Starting phenix.real_space_refine
on Fri Aug 22 19:45:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c08_45076/08_2025/9c08_45076.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c08_45076/08_2025/9c08_45076.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c08_45076/08_2025/9c08_45076.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c08_45076/08_2025/9c08_45076.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c08_45076/08_2025/9c08_45076.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c08_45076/08_2025/9c08_45076.cif"
  }
  resolution = 2.96
  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=  -0.001 sd=   0.070
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      20      5.16       5
     C    4892      2.51       5
     N    1172      2.21       5
     O    1336      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7420
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1855
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 10, 'TRANS': 212}
          Chain breaks: 2
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 1.37, per 1000 atoms: 0.18
  Number of scatterers: 7420
  At special positions: 0
  Unit cell: (111.1, 111.1, 58.3, 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      20     16.00
     O    1336      8.00
     N    1172      7.00
     C    4892      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: 0.52
  Conformation dependent library (CDL) restraints added in 313.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1712

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 4 sheets defined
      47.1% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 24
      removed outlier: 3.520A  pdb=" N   LEU A  22 " --> pdb=" O   GLY A  19 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   SER A  23 " --> pdb=" O   GLU A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 45
      removed outlier: 3.517A  pdb=" N   PHE A  44 " --> pdb=" O   GLN A  41 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   GLU A  45 " --> pdb=" O   PHE A  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 41 through 45'
    Processing helix  chain 'A' and resid 64 through 77
      removed outlier: 3.677A  pdb=" N   THR A  70 " --> pdb=" O   GLU A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 107
      removed outlier: 3.532A  pdb=" N   GLN A 101 " --> pdb=" O   LEU A  97 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU A 106 " --> pdb=" O   LYS A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 117
    Processing helix  chain 'A' and resid 118 through 120
      No H-bonds generated for 'chain 'A' and resid 118 through 120'
    Processing helix  chain 'A' and resid 121 through 136
      removed outlier: 3.584A  pdb=" N   ASN A 136 " --> pdb=" O   GLU A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 152
    Processing helix  chain 'A' and resid 199 through 215
      removed outlier: 3.831A  pdb=" N   ASP A 203 " --> pdb=" O   SER A 199 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU A 204 " --> pdb=" O   LYS A 200 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLU A 205 " --> pdb=" O   ASP A 201 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   HIS A 215 " --> pdb=" O   GLN A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 230
    Processing helix  chain 'A' and resid 260 through 267
      removed outlier: 4.267A  pdb=" N   TYR A 264 " --> pdb=" O   PRO A 260 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   GLU A 265 " --> pdb=" O   HIS A 261 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU A 267 " --> pdb=" O   VAL A 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 24
      removed outlier: 3.520A  pdb=" N   LEU B  22 " --> pdb=" O   GLY B  19 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   SER B  23 " --> pdb=" O   GLU B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 45
      removed outlier: 3.517A  pdb=" N   PHE B  44 " --> pdb=" O   GLN B  41 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   GLU B  45 " --> pdb=" O   PHE B  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 41 through 45'
    Processing helix  chain 'B' and resid 64 through 77
      removed outlier: 3.677A  pdb=" N   THR B  70 " --> pdb=" O   GLU B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 107
      removed outlier: 3.532A  pdb=" N   GLN B 101 " --> pdb=" O   LEU B  97 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU B 106 " --> pdb=" O   LYS B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 117
    Processing helix  chain 'B' and resid 118 through 120
      No H-bonds generated for 'chain 'B' and resid 118 through 120'
    Processing helix  chain 'B' and resid 121 through 136
      removed outlier: 3.584A  pdb=" N   ASN B 136 " --> pdb=" O   GLU B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 152
    Processing helix  chain 'B' and resid 199 through 215
      removed outlier: 3.831A  pdb=" N   ASP B 203 " --> pdb=" O   SER B 199 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU B 204 " --> pdb=" O   LYS B 200 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLU B 205 " --> pdb=" O   ASP B 201 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   HIS B 215 " --> pdb=" O   GLN B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 230
    Processing helix  chain 'B' and resid 260 through 267
      removed outlier: 4.267A  pdb=" N   TYR B 264 " --> pdb=" O   PRO B 260 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   GLU B 265 " --> pdb=" O   HIS B 261 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU B 267 " --> pdb=" O   VAL B 263 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 19 through 24
      removed outlier: 3.520A  pdb=" N   LEU C  22 " --> pdb=" O   GLY C  19 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   SER C  23 " --> pdb=" O   GLU C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 45
      removed outlier: 3.517A  pdb=" N   PHE C  44 " --> pdb=" O   GLN C  41 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   GLU C  45 " --> pdb=" O   PHE C  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 41 through 45'
    Processing helix  chain 'C' and resid 64 through 77
      removed outlier: 3.677A  pdb=" N   THR C  70 " --> pdb=" O   GLU C  66 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 107
      removed outlier: 3.532A  pdb=" N   GLN C 101 " --> pdb=" O   LEU C  97 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU C 106 " --> pdb=" O   LYS C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 117
    Processing helix  chain 'C' and resid 118 through 120
      No H-bonds generated for 'chain 'C' and resid 118 through 120'
    Processing helix  chain 'C' and resid 121 through 136
      removed outlier: 3.584A  pdb=" N   ASN C 136 " --> pdb=" O   GLU C 132 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 152
    Processing helix  chain 'C' and resid 199 through 215
      removed outlier: 3.831A  pdb=" N   ASP C 203 " --> pdb=" O   SER C 199 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU C 204 " --> pdb=" O   LYS C 200 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLU C 205 " --> pdb=" O   ASP C 201 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   HIS C 215 " --> pdb=" O   GLN C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 225 through 230
    Processing helix  chain 'C' and resid 260 through 267
      removed outlier: 4.267A  pdb=" N   TYR C 264 " --> pdb=" O   PRO C 260 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   GLU C 265 " --> pdb=" O   HIS C 261 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU C 267 " --> pdb=" O   VAL C 263 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 24
      removed outlier: 3.520A  pdb=" N   LEU D  22 " --> pdb=" O   GLY D  19 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   SER D  23 " --> pdb=" O   GLU D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 41 through 45
      removed outlier: 3.517A  pdb=" N   PHE D  44 " --> pdb=" O   GLN D  41 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   GLU D  45 " --> pdb=" O   PHE D  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 41 through 45'
    Processing helix  chain 'D' and resid 64 through 77
      removed outlier: 3.677A  pdb=" N   THR D  70 " --> pdb=" O   GLU D  66 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 96 through 107
      removed outlier: 3.532A  pdb=" N   GLN D 101 " --> pdb=" O   LEU D  97 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU D 106 " --> pdb=" O   LYS D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 113 through 117
    Processing helix  chain 'D' and resid 118 through 120
      No H-bonds generated for 'chain 'D' and resid 118 through 120'
    Processing helix  chain 'D' and resid 121 through 136
      removed outlier: 3.584A  pdb=" N   ASN D 136 " --> pdb=" O   GLU D 132 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 152
    Processing helix  chain 'D' and resid 199 through 215
      removed outlier: 3.831A  pdb=" N   ASP D 203 " --> pdb=" O   SER D 199 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU D 204 " --> pdb=" O   LYS D 200 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLU D 205 " --> pdb=" O   ASP D 201 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   HIS D 215 " --> pdb=" O   GLN D 211 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 225 through 230
    Processing helix  chain 'D' and resid 260 through 267
      removed outlier: 4.267A  pdb=" N   TYR D 264 " --> pdb=" O   PRO D 260 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   GLU D 265 " --> pdb=" O   HIS D 261 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU D 267 " --> pdb=" O   VAL D 263 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 112
      removed outlier: 9.018A  pdb=" N   LYS A  53 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
      removed outlier: 9.929A  pdb=" N   ASN A  84 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   LYS A  55 " --> pdb=" O   ASN A  84 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   ILE A  86 " --> pdb=" O   LYS A  55 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   VAL A  57 " --> pdb=" O   ILE A  86 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  55 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   VAL A  57 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ARG A  38 " --> pdb=" O   VAL A  57 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   PHE A  59 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ASP A  35 " --> pdb=" O   ALA A  12 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   CYS A  39 " --> pdb=" O   ALA A  16 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   VAL A  13 " --> pdb=" O   TYR A 158 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   THR A 160 " --> pdb=" O   VAL A  13 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   VAL A  15 " --> pdb=" O   THR A 160 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 111 through 112
      removed outlier: 9.018A  pdb=" N   LYS B  53 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
      removed outlier: 9.929A  pdb=" N   ASN B  84 " --> pdb=" O   LYS B  53 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   LYS B  55 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   ILE B  86 " --> pdb=" O   LYS B  55 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   VAL B  57 " --> pdb=" O   ILE B  86 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   VAL B  36 " --> pdb=" O   LYS B  55 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   VAL B  57 " --> pdb=" O   VAL B  36 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ARG B  38 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   PHE B  59 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ASP B  35 " --> pdb=" O   ALA B  12 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   CYS B  39 " --> pdb=" O   ALA B  16 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   VAL B  13 " --> pdb=" O   TYR B 158 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   THR B 160 " --> pdb=" O   VAL B  13 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   VAL B  15 " --> pdb=" O   THR B 160 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 111 through 112
      removed outlier: 9.018A  pdb=" N   LYS C  53 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
      removed outlier: 9.929A  pdb=" N   ASN C  84 " --> pdb=" O   LYS C  53 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   LYS C  55 " --> pdb=" O   ASN C  84 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   ILE C  86 " --> pdb=" O   LYS C  55 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   VAL C  57 " --> pdb=" O   ILE C  86 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   VAL C  36 " --> pdb=" O   LYS C  55 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   VAL C  57 " --> pdb=" O   VAL C  36 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ARG C  38 " --> pdb=" O   VAL C  57 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   PHE C  59 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ASP C  35 " --> pdb=" O   ALA C  12 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   CYS C  39 " --> pdb=" O   ALA C  16 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   VAL C  13 " --> pdb=" O   TYR C 158 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   THR C 160 " --> pdb=" O   VAL C  13 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   VAL C  15 " --> pdb=" O   THR C 160 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 111 through 112
      removed outlier: 9.018A  pdb=" N   LYS D  53 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
      removed outlier: 9.929A  pdb=" N   ASN D  84 " --> pdb=" O   LYS D  53 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   LYS D  55 " --> pdb=" O   ASN D  84 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   ILE D  86 " --> pdb=" O   LYS D  55 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   VAL D  57 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   VAL D  36 " --> pdb=" O   LYS D  55 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   VAL D  57 " --> pdb=" O   VAL D  36 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ARG D  38 " --> pdb=" O   VAL D  57 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   PHE D  59 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ASP D  35 " --> pdb=" O   ALA D  12 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   CYS D  39 " --> pdb=" O   ALA D  16 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   VAL D  13 " --> pdb=" O   TYR D 158 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   THR D 160 " --> pdb=" O   VAL D  13 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   VAL D  15 " --> pdb=" O   THR D 160 " (cutoff:3.500A)

    232 hydrogen bonds defined for protein.
    636 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.72

  Time building geometry restraints manager: 0.72 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: 2268
        1.34 -     1.46: 1952
        1.46 -     1.58: 3384
        1.58 -     1.69: 0
        1.69 -     1.81: 32
  Bond restraints: 7636
  Sorted by residual:
  bond pdb=" N   ASN B 251 "
       pdb=" CA  ASN B 251 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.014 1.29e-02 6.01e+03 1.10e+00
  bond pdb=" N   ASN A 251 "
       pdb=" CA  ASN A 251 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.014 1.29e-02 6.01e+03 1.10e+00
  bond pdb=" N   ASN C 251 "
       pdb=" CA  ASN C 251 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.014 1.29e-02 6.01e+03 1.10e+00
  bond pdb=" N   ASN D 251 "
       pdb=" CA  ASN D 251 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.014 1.29e-02 6.01e+03 1.10e+00
  bond pdb=" N   GLY A  17 "
       pdb=" CA  GLY A  17 "
    ideal  model  delta    sigma   weight residual
    1.438  1.448 -0.010 1.41e-02 5.03e+03 5.07e-01
  ... (remaining 7631 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.59: 9076
        0.59 -     1.18: 1024
        1.18 -     1.77: 156
        1.77 -     2.36: 40
        2.36 -     2.95: 56
  Bond angle restraints: 10352
  Sorted by residual:
  angle pdb=" N   ILE B 202 "
        pdb=" CA  ILE B 202 "
        pdb=" C   ILE B 202 "
      ideal   model   delta    sigma   weight residual
     111.90  109.01    2.89 8.10e-01 1.52e+00 1.28e+01
  angle pdb=" N   ILE C 202 "
        pdb=" CA  ILE C 202 "
        pdb=" C   ILE C 202 "
      ideal   model   delta    sigma   weight residual
     111.90  109.01    2.89 8.10e-01 1.52e+00 1.28e+01
  angle pdb=" N   ILE D 202 "
        pdb=" CA  ILE D 202 "
        pdb=" C   ILE D 202 "
      ideal   model   delta    sigma   weight residual
     111.90  109.01    2.89 8.10e-01 1.52e+00 1.28e+01
  angle pdb=" N   ILE A 202 "
        pdb=" CA  ILE A 202 "
        pdb=" C   ILE A 202 "
      ideal   model   delta    sigma   weight residual
     111.90  109.01    2.89 8.10e-01 1.52e+00 1.28e+01
  angle pdb=" CA  GLY C  17 "
        pdb=" C   GLY C  17 "
        pdb=" N   ASN C  18 "
      ideal   model   delta    sigma   weight residual
     115.27  116.98   -1.71 7.60e-01 1.73e+00 5.07e+00
  ... (remaining 10347 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.33: 4156
       11.33 -    22.66: 216
       22.66 -    33.99: 88
       33.99 -    45.32: 8
       45.32 -    56.66: 4
  Dihedral angle restraints: 4472
    sinusoidal: 1796
      harmonic: 2676
  Sorted by residual:
  dihedral pdb=" CB  LYS B 200 "
           pdb=" CG  LYS B 200 "
           pdb=" CD  LYS B 200 "
           pdb=" CE  LYS B 200 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  116.66  -56.66     3      1.50e+01 4.44e-03 9.41e+00
  dihedral pdb=" CB  LYS A 200 "
           pdb=" CG  LYS A 200 "
           pdb=" CD  LYS A 200 "
           pdb=" CE  LYS A 200 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  116.66  -56.66     3      1.50e+01 4.44e-03 9.41e+00
  dihedral pdb=" CB  LYS C 200 "
           pdb=" CG  LYS C 200 "
           pdb=" CD  LYS C 200 "
           pdb=" CE  LYS C 200 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  116.66  -56.66     3      1.50e+01 4.44e-03 9.41e+00
  ... (remaining 4469 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 568
       0.028 -    0.056: 352
       0.056 -    0.084: 100
       0.084 -    0.112: 72
       0.112 -    0.140: 16
  Chirality restraints: 1108
  Sorted by residual:
  chirality pdb=" CA  ILE D 233 "
            pdb=" N   ILE D 233 "
            pdb=" C   ILE D 233 "
            pdb=" CB  ILE D 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  chirality pdb=" CA  ILE A 233 "
            pdb=" N   ILE A 233 "
            pdb=" C   ILE A 233 "
            pdb=" CB  ILE A 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  chirality pdb=" CA  ILE B 233 "
            pdb=" N   ILE B 233 "
            pdb=" C   ILE B 233 "
            pdb=" CB  ILE B 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  ... (remaining 1105 not shown)

  Planarity restraints: 1308
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 259 "   -0.015 5.00e-02 4.00e+02   2.34e-02 8.75e-01
        pdb=" N   PRO B 260 "    0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO B 260 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO B 260 "   -0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 259 "    0.015 5.00e-02 4.00e+02   2.34e-02 8.75e-01
        pdb=" N   PRO A 260 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO A 260 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 260 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO D 259 "    0.015 5.00e-02 4.00e+02   2.34e-02 8.75e-01
        pdb=" N   PRO D 260 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO D 260 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO D 260 "    0.013 5.00e-02 4.00e+02
  ... (remaining 1305 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2032
        2.81 -     3.33: 6180
        3.33 -     3.85: 11128
        3.85 -     4.38: 13287
        4.38 -     4.90: 23917
  Nonbonded interactions: 56544
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 136 "
            pdb=" NZ  LYS B 266 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" OD1 ASN B 136 "
            pdb=" NZ  LYS C 266 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" NZ  LYS A 266 "
            pdb=" OD1 ASN D 136 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" OD1 ASN C 136 "
            pdb=" NZ  LYS D 266 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" OG  SER C  21 "
            pdb=" OD1 ASP C 163 "
     model   vdw
     2.364 3.040
  ... (remaining 56539 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.030
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.950
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
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   0.034   7636  Z= 0.093
  Angle     :  0.442   2.950  10352  Z= 0.276
  Chirality :  0.044   0.140   1108
  Planarity :  0.003   0.023   1308
  Dihedral  :  8.367  56.655   2760
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  3.43 %
    Favored  : 95.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.30), residues: 868
  helix:  1.05 (0.35), residues: 264
  sheet:  1.25 (0.50), residues: 108
  loop :  0.15 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  47 
 TYR   0.011   0.001   TYR B 127 
 PHE   0.007   0.001   PHE A 262 
 HIS   0.001   0.000   HIS B 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00185 ( 7636)
  covalent geometry    : angle       0.44211 (10352)
  hydrogen bonds       : bond        0.21687 (  232)
  hydrogen bonds       : angle       6.40590 (  636)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A  266 LYS cc_start: 0.7975 (ptpt) cc_final: 0.7765 (ptpt)
  outliers start: 12
  outliers final: 4
  residues processed: 147
  average time/residue: 0.6500
  time to fit residues: 99.9171
Evaluate side-chains
  88 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain D residue   63 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  73 HIS
A 104 GLN
A 112 ASN
A 212 GLN
B 104 GLN
B 112 ASN
B 212 GLN
C 104 GLN
C 112 ASN
C 212 GLN
D 104 GLN
D 112 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.173247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.137777 restraints weight = 7510.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 2.18
r_work: 0.3425 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7636  Z= 0.126
  Angle     :  0.504   4.071  10352  Z= 0.277
  Chirality :  0.047   0.154   1108
  Planarity :  0.004   0.023   1308
  Dihedral  :  4.014  19.720    992
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  8.82 %
    Favored  : 89.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.29), residues: 868
  helix:  1.08 (0.32), residues: 300
  sheet:  1.02 (0.48), residues: 108
  loop :  0.00 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  76 
 TYR   0.015   0.001   TYR C 127 
 PHE   0.013   0.001   PHE D 218 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7636)
  covalent geometry    : angle       0.50435 (10352)
  hydrogen bonds       : bond        0.04887 (  232)
  hydrogen bonds       : angle       3.92403 (  636)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7574 (mt0)
REVERT: B   24 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7573 (mt0)
REVERT: C   24 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7567 (mt0)
  outliers start: 16
  outliers final: 8
  residues processed: 106
  average time/residue: 0.7321
  time to fit residues: 81.1020
Evaluate side-chains
  105 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  102 LYS
Chi-restraints excluded: chain B residue   24 GLN
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  102 LYS
Chi-restraints excluded: chain C residue   24 GLN
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue  102 LYS
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue  102 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 64 optimal weight:    0.3980
   chunk 51 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 212 GLN
B  73 HIS
B 212 GLN
C  73 HIS
C 212 GLN
D  73 HIS
D 211 GLN
D 212 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.170263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.134322 restraints weight = 7627.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.32
r_work: 0.3355 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7636  Z= 0.156
  Angle     :  0.542   4.869  10352  Z= 0.296
  Chirality :  0.048   0.149   1108
  Planarity :  0.004   0.025   1308
  Dihedral  :  4.394  20.231    992
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  :  8.82 %
    Favored  : 88.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.28), residues: 868
  helix:  0.94 (0.31), residues: 300
  sheet:  0.76 (0.48), residues: 108
  loop : -0.47 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  76 
 TYR   0.016   0.002   TYR D 127 
 PHE   0.013   0.001   PHE A 218 
 HIS   0.004   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 7636)
  covalent geometry    : angle       0.54170 (10352)
  hydrogen bonds       : bond        0.05407 (  232)
  hydrogen bonds       : angle       3.97830 (  636)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7471 (mt0)
REVERT: B   24 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7471 (mt0)
REVERT: C   24 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7469 (mt0)
REVERT: D   24 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.7026 (mt0)
  outliers start: 24
  outliers final: 12
  residues processed: 97
  average time/residue: 0.7371
  time to fit residues: 74.7357
Evaluate side-chains
  102 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  102 LYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain B residue   24 GLN
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  102 LYS
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain C residue   24 GLN
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue  102 LYS
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain D residue   24 GLN
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue  102 LYS
Chi-restraints excluded: chain D residue  227 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 9 optimal weight:    0.0470
   chunk 49 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    1.1282

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

Flipped N/Q/H residues before XYZ refinement:
A 212 GLN
B 212 GLN
C 212 GLN
D 212 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.168341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.131830 restraints weight = 7731.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 2.36
r_work: 0.3365 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7636  Z= 0.148
  Angle     :  0.520   4.306  10352  Z= 0.285
  Chirality :  0.048   0.137   1108
  Planarity :  0.003   0.028   1308
  Dihedral  :  4.418  20.156    992
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 11.27 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.28), residues: 868
  helix:  0.90 (0.30), residues: 300
  sheet:  0.63 (0.48), residues: 108
  loop : -0.65 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  76 
 TYR   0.015   0.001   TYR D 127 
 PHE   0.011   0.001   PHE C 218 
 HIS   0.003   0.001   HIS D 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 7636)
  covalent geometry    : angle       0.51984 (10352)
  hydrogen bonds       : bond        0.05016 (  232)
  hydrogen bonds       : angle       3.93520 (  636)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7490 (mt0)
REVERT: B   24 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7489 (mt0)
REVERT: C   24 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7488 (mt0)
REVERT: D   24 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7058 (mt0)
  outliers start: 20
  outliers final: 4
  residues processed: 94
  average time/residue: 0.7307
  time to fit residues: 71.7609
Evaluate side-chains
  97 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain B residue   24 GLN
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain C residue   24 GLN
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain D residue   24 GLN
Chi-restraints excluded: chain D residue   63 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 82 optimal weight:    0.4980
   chunk 15 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3821 r_free = 0.3821 target = 0.163049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.127946 restraints weight = 7735.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 2.07
r_work: 0.3367 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7636  Z= 0.143
  Angle     :  0.512   4.248  10352  Z= 0.280
  Chirality :  0.047   0.138   1108
  Planarity :  0.003   0.028   1308
  Dihedral  :  4.418  19.957    992
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 10.29 %
    Favored  : 86.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.01 (0.28), residues: 868
  helix:  0.88 (0.30), residues: 300
  sheet:  0.50 (0.47), residues: 108
  loop : -0.71 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  28 
 TYR   0.015   0.001   TYR C 127 
 PHE   0.010   0.001   PHE A 218 
 HIS   0.003   0.001   HIS D 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 7636)
  covalent geometry    : angle       0.51179 (10352)
  hydrogen bonds       : bond        0.04874 (  232)
  hydrogen bonds       : angle       3.94393 (  636)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7542 (mt0)
REVERT: B   24 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7537 (mt0)
REVERT: C   24 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7524 (mt0)
REVERT: D   24 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7065 (mt0)
  outliers start: 24
  outliers final: 14
  residues processed: 93
  average time/residue: 0.7249
  time to fit residues: 70.5334
Evaluate side-chains
  103 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   76 ARG
Chi-restraints excluded: chain A residue  102 LYS
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain B residue   24 GLN
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  102 LYS
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain C residue   24 GLN
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue  102 LYS
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain D residue   24 GLN
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   76 ARG
Chi-restraints excluded: chain D residue  102 LYS
Chi-restraints excluded: chain D residue  248 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 75 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  41 GLN
B  41 GLN
C  41 GLN
D  41 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.167113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.133663 restraints weight = 7718.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.00
r_work: 0.3323 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   7636  Z= 0.189
  Angle     :  0.568   5.266  10352  Z= 0.308
  Chirality :  0.049   0.138   1108
  Planarity :  0.004   0.029   1308
  Dihedral  :  4.643  19.992    992
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 11.15 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.28), residues: 868
  helix:  0.85 (0.30), residues: 292
  sheet:  0.34 (0.47), residues: 108
  loop : -0.84 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  28 
 TYR   0.016   0.002   TYR A 127 
 PHE   0.010   0.001   PHE A 218 
 HIS   0.003   0.001   HIS D 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 7636)
  covalent geometry    : angle       0.56784 (10352)
  hydrogen bonds       : bond        0.05710 (  232)
  hydrogen bonds       : angle       4.14308 (  636)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 93
  time to evaluate  : 0.371 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7581 (mt0)
REVERT: B   24 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7578 (mt0)
REVERT: C   24 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7563 (mt0)
REVERT: D   24 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7136 (mt0)
  outliers start: 29
  outliers final: 20
  residues processed: 101
  average time/residue: 0.7036
  time to fit residues: 74.4743
Evaluate side-chains
  117 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   76 ARG
Chi-restraints excluded: chain A residue  102 LYS
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain B residue   24 GLN
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   76 ARG
Chi-restraints excluded: chain B residue  102 LYS
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain C residue   24 GLN
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   76 ARG
Chi-restraints excluded: chain C residue  102 LYS
Chi-restraints excluded: chain C residue  108 ILE
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain D residue   24 GLN
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   76 ARG
Chi-restraints excluded: chain D residue  102 LYS
Chi-restraints excluded: chain D residue  108 ILE
Chi-restraints excluded: chain D residue  248 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0980
   chunk 43 optimal weight:    4.9990
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0770
   chunk 12 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
A  41 GLN
B  41 GLN
C  41 GLN
D  41 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.170472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.136064 restraints weight = 7707.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 2.14
r_work: 0.3444 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7636  Z= 0.087
  Angle     :  0.438   3.596  10352  Z= 0.242
  Chirality :  0.045   0.136   1108
  Planarity :  0.003   0.027   1308
  Dihedral  :  4.153  19.829    992
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 11.64 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.28), residues: 868
  helix:  1.04 (0.30), residues: 300
  sheet:  0.56 (0.47), residues: 108
  loop : -0.60 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 138 
 TYR   0.011   0.001   TYR B 127 
 PHE   0.007   0.001   PHE C 209 
 HIS   0.002   0.001   HIS B 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 7636)
  covalent geometry    : angle       0.43776 (10352)
  hydrogen bonds       : bond        0.03535 (  232)
  hydrogen bonds       : angle       3.77576 (  636)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.7717 (mt0) cc_final: 0.7496 (mt0)
REVERT: B   24 GLN cc_start: 0.7718 (mt0) cc_final: 0.7497 (mt0)
REVERT: C   24 GLN cc_start: 0.7708 (mt0) cc_final: 0.7492 (mt0)
  outliers start: 25
  outliers final: 20
  residues processed: 104
  average time/residue: 0.6672
  time to fit residues: 72.5986
Evaluate side-chains
  114 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  102 LYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  102 LYS
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue  102 LYS
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue  102 LYS
Chi-restraints excluded: chain D residue  227 LEU
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  248 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   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  41 GLN
B  41 GLN
C  41 GLN
D  41 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.170113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.136126 restraints weight = 7739.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 2.09
r_work: 0.3374 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7636  Z= 0.123
  Angle     :  0.483   3.888  10352  Z= 0.265
  Chirality :  0.046   0.136   1108
  Planarity :  0.003   0.028   1308
  Dihedral  :  4.277  19.939    992
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.38 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.28), residues: 868
  helix:  1.07 (0.30), residues: 292
  sheet:  0.51 (0.47), residues: 108
  loop : -0.60 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  28 
 TYR   0.014   0.001   TYR A 127 
 PHE   0.009   0.001   PHE B 218 
 HIS   0.002   0.001   HIS D 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7636)
  covalent geometry    : angle       0.48307 (10352)
  hydrogen bonds       : bond        0.04384 (  232)
  hydrogen bonds       : angle       3.91044 (  636)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7568 (mt0)
REVERT: B   24 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7570 (mt0)
REVERT: C   24 GLN cc_start: 0.7776 (mt0) cc_final: 0.7559 (mt0)
  outliers start: 19
  outliers final: 20
  residues processed: 96
  average time/residue: 0.6487
  time to fit residues: 65.2449
Evaluate side-chains
  117 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  102 LYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain B residue   24 GLN
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  102 LYS
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue  102 LYS
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue  102 LYS
Chi-restraints excluded: chain D residue  227 LEU
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  248 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 54 optimal weight:    0.2980
   chunk 46 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  41 GLN
B  41 GLN
C  41 GLN
D  41 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.171259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.138050 restraints weight = 7661.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.01
r_work: 0.3399 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7636  Z= 0.106
  Angle     :  0.463   4.056  10352  Z= 0.255
  Chirality :  0.046   0.136   1108
  Planarity :  0.003   0.028   1308
  Dihedral  :  4.218  19.908    992
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 13.11 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.28), residues: 868
  helix:  1.12 (0.30), residues: 292
  sheet:  0.53 (0.47), residues: 108
  loop : -0.55 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  28 
 TYR   0.013   0.001   TYR D 127 
 PHE   0.008   0.001   PHE D 218 
 HIS   0.002   0.001   HIS D 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 7636)
  covalent geometry    : angle       0.46269 (10352)
  hydrogen bonds       : bond        0.04004 (  232)
  hydrogen bonds       : angle       3.90237 (  636)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.7775 (mt0) cc_final: 0.7555 (mt0)
REVERT: B   24 GLN cc_start: 0.7768 (mt0) cc_final: 0.7545 (mt0)
REVERT: C   24 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7538 (mt0)
  outliers start: 17
  outliers final: 20
  residues processed: 98
  average time/residue: 0.7082
  time to fit residues: 72.6183
Evaluate side-chains
  116 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  102 LYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  102 LYS
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain C residue   24 GLN
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue  102 LYS
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue  102 LYS
Chi-restraints excluded: chain D residue  227 LEU
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  248 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 26 optimal weight:    0.1980
   chunk 29 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A  41 GLN
B  41 GLN
C  41 GLN
D  41 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.170372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.136452 restraints weight = 7656.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 2.08
r_work: 0.3366 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7636  Z= 0.116
  Angle     :  0.476   4.198  10352  Z= 0.262
  Chirality :  0.046   0.137   1108
  Planarity :  0.003   0.028   1308
  Dihedral  :  4.258  19.934    992
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 12.38 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.28), residues: 868
  helix:  1.11 (0.30), residues: 292
  sheet:  0.53 (0.47), residues: 108
  loop : -0.58 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  28 
 TYR   0.014   0.001   TYR A 127 
 PHE   0.011   0.001   PHE B  81 
 HIS   0.002   0.001   HIS D 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7636)
  covalent geometry    : angle       0.47581 (10352)
  hydrogen bonds       : bond        0.04254 (  232)
  hydrogen bonds       : angle       3.93700 (  636)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7484 (mt0)
REVERT: B   24 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7488 (mt0)
REVERT: C   24 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7472 (mt0)
  outliers start: 23
  outliers final: 20
  residues processed: 99
  average time/residue: 0.6848
  time to fit residues: 71.0210
Evaluate side-chains
  114 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 GLN
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  102 LYS
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain B residue   24 GLN
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  102 LYS
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain C residue   24 GLN
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue  102 LYS
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue  102 LYS
Chi-restraints excluded: chain D residue  227 LEU
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  248 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  41 GLN
B  41 GLN
C  41 GLN
D  41 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.168997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.135681 restraints weight = 7634.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.00
r_work: 0.3367 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7636  Z= 0.143
  Angle     :  0.510   4.180  10352  Z= 0.279
  Chirality :  0.047   0.138   1108
  Planarity :  0.003   0.029   1308
  Dihedral  :  4.414  19.975    992
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.11 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.28), residues: 868
  helix:  0.98 (0.30), residues: 292
  sheet:  0.44 (0.47), residues: 108
  loop : -0.66 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  28 
 TYR   0.015   0.001   TYR A 127 
 PHE   0.008   0.001   PHE A 218 
 HIS   0.002   0.001   HIS D 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 7636)
  covalent geometry    : angle       0.51001 (10352)
  hydrogen bonds       : bond        0.04837 (  232)
  hydrogen bonds       : angle       4.05013 (  636)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2658.84 seconds
wall clock time: 46 minutes 5.12 seconds (2765.12 seconds total)