Starting phenix.real_space_refine
on Wed Sep 17 12:37:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zzy_15041/09_2025/7zzy_15041.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zzy_15041/09_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_15041/09_2025/7zzy_15041.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zzy_15041/09_2025/7zzy_15041.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zzy_15041/09_2025/7zzy_15041.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zzy_15041/09_2025/7zzy_15041.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.013
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.82, per 1000 atoms: 0.43
  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: 0.79
  Conformation dependent library (CDL) restraints added in 635.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.25
  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: 1.30

  Time building geometry restraints manager: 1.07 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: 0.00
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:             3.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.760
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.750
-------------------------------------------------------------------------------
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= 0.098
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (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
 ARG   0.002   0.000   ARG G 114 
 TYR   0.004   0.001   TYR A 112 
 PHE   0.002   0.000   PHE G  10 
 TRP   0.005   0.001   TRP A 103 
 HIS   0.001   0.000   HIS C  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00194 ( 8928)
  covalent geometry    : angle       0.47013 (12152)
  hydrogen bonds       : bond        0.14438 (  497)
  hydrogen bonds       : angle       4.53311 ( 1395)

*********************** 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  : 0.292 
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: 0.0971
  time to fit residues: 29.4074
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  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.3980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
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 = 0.3165 r_free = 0.3165 target = 0.057609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.042824 restraints weight = 159973.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.2761 rms_B_bonded: 9.41
r_work: 0.2494 rms_B_bonded: 8.40 restraints_weight: 2.0000
r_work: 0.2666 rms_B_bonded: 5.19 restraints_weight: 4.0000
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2632
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2632 r_free = 0.2632    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2630 r_free = 0.2630    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2630
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.2738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8928  Z= 0.168
  Angle     :  0.648   7.019  12152  Z= 0.337
  Chirality :  0.040   0.148   1416
  Planarity :  0.005   0.028   1552
  Dihedral  :  3.394  13.700   1192
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 11.57 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.25), residues: 1080
  helix:  2.13 (0.22), residues: 488
  sheet:  1.09 (0.31), residues: 232
  loop : -1.08 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 114 
 TYR   0.008   0.001   TYR A 112 
 PHE   0.003   0.001   PHE B  10 
 TRP   0.008   0.001   TRP A 103 
 HIS   0.001   0.001   HIS B  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8928)
  covalent geometry    : angle       0.64812 (12152)
  hydrogen bonds       : bond        0.04524 (  497)
  hydrogen bonds       : angle       3.83149 ( 1395)

*********************** 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
  191 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 183
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8655 (mmmt) cc_final: 0.8333 (mmtt)
REVERT: A   20 GLU cc_start: 0.9199 (tp30) cc_final: 0.8994 (tp30)
REVERT: A   59 GLU cc_start: 0.9322 (mm-30) cc_final: 0.9103 (mm-30)
REVERT: A  123 PHE cc_start: 0.8409 (t80) cc_final: 0.8167 (t80)
REVERT: A  149 MET cc_start: 0.9392 (tpp) cc_final: 0.8806 (tpt)
REVERT: G    7 LYS cc_start: 0.8525 (mmmt) cc_final: 0.8018 (mmtm)
REVERT: G   20 GLU cc_start: 0.9253 (tp30) cc_final: 0.9051 (tp30)
REVERT: G   59 GLU cc_start: 0.9335 (mm-30) cc_final: 0.9106 (mm-30)
REVERT: G  123 PHE cc_start: 0.8336 (t80) cc_final: 0.8127 (t80)
REVERT: G  149 MET cc_start: 0.9538 (mmm) cc_final: 0.8862 (mmm)
REVERT: E   20 GLU cc_start: 0.9194 (tp30) cc_final: 0.8983 (tp30)
REVERT: E  123 PHE cc_start: 0.8384 (t80) cc_final: 0.8146 (t80)
REVERT: E  149 MET cc_start: 0.9426 (tpp) cc_final: 0.8907 (tpt)
REVERT: C    7 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8331 (mmtt)
REVERT: C   20 GLU cc_start: 0.9190 (tp30) cc_final: 0.8983 (tp30)
REVERT: C   36 GLU cc_start: 0.9290 (mm-30) cc_final: 0.8984 (mm-30)
REVERT: C   59 GLU cc_start: 0.9335 (mm-30) cc_final: 0.8973 (mm-30)
REVERT: C  123 PHE cc_start: 0.8391 (t80) cc_final: 0.8153 (t80)
REVERT: C  149 MET cc_start: 0.9403 (tpp) cc_final: 0.8817 (tpt)
REVERT: H    7 LYS cc_start: 0.8508 (mmmt) cc_final: 0.8010 (mmtm)
REVERT: H   20 GLU cc_start: 0.9203 (tp30) cc_final: 0.8990 (tp30)
REVERT: H  123 PHE cc_start: 0.8404 (t80) cc_final: 0.8168 (t80)
REVERT: H  149 MET cc_start: 0.9399 (tpp) cc_final: 0.8811 (tpt)
REVERT: B    7 LYS cc_start: 0.8674 (mmmt) cc_final: 0.8343 (mmtt)
REVERT: B   20 GLU cc_start: 0.9216 (tp30) cc_final: 0.8981 (tp30)
REVERT: B   59 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9121 (mm-30)
REVERT: B  123 PHE cc_start: 0.8330 (t80) cc_final: 0.8114 (t80)
REVERT: B  149 MET cc_start: 0.9435 (tpp) cc_final: 0.8911 (tpt)
REVERT: D   20 GLU cc_start: 0.9188 (tp30) cc_final: 0.8985 (tp30)
REVERT: D   36 GLU cc_start: 0.9302 (mm-30) cc_final: 0.9068 (mm-30)
REVERT: D  123 PHE cc_start: 0.8364 (t80) cc_final: 0.8132 (t80)
REVERT: D  149 MET cc_start: 0.9441 (tpp) cc_final: 0.8922 (tpt)
REVERT: F    7 LYS cc_start: 0.8530 (mmmt) cc_final: 0.8031 (mmtm)
REVERT: F   20 GLU cc_start: 0.9244 (tp30) cc_final: 0.9039 (tp30)
REVERT: F   59 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9105 (mm-30)
REVERT: F  123 PHE cc_start: 0.8351 (t80) cc_final: 0.8131 (t80)
  outliers start: 8
  outliers final: 0
  residues processed: 183
  average time/residue: 0.0907
  time to fit residues: 23.1638
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  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 77 optimal weight:   20.0000
   chunk 46 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   chunk 59 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 102 optimal weight:    0.6980
   chunk 25 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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 = 0.056488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.042286 restraints weight = 171722.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.2732 rms_B_bonded: 9.43
r_work: 0.2459 rms_B_bonded: 8.44 restraints_weight: 2.0000
r_work: 0.2622 rms_B_bonded: 5.27 restraints_weight: 4.0000
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2585
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2585 r_free = 0.2585    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2584 r_free = 0.2584    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2584
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   8928  Z= 0.168
  Angle     :  0.626   5.264  12152  Z= 0.327
  Chirality :  0.040   0.118   1416
  Planarity :  0.004   0.027   1552
  Dihedral  :  3.512  12.790   1192
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 14.05 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.25), residues: 1080
  helix:  2.18 (0.23), residues: 488
  sheet:  1.22 (0.29), residues: 232
  loop : -1.09 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G  39 
 TYR   0.005   0.001   TYR G 112 
 PHE   0.006   0.001   PHE B 123 
 TRP   0.007   0.001   TRP F  19 
 HIS   0.002   0.001   HIS B  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 8928)
  covalent geometry    : angle       0.62607 (12152)
  hydrogen bonds       : bond        0.04324 (  497)
  hydrogen bonds       : angle       3.87665 ( 1395)

*********************** 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
  183 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 176
  time to evaluate  : 0.363 
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
REVERT: A    7 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8408 (mmtt)
REVERT: A   20 GLU cc_start: 0.9226 (tp30) cc_final: 0.9001 (tp30)
REVERT: A   59 GLU cc_start: 0.9370 (mm-30) cc_final: 0.9123 (mm-30)
REVERT: A  149 MET cc_start: 0.9399 (tpp) cc_final: 0.8519 (mmm)
REVERT: G    7 LYS cc_start: 0.8696 (mmmt) cc_final: 0.8219 (mmtt)
REVERT: G   20 GLU cc_start: 0.9256 (tp30) cc_final: 0.9003 (tp30)
REVERT: G   59 GLU cc_start: 0.9388 (mm-30) cc_final: 0.9154 (mm-30)
REVERT: G  149 MET cc_start: 0.9475 (mmm) cc_final: 0.8753 (mmm)
REVERT: E   20 GLU cc_start: 0.9261 (tp30) cc_final: 0.9034 (tp30)
REVERT: E  149 MET cc_start: 0.9395 (tpp) cc_final: 0.8865 (tpt)
REVERT: C    7 LYS cc_start: 0.8882 (mmmt) cc_final: 0.8412 (mmtt)
REVERT: C   20 GLU cc_start: 0.9239 (tp30) cc_final: 0.9016 (tp30)
REVERT: C   59 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9133 (mm-30)
REVERT: C  149 MET cc_start: 0.9379 (tpp) cc_final: 0.8857 (tpt)
REVERT: H    7 LYS cc_start: 0.8654 (mmmt) cc_final: 0.8180 (mmtt)
REVERT: H   20 GLU cc_start: 0.9236 (tp30) cc_final: 0.8987 (tp30)
REVERT: H   59 GLU cc_start: 0.9319 (mm-30) cc_final: 0.9057 (mm-30)
REVERT: H  149 MET cc_start: 0.9384 (tpp) cc_final: 0.8843 (tpt)
REVERT: B    7 LYS cc_start: 0.8887 (mmmt) cc_final: 0.8416 (mmtt)
REVERT: B   20 GLU cc_start: 0.9256 (tp30) cc_final: 0.9007 (tp30)
REVERT: B   59 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9128 (mm-30)
REVERT: B  149 MET cc_start: 0.9398 (tpp) cc_final: 0.8867 (tpt)
REVERT: D   20 GLU cc_start: 0.9253 (tp30) cc_final: 0.9035 (tp30)
REVERT: D  149 MET cc_start: 0.9423 (tpp) cc_final: 0.8884 (tpt)
REVERT: F    7 LYS cc_start: 0.8715 (mmmt) cc_final: 0.8212 (mmtt)
REVERT: F   20 GLU cc_start: 0.9270 (tp30) cc_final: 0.9031 (tp30)
REVERT: F   59 GLU cc_start: 0.9367 (mm-30) cc_final: 0.9139 (mm-30)
REVERT: F  149 MET cc_start: 0.9494 (mmm) cc_final: 0.8973 (tpt)
  outliers start: 7
  outliers final: 3
  residues processed: 179
  average time/residue: 0.0909
  time to fit residues: 22.9201
Evaluate side-chains
  166 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 163
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 64 optimal weight:    0.0670
   chunk 63 optimal weight:    5.9990
   chunk 35 optimal weight:    0.2980
   chunk 70 optimal weight:    0.8980
   chunk 100 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.5918

-------------------------------------------------------------------------------
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 = 0.3194 r_free = 0.3194 target = 0.057037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.042694 restraints weight = 145225.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.2761 rms_B_bonded: 8.99
r_work: 0.2502 rms_B_bonded: 8.24 restraints_weight: 2.0000
r_work: 0.2670 rms_B_bonded: 5.10 restraints_weight: 4.0000
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2636
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2636 r_free = 0.2636    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.27   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 = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2635
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.3300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8928  Z= 0.128
  Angle     :  0.616   5.998  12152  Z= 0.320
  Chirality :  0.041   0.123   1416
  Planarity :  0.004   0.027   1552
  Dihedral  :  3.453  11.564   1192
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 14.46 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.25), residues: 1080
  helix:  2.29 (0.23), residues: 488
  sheet:  1.38 (0.29), residues: 232
  loop : -1.16 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  35 
 TYR   0.005   0.001   TYR F 112 
 PHE   0.002   0.000   PHE A  10 
 TRP   0.007   0.001   TRP B  19 
 HIS   0.001   0.001   HIS D  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 8928)
  covalent geometry    : angle       0.61603 (12152)
  hydrogen bonds       : bond        0.03687 (  497)
  hydrogen bonds       : angle       3.78546 ( 1395)

*********************** 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: 1
    poor density    : 169
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8841 (mmmt) cc_final: 0.8433 (mmtt)
REVERT: A   20 GLU cc_start: 0.9258 (tp30) cc_final: 0.9013 (tp30)
REVERT: A   59 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9118 (mm-30)
REVERT: A  109 GLU cc_start: 0.8789 (tt0) cc_final: 0.8502 (tm-30)
REVERT: A  123 PHE cc_start: 0.8591 (t80) cc_final: 0.8377 (t80)
REVERT: A  149 MET cc_start: 0.9381 (tpp) cc_final: 0.8876 (tpt)
REVERT: G    7 LYS cc_start: 0.8706 (mmmt) cc_final: 0.8251 (mmtt)
REVERT: G   20 GLU cc_start: 0.9298 (tp30) cc_final: 0.8989 (tp30)
REVERT: G   59 GLU cc_start: 0.9404 (mm-30) cc_final: 0.9124 (mm-30)
REVERT: G  109 GLU cc_start: 0.8727 (tt0) cc_final: 0.8374 (tm-30)
REVERT: G  149 MET cc_start: 0.9428 (mmm) cc_final: 0.8739 (mmm)
REVERT: E   20 GLU cc_start: 0.9285 (tp30) cc_final: 0.9038 (tp30)
REVERT: E   59 GLU cc_start: 0.9333 (mm-30) cc_final: 0.9083 (mm-30)
REVERT: C    7 LYS cc_start: 0.8827 (mmmt) cc_final: 0.8414 (mmtt)
REVERT: C   20 GLU cc_start: 0.9261 (tp30) cc_final: 0.9015 (tp30)
REVERT: C   59 GLU cc_start: 0.9405 (mm-30) cc_final: 0.9119 (mm-30)
REVERT: H    7 LYS cc_start: 0.8662 (mmmt) cc_final: 0.8227 (mmtt)
REVERT: H   20 GLU cc_start: 0.9280 (tp30) cc_final: 0.9040 (tp30)
REVERT: H   59 GLU cc_start: 0.9326 (mm-30) cc_final: 0.9015 (mm-30)
REVERT: H  123 PHE cc_start: 0.8575 (t80) cc_final: 0.8355 (t80)
REVERT: B   20 GLU cc_start: 0.9289 (tp30) cc_final: 0.9050 (tp30)
REVERT: D   20 GLU cc_start: 0.9266 (tp30) cc_final: 0.9011 (tp30)
REVERT: D   59 GLU cc_start: 0.9321 (mm-30) cc_final: 0.9067 (mm-30)
REVERT: D  109 GLU cc_start: 0.8794 (tt0) cc_final: 0.8442 (tm-30)
REVERT: F   20 GLU cc_start: 0.9302 (tp30) cc_final: 0.9014 (tp30)
REVERT: F   59 GLU cc_start: 0.9384 (mm-30) cc_final: 0.9122 (mm-30)
REVERT: F  109 GLU cc_start: 0.8753 (tt0) cc_final: 0.8429 (tm-30)
REVERT: F  123 PHE cc_start: 0.8534 (t80) cc_final: 0.8333 (t80)
REVERT: F  149 MET cc_start: 0.9475 (mmm) cc_final: 0.9010 (tpt)
  outliers start: 1
  outliers final: 1
  residues processed: 170
  average time/residue: 0.0910
  time to fit residues: 21.6584
Evaluate side-chains
  160 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 64 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 4 optimal weight:    8.9990
   chunk 62 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   chunk 90 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.8780

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.056301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.041736 restraints weight = 161977.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.2746 rms_B_bonded: 9.43
r_work: 0.2476 rms_B_bonded: 8.56 restraints_weight: 2.0000
r_work: 0.2647 rms_B_bonded: 5.35 restraints_weight: 4.0000
r_work (final): 0.2647
-------------------------------------------------------------------------------
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 = 0.28   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 = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2615
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.3445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8928  Z= 0.140
  Angle     :  0.641   6.980  12152  Z= 0.332
  Chirality :  0.040   0.122   1416
  Planarity :  0.004   0.026   1552
  Dihedral  :  3.576  16.295   1192
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 15.91 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.25), residues: 1080
  helix:  2.33 (0.23), residues: 488
  sheet:  1.50 (0.30), residues: 232
  loop : -1.17 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 114 
 TYR   0.013   0.001   TYR D 126 
 PHE   0.023   0.002   PHE E 123 
 TRP   0.003   0.000   TRP C  69 
 HIS   0.002   0.001   HIS D  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8928)
  covalent geometry    : angle       0.64101 (12152)
  hydrogen bonds       : bond        0.03820 (  497)
  hydrogen bonds       : angle       3.79279 ( 1395)

*********************** 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
  171 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 170
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A    7 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8546 (mmtt)
REVERT: A   20 GLU cc_start: 0.9260 (tp30) cc_final: 0.9001 (tp30)
REVERT: A   59 GLU cc_start: 0.9398 (mm-30) cc_final: 0.9119 (mm-30)
REVERT: A  109 GLU cc_start: 0.8850 (tt0) cc_final: 0.8503 (tm-30)
REVERT: A  123 PHE cc_start: 0.8612 (t80) cc_final: 0.8398 (t80)
REVERT: A  149 MET cc_start: 0.9360 (tpp) cc_final: 0.8872 (tpt)
REVERT: G    7 LYS cc_start: 0.8693 (mmmt) cc_final: 0.8267 (mmtt)
REVERT: G   20 GLU cc_start: 0.9301 (tp30) cc_final: 0.8966 (tp30)
REVERT: G   59 GLU cc_start: 0.9410 (mm-30) cc_final: 0.9134 (mm-30)
REVERT: G  109 GLU cc_start: 0.8783 (tt0) cc_final: 0.8471 (tm-30)
REVERT: G  149 MET cc_start: 0.9440 (mmm) cc_final: 0.8776 (mmm)
REVERT: E   20 GLU cc_start: 0.9309 (tp30) cc_final: 0.9048 (tp30)
REVERT: E  109 GLU cc_start: 0.8797 (tt0) cc_final: 0.8502 (tm-30)
REVERT: E  149 MET cc_start: 0.9358 (mmm) cc_final: 0.9029 (tpt)
REVERT: C    7 LYS cc_start: 0.8876 (mmmt) cc_final: 0.8530 (mmtt)
REVERT: C   20 GLU cc_start: 0.9287 (tp30) cc_final: 0.9023 (tp30)
REVERT: C   59 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9143 (mm-30)
REVERT: C  149 MET cc_start: 0.9329 (mmm) cc_final: 0.8980 (tpt)
REVERT: H    7 LYS cc_start: 0.8661 (mmmt) cc_final: 0.8234 (mmtt)
REVERT: H   20 GLU cc_start: 0.9294 (tp30) cc_final: 0.9022 (tp30)
REVERT: H   59 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9100 (mm-30)
REVERT: H  109 GLU cc_start: 0.8785 (tt0) cc_final: 0.8496 (tm-30)
REVERT: H  123 PHE cc_start: 0.8581 (t80) cc_final: 0.8362 (t80)
REVERT: H  149 MET cc_start: 0.9360 (mmm) cc_final: 0.8980 (tpt)
REVERT: B    7 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8423 (mmtt)
REVERT: B   20 GLU cc_start: 0.9299 (tp30) cc_final: 0.9036 (tp30)
REVERT: B   59 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9146 (mm-30)
REVERT: B  109 GLU cc_start: 0.8791 (tt0) cc_final: 0.8488 (tm-30)
REVERT: B  149 MET cc_start: 0.9373 (mmm) cc_final: 0.9023 (tpt)
REVERT: D   20 GLU cc_start: 0.9266 (tp30) cc_final: 0.9017 (tp30)
REVERT: D   59 GLU cc_start: 0.9340 (mm-30) cc_final: 0.9040 (mm-30)
REVERT: D  109 GLU cc_start: 0.8812 (tt0) cc_final: 0.8487 (tm-30)
REVERT: D  149 MET cc_start: 0.9383 (mmm) cc_final: 0.9054 (tpt)
REVERT: F   20 GLU cc_start: 0.9311 (tp30) cc_final: 0.9004 (tp30)
REVERT: F   59 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9129 (mm-30)
REVERT: F  109 GLU cc_start: 0.8831 (tt0) cc_final: 0.8451 (tm-30)
REVERT: F  123 PHE cc_start: 0.8578 (t80) cc_final: 0.8360 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 171
  average time/residue: 0.0832
  time to fit residues: 20.2083
Evaluate side-chains
  159 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 86 optimal weight:    4.9990
   chunk 75 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 90 optimal weight:    6.9990
   chunk 66 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0870
   chunk 51 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    1.6962

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.053608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.039339 restraints weight = 165648.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.2685 rms_B_bonded: 9.23
r_work: 0.2414 rms_B_bonded: 8.38 restraints_weight: 2.0000
r_work: 0.2580 rms_B_bonded: 5.23 restraints_weight: 4.0000
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2542
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2542 r_free = 0.2542    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2542 r_free = 0.2542    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2542
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.3708

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= 0.184
  Angle     :  0.665   7.323  12152  Z= 0.346
  Chirality :  0.041   0.131   1416
  Planarity :  0.004   0.025   1552
  Dihedral  :  3.565  14.921   1192
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 15.91 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.26), residues: 1080
  helix:  2.21 (0.24), residues: 488
  sheet:  1.52 (0.30), residues: 232
  loop : -1.15 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  30 
 TYR   0.004   0.001   TYR C 112 
 PHE   0.022   0.002   PHE G 123 
 TRP   0.005   0.001   TRP F  69 
 HIS   0.004   0.002   HIS G  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 8928)
  covalent geometry    : angle       0.66548 (12152)
  hydrogen bonds       : bond        0.04639 (  497)
  hydrogen bonds       : angle       3.92642 ( 1395)

*********************** 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
  159 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 156
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.9297 (tp30) cc_final: 0.9009 (tp30)
REVERT: A   59 GLU cc_start: 0.9419 (mm-30) cc_final: 0.9150 (mm-30)
REVERT: A  109 GLU cc_start: 0.8890 (tt0) cc_final: 0.8521 (tm-30)
REVERT: A  123 PHE cc_start: 0.8690 (t80) cc_final: 0.8430 (t80)
REVERT: A  149 MET cc_start: 0.9331 (tpp) cc_final: 0.8821 (tpt)
REVERT: G   20 GLU cc_start: 0.9329 (tp30) cc_final: 0.8695 (tp30)
REVERT: G   59 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9160 (mm-30)
REVERT: E   20 GLU cc_start: 0.9340 (tp30) cc_final: 0.9057 (tp30)
REVERT: E  109 GLU cc_start: 0.8854 (tt0) cc_final: 0.8487 (tm-30)
REVERT: E  149 MET cc_start: 0.9336 (mmm) cc_final: 0.8871 (tpt)
REVERT: C   20 GLU cc_start: 0.9325 (tp30) cc_final: 0.9042 (tp30)
REVERT: C   59 GLU cc_start: 0.9433 (mm-30) cc_final: 0.9226 (mm-30)
REVERT: C  149 MET cc_start: 0.9326 (mmm) cc_final: 0.8831 (tpt)
REVERT: H   20 GLU cc_start: 0.9323 (tp30) cc_final: 0.9028 (tp30)
REVERT: H   59 GLU cc_start: 0.9363 (mm-30) cc_final: 0.9135 (mm-30)
REVERT: H  109 GLU cc_start: 0.8839 (tt0) cc_final: 0.8494 (tm-30)
REVERT: H  149 MET cc_start: 0.9359 (mmm) cc_final: 0.8960 (mmm)
REVERT: B   20 GLU cc_start: 0.9341 (tp30) cc_final: 0.9067 (tp30)
REVERT: B  109 GLU cc_start: 0.8841 (tt0) cc_final: 0.8487 (tm-30)
REVERT: B  149 MET cc_start: 0.9336 (mmm) cc_final: 0.8853 (tpt)
REVERT: D   20 GLU cc_start: 0.9335 (tp30) cc_final: 0.9055 (tp30)
REVERT: D  109 GLU cc_start: 0.8874 (tt0) cc_final: 0.8505 (tm-30)
REVERT: D  149 MET cc_start: 0.9361 (mmm) cc_final: 0.8886 (tpt)
REVERT: F   20 GLU cc_start: 0.9332 (tp30) cc_final: 0.8993 (tp30)
REVERT: F   59 GLU cc_start: 0.9406 (mm-30) cc_final: 0.9192 (mm-30)
REVERT: F  109 GLU cc_start: 0.8854 (tt0) cc_final: 0.8478 (tm-30)
REVERT: F  123 PHE cc_start: 0.8658 (t80) cc_final: 0.8395 (t80)
REVERT: F  149 MET cc_start: 0.9340 (mmm) cc_final: 0.8983 (tpt)
  outliers start: 3
  outliers final: 3
  residues processed: 159
  average time/residue: 0.0933
  time to fit residues: 20.7791
Evaluate side-chains
  158 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 155
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
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 93 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 43 optimal weight:    0.2980
   chunk 46 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 52 optimal weight:    0.3980
   chunk 45 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3122 r_free = 0.3122 target = 0.054515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.040104 restraints weight = 185949.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.2704 rms_B_bonded: 9.62
r_work: 0.2428 rms_B_bonded: 8.68 restraints_weight: 2.0000
r_work: 0.2594 rms_B_bonded: 5.40 restraints_weight: 4.0000
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2558
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2558 r_free = 0.2558    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2558 r_free = 0.2558    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2558
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.3814

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= 0.158
  Angle     :  0.689   8.679  12152  Z= 0.353
  Chirality :  0.041   0.132   1416
  Planarity :  0.004   0.026   1552
  Dihedral  :  3.535  13.902   1192
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 16.32 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.26), residues: 1080
  helix:  2.22 (0.24), residues: 488
  sheet:  1.61 (0.31), residues: 232
  loop : -1.10 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  30 
 TYR   0.005   0.001   TYR C 112 
 PHE   0.020   0.002   PHE D 123 
 TRP   0.004   0.000   TRP A  19 
 HIS   0.002   0.001   HIS E  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 8928)
  covalent geometry    : angle       0.68891 (12152)
  hydrogen bonds       : bond        0.04106 (  497)
  hydrogen bonds       : angle       3.86072 ( 1395)

*********************** 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
  171 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 168
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.9295 (tp30) cc_final: 0.9005 (tp30)
REVERT: A   59 GLU cc_start: 0.9420 (mm-30) cc_final: 0.9139 (mm-30)
REVERT: A  109 GLU cc_start: 0.8889 (tt0) cc_final: 0.8510 (tm-30)
REVERT: A  123 PHE cc_start: 0.8752 (t80) cc_final: 0.8523 (t80)
REVERT: G    7 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8346 (mmtt)
REVERT: G   20 GLU cc_start: 0.9097 (tp30) cc_final: 0.8785 (tp30)
REVERT: G   59 GLU cc_start: 0.9432 (mm-30) cc_final: 0.9167 (mm-30)
REVERT: E   20 GLU cc_start: 0.9327 (tp30) cc_final: 0.8739 (tp30)
REVERT: E  109 GLU cc_start: 0.8830 (tt0) cc_final: 0.8482 (tm-30)
REVERT: E  146 ILE cc_start: 0.9270 (mt) cc_final: 0.9030 (mm)
REVERT: E  149 MET cc_start: 0.9335 (mmm) cc_final: 0.8940 (mmm)
REVERT: C   20 GLU cc_start: 0.9325 (tp30) cc_final: 0.9014 (tp30)
REVERT: C   59 GLU cc_start: 0.9436 (mm-30) cc_final: 0.9225 (mm-30)
REVERT: C  149 MET cc_start: 0.9324 (mmm) cc_final: 0.8921 (mmm)
REVERT: H    7 LYS cc_start: 0.8589 (mmmt) cc_final: 0.8305 (mmtt)
REVERT: H   20 GLU cc_start: 0.9321 (tp30) cc_final: 0.9015 (tp30)
REVERT: H  109 GLU cc_start: 0.8836 (tt0) cc_final: 0.8482 (tm-30)
REVERT: H  123 PHE cc_start: 0.8741 (t80) cc_final: 0.8489 (t80)
REVERT: H  149 MET cc_start: 0.9345 (mmm) cc_final: 0.8925 (mmm)
REVERT: B   20 GLU cc_start: 0.9336 (tp30) cc_final: 0.8740 (tp30)
REVERT: B   59 GLU cc_start: 0.9385 (mm-30) cc_final: 0.9099 (mm-30)
REVERT: B  109 GLU cc_start: 0.8824 (tt0) cc_final: 0.8463 (tm-30)
REVERT: B  149 MET cc_start: 0.9343 (mmm) cc_final: 0.8940 (mmm)
REVERT: D   20 GLU cc_start: 0.9322 (tp30) cc_final: 0.9038 (tp30)
REVERT: D  109 GLU cc_start: 0.8875 (tt0) cc_final: 0.8497 (tm-30)
REVERT: D  146 ILE cc_start: 0.9277 (mt) cc_final: 0.9042 (mm)
REVERT: D  149 MET cc_start: 0.9380 (mmm) cc_final: 0.8901 (tpt)
REVERT: F   20 GLU cc_start: 0.9329 (tp30) cc_final: 0.8834 (tp30)
REVERT: F   59 GLU cc_start: 0.9416 (mm-30) cc_final: 0.9201 (mm-30)
REVERT: F  109 GLU cc_start: 0.8830 (tt0) cc_final: 0.8467 (tm-30)
REVERT: F  123 PHE cc_start: 0.8713 (t80) cc_final: 0.8462 (t80)
REVERT: F  149 MET cc_start: 0.9370 (mmm) cc_final: 0.9074 (mmm)
  outliers start: 3
  outliers final: 3
  residues processed: 171
  average time/residue: 0.0872
  time to fit residues: 21.0069
Evaluate side-chains
  163 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 160
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 87 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0030
   chunk 13 optimal weight:    4.9990
   overall best weight:    1.1594

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.055104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.041178 restraints weight = 158552.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.2702 rms_B_bonded: 9.04
r_work: 0.2438 rms_B_bonded: 8.26 restraints_weight: 2.0000
r_work: 0.2608 rms_B_bonded: 5.15 restraints_weight: 4.0000
r_work (final): 0.2608
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2573
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2573 r_free = 0.2573    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2573 r_free = 0.2573    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2573
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.3896

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= 0.163
  Angle     :  0.716   8.321  12152  Z= 0.370
  Chirality :  0.040   0.131   1416
  Planarity :  0.004   0.025   1552
  Dihedral  :  3.527  13.669   1192
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 17.98 %
    Favored  : 81.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.26), residues: 1080
  helix:  2.20 (0.23), residues: 488
  sheet:  1.59 (0.31), residues: 232
  loop : -1.10 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  30 
 TYR   0.004   0.001   TYR C 112 
 PHE   0.017   0.002   PHE G 123 
 TRP   0.004   0.000   TRP F  69 
 HIS   0.002   0.001   HIS G  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 8928)
  covalent geometry    : angle       0.71596 (12152)
  hydrogen bonds       : bond        0.04180 (  497)
  hydrogen bonds       : angle       3.85036 ( 1395)

*********************** 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
  173 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 170
  time to evaluate  : 0.421 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.9303 (tp30) cc_final: 0.8987 (tp30)
REVERT: A   59 GLU cc_start: 0.9434 (mm-30) cc_final: 0.9156 (mm-30)
REVERT: A  109 GLU cc_start: 0.8896 (tt0) cc_final: 0.8531 (tm-30)
REVERT: G    7 LYS cc_start: 0.8758 (mmmt) cc_final: 0.8485 (mmtt)
REVERT: G   20 GLU cc_start: 0.9064 (tp30) cc_final: 0.8736 (tp30)
REVERT: G   59 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9176 (mm-30)
REVERT: G  109 GLU cc_start: 0.8807 (tt0) cc_final: 0.8427 (tm-30)
REVERT: E   20 GLU cc_start: 0.9097 (tp30) cc_final: 0.8794 (tp30)
REVERT: E  109 GLU cc_start: 0.8852 (tt0) cc_final: 0.8477 (tm-30)
REVERT: E  146 ILE cc_start: 0.9300 (mt) cc_final: 0.9061 (mm)
REVERT: E  149 MET cc_start: 0.9335 (mmm) cc_final: 0.8948 (mmm)
REVERT: C   20 GLU cc_start: 0.9335 (tp30) cc_final: 0.8770 (tp30)
REVERT: C   59 GLU cc_start: 0.9458 (mm-30) cc_final: 0.9246 (mm-30)
REVERT: C  149 MET cc_start: 0.9325 (mmm) cc_final: 0.8934 (mmm)
REVERT: H    7 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8471 (mmtt)
REVERT: H   20 GLU cc_start: 0.9315 (tp30) cc_final: 0.8741 (tp30)
REVERT: H   59 GLU cc_start: 0.9384 (mm-30) cc_final: 0.9106 (mm-30)
REVERT: H  109 GLU cc_start: 0.8852 (tt0) cc_final: 0.8496 (tm-30)
REVERT: H  149 MET cc_start: 0.9349 (mmm) cc_final: 0.8940 (mmm)
REVERT: B   20 GLU cc_start: 0.9098 (tp30) cc_final: 0.8801 (tp30)
REVERT: B  109 GLU cc_start: 0.8837 (tt0) cc_final: 0.8473 (tm-30)
REVERT: B  149 MET cc_start: 0.9342 (mmm) cc_final: 0.8943 (mmm)
REVERT: D   20 GLU cc_start: 0.9338 (tp30) cc_final: 0.8753 (tp30)
REVERT: D  109 GLU cc_start: 0.8879 (tt0) cc_final: 0.8553 (tm-30)
REVERT: D  146 ILE cc_start: 0.9309 (mt) cc_final: 0.9081 (mm)
REVERT: D  149 MET cc_start: 0.9357 (mmm) cc_final: 0.8965 (mmm)
REVERT: F    7 LYS cc_start: 0.8707 (mmmt) cc_final: 0.8363 (mmtt)
REVERT: F   20 GLU cc_start: 0.9133 (tp30) cc_final: 0.8807 (tp30)
REVERT: F   59 GLU cc_start: 0.9431 (mm-30) cc_final: 0.9181 (mm-30)
REVERT: F  109 GLU cc_start: 0.8841 (tt0) cc_final: 0.8486 (tm-30)
REVERT: F  149 MET cc_start: 0.9365 (mmm) cc_final: 0.9082 (mmm)
  outliers start: 3
  outliers final: 3
  residues processed: 173
  average time/residue: 0.0891
  time to fit residues: 21.7892
Evaluate side-chains
  165 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 162
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 78 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   chunk 59 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3164 r_free = 0.3164 target = 0.055648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.041225 restraints weight = 190546.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.2720 rms_B_bonded: 9.82
r_work: 0.2443 rms_B_bonded: 8.83 restraints_weight: 2.0000
r_work: 0.2610 rms_B_bonded: 5.56 restraints_weight: 4.0000
r_work (final): 0.2610
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2572
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2572 r_free = 0.2572    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2572 r_free = 0.2572    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2572
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.3946

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= 0.154
  Angle     :  0.738   8.470  12152  Z= 0.381
  Chirality :  0.040   0.124   1416
  Planarity :  0.004   0.026   1552
  Dihedral  :  3.573  14.230   1192
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.26), residues: 1080
  helix:  2.22 (0.23), residues: 488
  sheet:  1.64 (0.31), residues: 232
  loop : -1.09 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  30 
 TYR   0.010   0.001   TYR F 126 
 PHE   0.017   0.002   PHE H 123 
 TRP   0.004   0.000   TRP H  19 
 HIS   0.002   0.001   HIS E  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 8928)
  covalent geometry    : angle       0.73812 (12152)
  hydrogen bonds       : bond        0.03979 (  497)
  hydrogen bonds       : angle       3.81172 ( 1395)

*********************** 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
  176 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 172
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.9306 (tp30) cc_final: 0.8722 (tp30)
REVERT: A  109 GLU cc_start: 0.8901 (tt0) cc_final: 0.8529 (tm-30)
REVERT: A  149 MET cc_start: 0.9391 (mmm) cc_final: 0.8982 (tpt)
REVERT: G    7 LYS cc_start: 0.8766 (mmmt) cc_final: 0.8498 (mmtt)
REVERT: G   20 GLU cc_start: 0.9071 (tp30) cc_final: 0.8821 (tp30)
REVERT: G   59 GLU cc_start: 0.9457 (mm-30) cc_final: 0.9237 (mm-30)
REVERT: G  109 GLU cc_start: 0.8821 (tt0) cc_final: 0.8449 (tm-30)
REVERT: G  149 MET cc_start: 0.9257 (tpp) cc_final: 0.8523 (mmm)
REVERT: E   20 GLU cc_start: 0.9021 (tp30) cc_final: 0.8738 (tp30)
REVERT: E  109 GLU cc_start: 0.8851 (tt0) cc_final: 0.8494 (tm-30)
REVERT: E  146 ILE cc_start: 0.9317 (mt) cc_final: 0.9086 (mm)
REVERT: E  149 MET cc_start: 0.9362 (mmm) cc_final: 0.9077 (mmm)
REVERT: C   20 GLU cc_start: 0.9022 (tp30) cc_final: 0.8750 (tp30)
REVERT: C   59 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9235 (mm-30)
REVERT: C  146 ILE cc_start: 0.9321 (mt) cc_final: 0.9096 (mm)
REVERT: C  149 MET cc_start: 0.9332 (mmm) cc_final: 0.8952 (mmm)
REVERT: H    7 LYS cc_start: 0.8759 (mmmt) cc_final: 0.8510 (mmtt)
REVERT: H   20 GLU cc_start: 0.9008 (tp30) cc_final: 0.8732 (tp30)
REVERT: H   59 GLU cc_start: 0.9378 (mm-30) cc_final: 0.9084 (mm-30)
REVERT: H  109 GLU cc_start: 0.8856 (tt0) cc_final: 0.8499 (tm-30)
REVERT: H  149 MET cc_start: 0.9344 (mmm) cc_final: 0.8980 (mmm)
REVERT: B   20 GLU cc_start: 0.9015 (tp30) cc_final: 0.8758 (tp30)
REVERT: B  109 GLU cc_start: 0.8831 (tt0) cc_final: 0.8466 (tm-30)
REVERT: B  149 MET cc_start: 0.9332 (mmm) cc_final: 0.9025 (mmm)
REVERT: D   20 GLU cc_start: 0.9033 (tp30) cc_final: 0.8753 (tp30)
REVERT: D  109 GLU cc_start: 0.8880 (tt0) cc_final: 0.8540 (tm-30)
REVERT: D  146 ILE cc_start: 0.9340 (mt) cc_final: 0.9114 (mm)
REVERT: D  149 MET cc_start: 0.9351 (mmm) cc_final: 0.8970 (mmm)
REVERT: F    7 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8422 (mmtt)
REVERT: F   20 GLU cc_start: 0.9120 (tp30) cc_final: 0.8888 (tp30)
REVERT: F   59 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9221 (mm-30)
REVERT: F  109 GLU cc_start: 0.8860 (tt0) cc_final: 0.8505 (tm-30)
REVERT: F  149 MET cc_start: 0.9376 (mmm) cc_final: 0.9012 (mmm)
  outliers start: 4
  outliers final: 4
  residues processed: 176
  average time/residue: 0.0885
  time to fit residues: 21.9700
Evaluate side-chains
  170 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 166
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 SER
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 90 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 102 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 50 optimal weight:    0.2980
   chunk 21 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 99 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3143 r_free = 0.3143 target = 0.054551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.039719 restraints weight = 174493.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.2668 rms_B_bonded: 9.97
r_work: 0.2416 rms_B_bonded: 9.04 restraints_weight: 2.0000
r_work: 0.2584 rms_B_bonded: 5.60 restraints_weight: 4.0000
r_work (final): 0.2584
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2559
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2559 r_free = 0.2559    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2559 r_free = 0.2559    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2559
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.4042

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= 0.157
  Angle     :  0.755   9.105  12152  Z= 0.391
  Chirality :  0.040   0.126   1416
  Planarity :  0.004   0.026   1552
  Dihedral  :  3.528  14.075   1192
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 18.60 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.62 (0.26), residues: 1080
  helix:  2.26 (0.23), residues: 488
  sheet:  1.65 (0.32), residues: 232
  loop : -1.08 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F  30 
 TYR   0.005   0.001   TYR F 126 
 PHE   0.018   0.002   PHE H 123 
 TRP   0.003   0.000   TRP G  69 
 HIS   0.002   0.001   HIS G  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 8928)
  covalent geometry    : angle       0.75484 (12152)
  hydrogen bonds       : bond        0.03948 (  497)
  hydrogen bonds       : angle       3.80523 ( 1395)

********************** 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
  172 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 168
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.9001 (tp30) cc_final: 0.8713 (tp30)
REVERT: A   59 GLU cc_start: 0.9379 (mm-30) cc_final: 0.9118 (mm-30)
REVERT: A  109 GLU cc_start: 0.8833 (tt0) cc_final: 0.8472 (tm-30)
REVERT: A  149 MET cc_start: 0.9326 (mmm) cc_final: 0.8842 (mmm)
REVERT: G    7 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8586 (mmtt)
REVERT: G   20 GLU cc_start: 0.9072 (tp30) cc_final: 0.8812 (tp30)
REVERT: G   59 GLU cc_start: 0.9462 (mm-30) cc_final: 0.9245 (mm-30)
REVERT: G  109 GLU cc_start: 0.8768 (tt0) cc_final: 0.8407 (tm-30)
REVERT: G  146 ILE cc_start: 0.9314 (mt) cc_final: 0.9085 (mm)
REVERT: E   20 GLU cc_start: 0.9010 (tp30) cc_final: 0.8741 (tp30)
REVERT: E  109 GLU cc_start: 0.8794 (tt0) cc_final: 0.8422 (tm-30)
REVERT: E  146 ILE cc_start: 0.9312 (mt) cc_final: 0.9087 (mm)
REVERT: E  149 MET cc_start: 0.9355 (mmm) cc_final: 0.9055 (mmm)
REVERT: C   20 GLU cc_start: 0.9000 (tp30) cc_final: 0.8725 (tp30)
REVERT: C   59 GLU cc_start: 0.9451 (mm-30) cc_final: 0.9239 (mm-30)
REVERT: C  146 ILE cc_start: 0.9309 (mt) cc_final: 0.9082 (mm)
REVERT: C  149 MET cc_start: 0.9318 (mmm) cc_final: 0.8917 (mmm)
REVERT: H    7 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8596 (mmtt)
REVERT: H   20 GLU cc_start: 0.9015 (tp30) cc_final: 0.8744 (tp30)
REVERT: H   59 GLU cc_start: 0.9387 (mm-30) cc_final: 0.9090 (mm-30)
REVERT: H  109 GLU cc_start: 0.8788 (tt0) cc_final: 0.8430 (tm-30)
REVERT: H  149 MET cc_start: 0.9336 (mmm) cc_final: 0.8956 (mmm)
REVERT: B   20 GLU cc_start: 0.9003 (tp30) cc_final: 0.8739 (tp30)
REVERT: B  109 GLU cc_start: 0.8797 (tt0) cc_final: 0.8435 (tm-30)
REVERT: B  149 MET cc_start: 0.9327 (mmm) cc_final: 0.9017 (mmm)
REVERT: D   20 GLU cc_start: 0.9026 (tp30) cc_final: 0.8739 (tp30)
REVERT: D  109 GLU cc_start: 0.8822 (tt0) cc_final: 0.8482 (tm-30)
REVERT: D  146 ILE cc_start: 0.9346 (mt) cc_final: 0.9114 (mm)
REVERT: D  149 MET cc_start: 0.9334 (mmm) cc_final: 0.8928 (mmm)
REVERT: F    7 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8489 (mmtt)
REVERT: F   20 GLU cc_start: 0.9078 (tp30) cc_final: 0.8823 (tp30)
REVERT: F   59 GLU cc_start: 0.9458 (mm-30) cc_final: 0.9242 (mm-30)
REVERT: F  109 GLU cc_start: 0.8788 (tt0) cc_final: 0.8428 (tm-30)
REVERT: F  149 MET cc_start: 0.9358 (mmm) cc_final: 0.8966 (mmm)
  outliers start: 4
  outliers final: 4
  residues processed: 172
  average time/residue: 0.0919
  time to fit residues: 22.1798
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  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 SER
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 27 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 64 optimal weight:   10.0000
   chunk 61 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 101 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    1.3988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.053127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.038693 restraints weight = 164157.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.2639 rms_B_bonded: 9.60
r_work: 0.2387 rms_B_bonded: 8.76 restraints_weight: 2.0000
r_work: 0.2552 rms_B_bonded: 5.45 restraints_weight: 4.0000
r_work (final): 0.2552
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2551
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2551 r_free = 0.2551    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2551 r_free = 0.2551    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2551
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.4120

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= 0.182
  Angle     :  0.755   8.958  12152  Z= 0.390
  Chirality :  0.040   0.123   1416
  Planarity :  0.004   0.025   1552
  Dihedral  :  3.548  13.771   1192
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  : 18.70 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.26), residues: 1080
  helix:  2.31 (0.23), residues: 488
  sheet:  1.48 (0.30), residues: 232
  loop : -1.08 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 130 
 TYR   0.004   0.001   TYR F 126 
 PHE   0.015   0.002   PHE A 123 
 TRP   0.004   0.001   TRP G  69 
 HIS   0.002   0.001   HIS E  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 8928)
  covalent geometry    : angle       0.75496 (12152)
  hydrogen bonds       : bond        0.04411 (  497)
  hydrogen bonds       : angle       3.87234 ( 1395)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2440.46 seconds
wall clock time: 42 minutes 19.00 seconds (2539.00 seconds total)