loop : -1.24 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  19 
 HIS   0.002   0.001   HIS H  87 
 PHE   0.017   0.002   PHE E 123 
 TYR   0.004   0.001   TYR H 112 
 ARG   0.002   0.000   ARG E 150 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 163
  time to evaluate  : 0.950 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.9259 (tp30) cc_final: 0.9014 (tp30)
REVERT: A   59 GLU cc_start: 0.9405 (mm-30) cc_final: 0.9129 (mm-30)
REVERT: A  109 GLU cc_start: 0.8885 (tt0) cc_final: 0.8553 (tm-30)
REVERT: A  149 MET cc_start: 0.9354 (tpp) cc_final: 0.8839 (tpt)
REVERT: G   20 GLU cc_start: 0.9308 (tp30) cc_final: 0.8988 (tp30)
REVERT: G   59 GLU cc_start: 0.9412 (mm-30) cc_final: 0.9155 (mm-30)
REVERT: G  109 GLU cc_start: 0.8818 (tt0) cc_final: 0.8450 (tm-30)
REVERT: G  149 MET cc_start: 0.9462 (mmm) cc_final: 0.8832 (mmm)
REVERT: E   20 GLU cc_start: 0.9324 (tp30) cc_final: 0.9063 (tp30)
REVERT: E  109 GLU cc_start: 0.8840 (tt0) cc_final: 0.8518 (tm-30)
REVERT: E  149 MET cc_start: 0.9368 (mmm) cc_final: 0.9077 (tpt)
REVERT: C   20 GLU cc_start: 0.9296 (tp30) cc_final: 0.9027 (tp30)
REVERT: C  149 MET cc_start: 0.9351 (mmm) cc_final: 0.9048 (tpt)
REVERT: H   20 GLU cc_start: 0.9313 (tp30) cc_final: 0.9033 (tp30)
REVERT: H   59 GLU cc_start: 0.9395 (mm-30) cc_final: 0.9124 (mm-30)
REVERT: H  109 GLU cc_start: 0.8810 (tt0) cc_final: 0.8458 (tm-30)
REVERT: H  149 MET cc_start: 0.9360 (tpp) cc_final: 0.8831 (tpt)
REVERT: B    7 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8528 (mmtt)
REVERT: B   20 GLU cc_start: 0.9322 (tp30) cc_final: 0.9043 (tp30)
REVERT: B   59 GLU cc_start: 0.9420 (mm-30) cc_final: 0.9174 (mm-30)
REVERT: B  109 GLU cc_start: 0.8833 (tt0) cc_final: 0.8501 (tm-30)
REVERT: B  149 MET cc_start: 0.9379 (mmm) cc_final: 0.9081 (tpt)
REVERT: D   59 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9107 (mm-30)
REVERT: D  109 GLU cc_start: 0.8855 (tt0) cc_final: 0.8492 (tm-30)
REVERT: D  149 MET cc_start: 0.9379 (mmm) cc_final: 0.9092 (tpt)
REVERT: F   20 GLU cc_start: 0.9308 (tp30) cc_final: 0.9012 (tp30)
REVERT: F   59 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9141 (mm-30)
REVERT: F  109 GLU cc_start: 0.8856 (tt0) cc_final: 0.8481 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 165
  average time/residue: 0.2121
  time to fit residues: 49.0684
Evaluate side-chains
  162 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 160
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  118 SER
Chi-restraints excluded: chain F residue  118 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 84 optimal weight:    0.0060
   chunk 45 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 9 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.6596

-------------------------------------------------------------------------------
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 = 0.3163 r_free = 0.3163 target = 0.055693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.041221 restraints weight = 180981.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.2749 rms_B_bonded: 9.57
r_work: 0.2474 rms_B_bonded: 8.64 restraints_weight: 2.0000
r_work: 0.2649 rms_B_bonded: 5.35 restraints_weight: 4.0000
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2615
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2615 r_free = 0.2615    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2615 r_free = 0.2615    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2615
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.3610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8928  Z= 0.218
  Angle     :  0.667   8.555  12152  Z= 0.342
  Chirality :  0.040   0.124   1416
  Planarity :  0.004   0.027   1552
  Dihedral  :  3.564  12.448   1192
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 15.29 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.26), residues: 1080
  helix:  2.28 (0.23), residues: 488
  sheet:  1.53 (0.29), residues: 232
  loop : -1.18 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP H  19 
 HIS   0.001   0.001   HIS B  87 
 PHE   0.015   0.002   PHE F 123 
 TYR   0.004   0.001   TYR C 112 
 ARG   0.005   0.000   ARG C  35 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 175
  time to evaluate  : 1.110 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8557 (mmmt) cc_final: 0.8286 (mmtt)
REVERT: A   20 GLU cc_start: 0.9300 (tp30) cc_final: 0.9028 (tp30)
REVERT: A  109 GLU cc_start: 0.8907 (tt0) cc_final: 0.8551 (tm-30)
REVERT: A  146 ILE cc_start: 0.9286 (mt) cc_final: 0.9059 (mm)
REVERT: A  149 MET cc_start: 0.9333 (tpp) cc_final: 0.8822 (tpt)
REVERT: G   20 GLU cc_start: 0.9305 (tp30) cc_final: 0.8693 (tp30)
REVERT: G   59 GLU cc_start: 0.9431 (mm-30) cc_final: 0.9141 (mm-30)
REVERT: E   20 GLU cc_start: 0.9334 (tp30) cc_final: 0.9022 (tp30)
REVERT: E  109 GLU cc_start: 0.8819 (tt0) cc_final: 0.8480 (tm-30)
REVERT: E  146 ILE cc_start: 0.9295 (mt) cc_final: 0.9062 (mm)
REVERT: E  149 MET cc_start: 0.9344 (mmm) cc_final: 0.8937 (tpt)
REVERT: C    7 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8353 (mmtt)
REVERT: C   20 GLU cc_start: 0.9310 (tp30) cc_final: 0.9001 (tp30)
REVERT: C   59 GLU cc_start: 0.9392 (mm-30) cc_final: 0.9082 (mm-30)
REVERT: C  109 GLU cc_start: 0.8847 (tt0) cc_final: 0.8498 (tm-30)
REVERT: C  146 ILE cc_start: 0.9286 (mt) cc_final: 0.9063 (mm)
REVERT: C  149 MET cc_start: 0.9326 (mmm) cc_final: 0.8890 (tpt)
REVERT: H   20 GLU cc_start: 0.9334 (tp30) cc_final: 0.9030 (tp30)
REVERT: H   59 GLU cc_start: 0.9399 (mm-30) cc_final: 0.9095 (mm-30)
REVERT: H  109 GLU cc_start: 0.8806 (tt0) cc_final: 0.8380 (tm-30)
REVERT: H  149 MET cc_start: 0.9335 (tpp) cc_final: 0.8803 (tpt)
REVERT: B   20 GLU cc_start: 0.9335 (tp30) cc_final: 0.9030 (tp30)
REVERT: B   59 GLU cc_start: 0.9434 (mm-30) cc_final: 0.9182 (mm-30)
REVERT: B  109 GLU cc_start: 0.8814 (tt0) cc_final: 0.8466 (tm-30)
REVERT: B  146 ILE cc_start: 0.9298 (mt) cc_final: 0.9064 (mm)
REVERT: B  149 MET cc_start: 0.9350 (mmm) cc_final: 0.8947 (tpt)
REVERT: D  109 GLU cc_start: 0.8853 (tt0) cc_final: 0.8491 (tm-30)
REVERT: D  146 ILE cc_start: 0.9286 (mt) cc_final: 0.9054 (mm)
REVERT: D  149 MET cc_start: 0.9346 (mmm) cc_final: 0.8908 (tpt)
REVERT: F    7 LYS cc_start: 0.8651 (mmmt) cc_final: 0.8416 (mmtt)
REVERT: F   20 GLU cc_start: 0.9324 (tp30) cc_final: 0.8998 (tp30)
REVERT: F   59 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9138 (mm-30)
REVERT: F  109 GLU cc_start: 0.8844 (tt0) cc_final: 0.8493 (tm-30)
REVERT: F  146 ILE cc_start: 0.9239 (mt) cc_final: 0.9003 (mm)
REVERT: F  149 MET cc_start: 0.9350 (mmm) cc_final: 0.8998 (tpt)
  outliers start: 3
  outliers final: 3
  residues processed: 177
  average time/residue: 0.1936
  time to fit residues: 47.8156
Evaluate side-chains
  167 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 164
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  118 SER
Chi-restraints excluded: chain H residue  118 SER
Chi-restraints excluded: chain F residue  118 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   chunk 98 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 16 optimal weight:    5.9990
   chunk 96 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
B  15 GLN
D  15 GLN
F  15 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.055520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.040895 restraints weight = 190193.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.2723 rms_B_bonded: 9.79
r_work: 0.2444 rms_B_bonded: 8.80 restraints_weight: 2.0000
r_work: 0.2614 rms_B_bonded: 5.55 restraints_weight: 4.0000
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2582
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2582 r_free = 0.2582    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2582 r_free = 0.2582    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2582
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8928  Z= 0.240
  Angle     :  0.680   8.302  12152  Z= 0.348
  Chirality :  0.040   0.129   1416
  Planarity :  0.004   0.026   1552
  Dihedral  :  3.493  12.089   1192
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 16.63 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.26), residues: 1080
  helix:  2.38 (0.24), residues: 488
  sheet:  1.62 (0.30), residues: 232
  loop : -1.13 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP F  69 
 HIS   0.002   0.001   HIS E  87 
 PHE   0.013   0.002   PHE E 123 
 TYR   0.004   0.001   TYR C 112 
 ARG   0.006   0.000   ARG B  30 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 167
  time to evaluate  : 0.951 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8667 (mmmt) cc_final: 0.8375 (mmtt)
REVERT: A   20 GLU cc_start: 0.9296 (tp30) cc_final: 0.9004 (tp30)
REVERT: A   59 GLU cc_start: 0.9369 (mm-30) cc_final: 0.9081 (mm-30)
REVERT: A  109 GLU cc_start: 0.8848 (tt0) cc_final: 0.8543 (tm-30)
REVERT: A  149 MET cc_start: 0.9334 (tpp) cc_final: 0.8822 (tpt)
REVERT: G   20 GLU cc_start: 0.9055 (tp30) cc_final: 0.8829 (tp30)
REVERT: G   59 GLU cc_start: 0.9431 (mm-30) cc_final: 0.9218 (mm-30)
REVERT: G  149 MET cc_start: 0.9327 (mmm) cc_final: 0.9034 (tpp)
REVERT: E   20 GLU cc_start: 0.9303 (tp30) cc_final: 0.8715 (tp30)
REVERT: E  109 GLU cc_start: 0.8786 (tt0) cc_final: 0.8505 (tm-30)
REVERT: E  149 MET cc_start: 0.9322 (mmm) cc_final: 0.8941 (mmm)
REVERT: C    7 LYS cc_start: 0.8731 (mmmt) cc_final: 0.8462 (mmtt)
REVERT: C   20 GLU cc_start: 0.9316 (tp30) cc_final: 0.8722 (tp30)
REVERT: C   59 GLU cc_start: 0.9379 (mm-30) cc_final: 0.9166 (mm-30)
REVERT: C  109 GLU cc_start: 0.8814 (tt0) cc_final: 0.8535 (tm-30)
REVERT: C  149 MET cc_start: 0.9319 (mmm) cc_final: 0.8943 (mmm)
REVERT: H   20 GLU cc_start: 0.9306 (tp30) cc_final: 0.8719 (tp30)
REVERT: H  109 GLU cc_start: 0.8774 (tt0) cc_final: 0.8358 (tm-30)
REVERT: H  149 MET cc_start: 0.9324 (tpp) cc_final: 0.8789 (tpt)
REVERT: B   20 GLU cc_start: 0.9309 (tp30) cc_final: 0.8720 (tp30)
REVERT: B   59 GLU cc_start: 0.9438 (mm-30) cc_final: 0.9183 (mm-30)
REVERT: B  109 GLU cc_start: 0.8789 (tt0) cc_final: 0.8501 (tm-30)
REVERT: B  149 MET cc_start: 0.9329 (mmm) cc_final: 0.8945 (mmm)
REVERT: D  109 GLU cc_start: 0.8823 (tt0) cc_final: 0.8495 (tm-30)
REVERT: D  149 MET cc_start: 0.9329 (mmm) cc_final: 0.8950 (mmm)
REVERT: F    7 LYS cc_start: 0.8708 (mmmt) cc_final: 0.8474 (mmtt)
REVERT: F   20 GLU cc_start: 0.9318 (tp30) cc_final: 0.8774 (tp30)
REVERT: F   59 GLU cc_start: 0.9410 (mm-30) cc_final: 0.9193 (mm-30)
REVERT: F  109 GLU cc_start: 0.8841 (tt0) cc_final: 0.8485 (tm-30)
REVERT: F  146 ILE cc_start: 0.9207 (mt) cc_final: 0.8979 (mm)
REVERT: F  149 MET cc_start: 0.9361 (mmm) cc_final: 0.8868 (tpt)
  outliers start: 2
  outliers final: 2
  residues processed: 168
  average time/residue: 0.1970
  time to fit residues: 46.0753
Evaluate side-chains
  161 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 159
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  118 SER
Chi-restraints excluded: chain F residue  118 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 95 optimal weight:    0.8980
   chunk 88 optimal weight:    0.6980
   chunk 100 optimal weight:    6.9990
   chunk 69 optimal weight:    0.0050
   chunk 53 optimal weight:    0.7980
   chunk 91 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.6796

-------------------------------------------------------------------------------
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 = 0.3191 r_free = 0.3191 target = 0.056676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.042778 restraints weight = 128612.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.2759 rms_B_bonded: 8.59
r_work: 0.2504 rms_B_bonded: 8.09 restraints_weight: 2.0000
r_work: 0.2667 rms_B_bonded: 5.06 restraints_weight: 4.0000
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2635
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2635 r_free = 0.2635    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2635 r_free = 0.2635    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2635
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.3836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8928  Z= 0.233
  Angle     :  0.703   8.162  12152  Z= 0.364
  Chirality :  0.040   0.130   1416
  Planarity :  0.004   0.027   1552
  Dihedral  :  3.482  12.150   1192
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 17.36 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.26), residues: 1080
  helix:  2.28 (0.23), residues: 488
  sheet:  1.65 (0.30), residues: 232
  loop : -1.12 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP D  69 
 HIS   0.002   0.001   HIS B  87 
 PHE   0.012   0.002   PHE B 123 
 TYR   0.004   0.001   TYR A 112 
 ARG   0.004   0.000   ARG G  30 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 173
  time to evaluate  : 1.288 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8724 (mmmt) cc_final: 0.8469 (mmtt)
REVERT: A   20 GLU cc_start: 0.9281 (tp30) cc_final: 0.8644 (tp30)
REVERT: A   59 GLU cc_start: 0.9352 (mm-30) cc_final: 0.9025 (mm-30)
REVERT: A  109 GLU cc_start: 0.8825 (tt0) cc_final: 0.8517 (tm-30)
REVERT: G    7 LYS cc_start: 0.8590 (mmmt) cc_final: 0.8262 (mmtt)
REVERT: G   20 GLU cc_start: 0.9067 (tp30) cc_final: 0.8838 (tp30)
REVERT: G   59 GLU cc_start: 0.9439 (mm-30) cc_final: 0.9145 (mm-30)
REVERT: G  149 MET cc_start: 0.9292 (mmm) cc_final: 0.9002 (tpp)
REVERT: E   20 GLU cc_start: 0.9056 (tp30) cc_final: 0.8749 (tp30)
REVERT: E  109 GLU cc_start: 0.8806 (tt0) cc_final: 0.8456 (tm-30)
REVERT: E  149 MET cc_start: 0.9332 (mmm) cc_final: 0.8983 (mmm)
REVERT: C    7 LYS cc_start: 0.8725 (mmmt) cc_final: 0.8469 (mmtt)
REVERT: C   20 GLU cc_start: 0.9007 (tp30) cc_final: 0.8724 (tp30)
REVERT: C   59 GLU cc_start: 0.9376 (mm-30) cc_final: 0.9147 (mm-30)
REVERT: C  109 GLU cc_start: 0.8831 (tt0) cc_final: 0.8493 (tm-30)
REVERT: C  149 MET cc_start: 0.9315 (mmm) cc_final: 0.8954 (mmm)
REVERT: H    7 LYS cc_start: 0.8599 (mmmt) cc_final: 0.8312 (mmtt)
REVERT: H   20 GLU cc_start: 0.9059 (tp30) cc_final: 0.8752 (tp30)
REVERT: H   59 GLU cc_start: 0.9351 (mm-30) cc_final: 0.9060 (mm-30)
REVERT: H  109 GLU cc_start: 0.8806 (tt0) cc_final: 0.8377 (tm-30)
REVERT: H  149 MET cc_start: 0.9317 (tpp) cc_final: 0.8811 (tpt)
REVERT: B   20 GLU cc_start: 0.9037 (tp30) cc_final: 0.8751 (tp30)
REVERT: B   59 GLU cc_start: 0.9434 (mm-30) cc_final: 0.9214 (mm-30)
REVERT: B  109 GLU cc_start: 0.8800 (tt0) cc_final: 0.8439 (tm-30)
REVERT: B  149 MET cc_start: 0.9305 (mmm) cc_final: 0.8937 (mmm)
REVERT: D   20 GLU cc_start: 0.9291 (tp30) cc_final: 0.8858 (tp30)
REVERT: D  109 GLU cc_start: 0.8833 (tt0) cc_final: 0.8494 (tm-30)
REVERT: D  149 MET cc_start: 0.9332 (mmm) cc_final: 0.8957 (mmm)
REVERT: F    7 LYS cc_start: 0.8734 (mmmt) cc_final: 0.8509 (mmtt)
REVERT: F   20 GLU cc_start: 0.9102 (tp30) cc_final: 0.8863 (tp30)
REVERT: F   59 GLU cc_start: 0.9411 (mm-30) cc_final: 0.9179 (mm-30)
REVERT: F  109 GLU cc_start: 0.8831 (tt0) cc_final: 0.8486 (tm-30)
REVERT: F  146 ILE cc_start: 0.9266 (mt) cc_final: 0.9041 (mm)
REVERT: F  149 MET cc_start: 0.9358 (mmm) cc_final: 0.9013 (mmm)
  outliers start: 2
  outliers final: 2
  residues processed: 174
  average time/residue: 0.2063
  time to fit residues: 50.3908
Evaluate side-chains
  166 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 164
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  118 SER
Chi-restraints excluded: chain F residue  118 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0270
   chunk 35 optimal weight:    0.2980
   chunk 26 optimal weight:    4.9990
   chunk 23 optimal weight:    0.5980
   chunk 54 optimal weight:    0.3980
   chunk 7 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 101 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    1.0640

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

Flipped N/Q/H residues before XYZ refinement:
H  15 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.054915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.040685 restraints weight = 167276.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.2710 rms_B_bonded: 9.70
r_work: 0.2439 rms_B_bonded: 8.73 restraints_weight: 2.0000
r_work: 0.2608 rms_B_bonded: 5.45 restraints_weight: 4.0000
r_work (final): 0.2608
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2608
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2608 r_free = 0.2608    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2608 r_free = 0.2608    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2608
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.3922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8928  Z= 0.264
  Angle     :  0.730   8.222  12152  Z= 0.378
  Chirality :  0.040   0.124   1416
  Planarity :  0.004   0.026   1552
  Dihedral  :  3.497  12.258   1192
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 17.98 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.26), residues: 1080
  helix:  2.24 (0.23), residues: 488
  sheet:  1.62 (0.30), residues: 232
  loop : -1.10 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP D  69 
 HIS   0.002   0.001   HIS E  87 
 PHE   0.011   0.001   PHE D 123 
 TYR   0.005   0.001   TYR D 148 
 ARG   0.002   0.000   ARG G  30 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 168
  time to evaluate  : 0.938 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8786 (mmmt) cc_final: 0.8539 (mmtt)
REVERT: A   20 GLU cc_start: 0.9008 (tp30) cc_final: 0.8725 (tp30)
REVERT: A   59 GLU cc_start: 0.9373 (mm-30) cc_final: 0.9053 (mm-30)
REVERT: A  109 GLU cc_start: 0.8779 (tt0) cc_final: 0.8436 (tm-30)
REVERT: A  149 MET cc_start: 0.9372 (mmm) cc_final: 0.9016 (tpt)
REVERT: G    7 LYS cc_start: 0.8684 (mmmt) cc_final: 0.8406 (mmtt)
REVERT: G   20 GLU cc_start: 0.9075 (tp30) cc_final: 0.8817 (tp30)
REVERT: G   59 GLU cc_start: 0.9447 (mm-30) cc_final: 0.9179 (mm-30)
REVERT: E   20 GLU cc_start: 0.9026 (tp30) cc_final: 0.8749 (tp30)
REVERT: E  109 GLU cc_start: 0.8784 (tt0) cc_final: 0.8402 (tm-30)
REVERT: E  149 MET cc_start: 0.9326 (mmm) cc_final: 0.9053 (mmm)
REVERT: C    7 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8566 (mmtt)
REVERT: C   20 GLU cc_start: 0.8990 (tp30) cc_final: 0.8701 (tp30)
REVERT: C   59 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9178 (mm-30)
REVERT: C  109 GLU cc_start: 0.8809 (tt0) cc_final: 0.8468 (tm-30)
REVERT: C  149 MET cc_start: 0.9302 (mmm) cc_final: 0.9028 (mmm)
REVERT: H    7 LYS cc_start: 0.8715 (mmmt) cc_final: 0.8436 (mmtt)
REVERT: H   20 GLU cc_start: 0.9023 (tp30) cc_final: 0.8746 (tp30)
REVERT: H   59 GLU cc_start: 0.9363 (mm-30) cc_final: 0.9068 (mm-30)
REVERT: H  109 GLU cc_start: 0.8783 (tt0) cc_final: 0.8344 (tm-30)
REVERT: H  149 MET cc_start: 0.9275 (tpp) cc_final: 0.8771 (tpt)
REVERT: B   20 GLU cc_start: 0.9021 (tp30) cc_final: 0.8739 (tp30)
REVERT: B   59 GLU cc_start: 0.9443 (mm-30) cc_final: 0.9231 (mm-30)
REVERT: B  109 GLU cc_start: 0.8791 (tt0) cc_final: 0.8404 (tm-30)
REVERT: B  149 MET cc_start: 0.9307 (mmm) cc_final: 0.9022 (mmm)
REVERT: D  109 GLU cc_start: 0.8789 (tt0) cc_final: 0.8400 (tm-30)
REVERT: D  146 ILE cc_start: 0.9265 (mt) cc_final: 0.9024 (mm)
REVERT: D  149 MET cc_start: 0.9339 (mmm) cc_final: 0.9065 (mmm)
REVERT: F   20 GLU cc_start: 0.9087 (tp30) cc_final: 0.8777 (tp30)
REVERT: F   59 GLU cc_start: 0.9435 (mm-30) cc_final: 0.9219 (mm-30)
REVERT: F  109 GLU cc_start: 0.8819 (tt0) cc_final: 0.8461 (tm-30)
REVERT: F  146 ILE cc_start: 0.9229 (mt) cc_final: 0.9002 (mm)
REVERT: F  149 MET cc_start: 0.9333 (mmm) cc_final: 0.8932 (mmm)
  outliers start: 4
  outliers final: 4
  residues processed: 170
  average time/residue: 0.2160
  time to fit residues: 51.1375
Evaluate side-chains
  171 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 167
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  118 SER
Chi-restraints excluded: chain H residue   22 ASP
Chi-restraints excluded: chain H residue  118 SER
Chi-restraints excluded: chain F residue  118 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 99 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3151 r_free = 0.3151 target = 0.054865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.040481 restraints weight = 140708.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.2694 rms_B_bonded: 9.32
r_work: 0.2445 rms_B_bonded: 8.55 restraints_weight: 2.0000
r_work: 0.2614 rms_B_bonded: 5.32 restraints_weight: 4.0000
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2612
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2612 r_free = 0.2612    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2611 r_free = 0.2611    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2611
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.3976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8928  Z= 0.249
  Angle     :  0.733   8.795  12152  Z= 0.381
  Chirality :  0.040   0.121   1416
  Planarity :  0.004   0.026   1552
  Dihedral  :  3.482  12.294   1192
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 17.87 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.26), residues: 1080
  helix:  2.26 (0.23), residues: 488
  sheet:  1.60 (0.30), residues: 232
  loop : -1.07 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A  19 
 HIS   0.002   0.001   HIS D  87 
 PHE   0.011   0.001   PHE D 123 
 TYR   0.004   0.001   TYR D 112 
 ARG   0.002   0.000   ARG H  30 

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

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

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2160 Ramachandran restraints generated.
    1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 175
  time to evaluate  : 0.920 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.8961 (tp30) cc_final: 0.8690 (tp30)
REVERT: A   59 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9067 (mm-30)
REVERT: A  109 GLU cc_start: 0.8828 (tt0) cc_final: 0.8508 (tm-30)
REVERT: A  146 ILE cc_start: 0.9289 (mt) cc_final: 0.9068 (mm)
REVERT: A  149 MET cc_start: 0.9374 (mmm) cc_final: 0.8969 (tpt)
REVERT: G    7 LYS cc_start: 0.8722 (mmmt) cc_final: 0.8440 (mmtt)
REVERT: G   20 GLU cc_start: 0.9099 (tp30) cc_final: 0.8847 (tp30)
REVERT: G   59 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9249 (mm-30)
REVERT: E   20 GLU cc_start: 0.9005 (tp30) cc_final: 0.8719 (tp30)
REVERT: E  149 MET cc_start: 0.9333 (mmm) cc_final: 0.9069 (mmm)
REVERT: C   20 GLU cc_start: 0.8999 (tp30) cc_final: 0.8702 (tp30)
REVERT: C   59 GLU cc_start: 0.9423 (mm-30) cc_final: 0.9191 (mm-30)
REVERT: C  109 GLU cc_start: 0.8818 (tt0) cc_final: 0.8490 (tm-30)
REVERT: C  146 ILE cc_start: 0.9324 (mt) cc_final: 0.9089 (mm)
REVERT: C  149 MET cc_start: 0.9323 (mmm) cc_final: 0.9066 (mmm)
REVERT: H    7 LYS cc_start: 0.8725 (mmmt) cc_final: 0.8463 (mmtt)
REVERT: H   20 GLU cc_start: 0.8996 (tp30) cc_final: 0.8706 (tp30)
REVERT: H   59 GLU cc_start: 0.9379 (mm-30) cc_final: 0.9085 (mm-30)
REVERT: H  109 GLU cc_start: 0.8776 (tt0) cc_final: 0.8362 (tm-30)
REVERT: B   20 GLU cc_start: 0.9010 (tp30) cc_final: 0.8710 (tp30)
REVERT: B   59 GLU cc_start: 0.9459 (mm-30) cc_final: 0.9243 (mm-30)
REVERT: B  109 GLU cc_start: 0.8800 (tt0) cc_final: 0.8426 (tm-30)
REVERT: B  146 ILE cc_start: 0.9338 (mt) cc_final: 0.9095 (mm)
REVERT: B  149 MET cc_start: 0.9313 (mmm) cc_final: 0.9046 (mmm)
REVERT: D  109 GLU cc_start: 0.8801 (tt0) cc_final: 0.8463 (tm-30)
REVERT: D  146 ILE cc_start: 0.9297 (mt) cc_final: 0.9041 (mm)
REVERT: D  149 MET cc_start: 0.9312 (mmm) cc_final: 0.8919 (mmm)
REVERT: F   20 GLU cc_start: 0.9108 (tp30) cc_final: 0.8836 (tp30)
REVERT: F   59 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9227 (mm-30)
REVERT: F  109 GLU cc_start: 0.8820 (tt0) cc_final: 0.8454 (tm-30)
REVERT: F  146 ILE cc_start: 0.9299 (mt) cc_final: 0.9076 (mm)
REVERT: F  149 MET cc_start: 0.9337 (mmm) cc_final: 0.8967 (mmm)
  outliers start: 3
  outliers final: 3
  residues processed: 175
  average time/residue: 0.1941
  time to fit residues: 47.2917
Evaluate side-chains
  175 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 172
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  118 SER
Chi-restraints excluded: chain H residue  118 SER
Chi-restraints excluded: chain F residue  118 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   chunk 19 optimal weight:    0.4980
   chunk 70 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 99 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.3145 r_free = 0.3145 target = 0.054681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.040224 restraints weight = 169183.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.2685 rms_B_bonded: 9.86
r_work: 0.2431 rms_B_bonded: 8.86 restraints_weight: 2.0000
r_work: 0.2593 rms_B_bonded: 5.56 restraints_weight: 4.0000
r_work (final): 0.2593
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2584
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2584 r_free = 0.2584    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2584 r_free = 0.2584    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2584
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.4044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8928  Z= 0.255
  Angle     :  0.739   9.084  12152  Z= 0.382
  Chirality :  0.040   0.122   1416
  Planarity :  0.004   0.026   1552
  Dihedral  :  3.455  12.193   1192
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 18.29 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.26), residues: 1080
  helix:  2.30 (0.23), residues: 488
  sheet:  1.65 (0.31), residues: 232
  loop : -1.05 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP D  69 
 HIS   0.002   0.001   HIS D  87 
 PHE   0.009   0.001   PHE F 123 
 TYR   0.004   0.001   TYR D 112 
 ARG   0.002   0.000   ARG H  30 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4993.38 seconds
wall clock time: 88 minutes 13.25 seconds (5293.25 seconds total)