Starting phenix.real_space_refine
on Wed Jun  4 11:51:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wmm_32615/06_2025/7wmm_32615_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wmm_32615/06_2025/7wmm_32615.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wmm_32615/06_2025/7wmm_32615.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wmm_32615/06_2025/7wmm_32615.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wmm_32615/06_2025/7wmm_32615_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wmm_32615/06_2025/7wmm_32615_neut.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 6
    Type Number    sf(0)   Gaussians
     Br      2      7.06       5
     S       2      5.16       5
     C    1650      2.51       5
     N     448      2.21       5
     O     514      1.98       5
     F       2      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 2618
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 427
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
      Conformer: "B"
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
          bond proxies already assigned to first conformer: 416
    Chain: "B"
      Number of atoms: 427
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
      Conformer: "B"
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
          bond proxies already assigned to first conformer: 416
    Chain: "C"
      Number of atoms: 427
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
      Conformer: "B"
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
          bond proxies already assigned to first conformer: 416
    Chain: "D"
      Number of atoms: 427
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
      Conformer: "B"
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
          bond proxies already assigned to first conformer: 416
    Chain: "E"
      Number of atoms: 427
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
      Conformer: "B"
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
          bond proxies already assigned to first conformer: 416
    Chain: "F"
      Number of atoms: 427
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
      Conformer: "B"
        Number of residues, atoms: 61, 421
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
          bond proxies already assigned to first conformer: 416
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'1KI': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'1KI': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 6
    residue:
      pdb=" N  ASER A  42 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER A  42 " occ=0.50
    residue:
      pdb=" N  ASER B  42 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER B  42 " occ=0.50
    residue:
      pdb=" N  ASER C  42 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER C  42 " occ=0.50
    residue:
      pdb=" N  ASER D  42 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER D  42 " occ=0.50
    residue:
      pdb=" N  ASER E  42 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER E  42 " occ=0.50
    residue:
      pdb=" N  ASER F  42 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER F  42 " occ=0.50
  Time building chain proxies: 4.64, per 1000 atoms: 1.77
  Number of scatterers: 2618
  At special positions: 0
  Unit cell: (98.77, 105.41, 30.71, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Br      2     34.99
     S       2     16.00
     F       2      9.00
     O     514      8.00
     N     448      7.00
     C    1650      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: 0.76
  Conformation dependent library (CDL) restraints added in 700.0 milliseconds
  

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  636

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 70.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 39 through 42
      removed outlier: 6.746A  pdb=" N   TYR A  39 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
      removed outlier: 7.968A  pdb=" N  ASER B  42 " --> pdb=" O   TYR A  39 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   GLY A  41 " --> pdb=" O  ASER B  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 66
      removed outlier: 6.966A  pdb=" N   GLU B  46 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   GLY A  47 " --> pdb=" O   GLU B  46 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   VAL B  52 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   ALA A  53 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   THR B  54 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   VAL A  55 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   ALA B  56 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   GLU A  57 " --> pdb=" O   ALA B  56 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   LYS B  58 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   THR A  59 " --> pdb=" O   LYS B  58 " (cutoff:3.500A)
      removed outlier: 5.721A  pdb=" N   GLU A  46 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 8.800A  pdb=" N   VAL E  49 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   VAL A  48 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 8.292A  pdb=" N   GLY E  51 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 8.682A  pdb=" N   HIS A  50 " --> pdb=" O   GLY E  51 " (cutoff:3.500A)
      removed outlier: 8.211A  pdb=" N   ALA E  53 " --> pdb=" O   HIS A  50 " (cutoff:3.500A)
      removed outlier: 9.105A  pdb=" N   VAL A  52 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 10.408A  pdb=" N   VAL E  55 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 8.958A  pdb=" N   THR A  54 " --> pdb=" O   VAL E  55 " (cutoff:3.500A)
      removed outlier: 10.149A  pdb=" N   GLU E  57 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
      removed outlier: 9.087A  pdb=" N   ALA A  56 " --> pdb=" O   GLU E  57 " (cutoff:3.500A)
      removed outlier: 9.637A  pdb=" N   THR E  59 " --> pdb=" O   ALA A  56 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   LYS A  58 " --> pdb=" O   THR E  59 " (cutoff:3.500A)
      removed outlier: 8.084A  pdb=" N   GLU E  61 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   LYS A  60 " --> pdb=" O   GLU E  61 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   VAL E  63 " --> pdb=" O   LYS A  60 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   GLN A  62 " --> pdb=" O   VAL E  63 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   ASN E  65 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   THR A  64 " --> pdb=" O   ASN E  65 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 82
      removed outlier: 6.898A  pdb=" N   VAL B  70 " --> pdb=" O   ALA A  69 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   VAL A  71 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   THR B  72 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   GLY A  73 " --> pdb=" O   THR B  72 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   VAL A  77 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   ALA B  78 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   GLN A  79 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   LYS B  80 " --> pdb=" O   GLN A  79 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   THR A  81 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   VAL B  82 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 9.137A  pdb=" N   VAL A  70 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 10.236A  pdb=" N   GLY E  73 " --> pdb=" O   VAL A  70 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   THR A  72 " --> pdb=" O   GLY E  73 " (cutoff:3.500A)
      removed outlier: 9.127A  pdb=" N   THR E  75 " --> pdb=" O   THR A  72 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   VAL A  74 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   VAL E  77 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   ALA A  76 " --> pdb=" O   VAL E  77 " (cutoff:3.500A)
      removed outlier: 10.157A  pdb=" N   GLN E  79 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 8.722A  pdb=" N   ALA A  78 " --> pdb=" O   GLN E  79 " (cutoff:3.500A)
      removed outlier: 10.581A  pdb=" N   THR E  81 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 9.033A  pdb=" N   LYS A  80 " --> pdb=" O   THR E  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 86 through 92
      removed outlier: 8.966A  pdb=" N   GLY A  86 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
      removed outlier: 9.508A  pdb=" N   ALA B  89 " --> pdb=" O   GLY A  86 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   ILE A  88 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   ALA B  91 " --> pdb=" O   ILE A  88 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ALA A  90 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   SER A  87 " --> pdb=" O   GLY E  86 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ILE E  88 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 39 through 42
      removed outlier: 6.685A  pdb=" N   TYR C  39 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 7.986A  pdb=" N  ASER D  42 " --> pdb=" O   TYR C  39 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   GLY C  41 " --> pdb=" O  ASER D  42 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 45 through 66
      removed outlier: 6.967A  pdb=" N   GLU D  46 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   GLY C  47 " --> pdb=" O   GLU D  46 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   VAL D  52 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   ALA C  53 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   THR D  54 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   VAL C  55 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   ALA D  56 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   GLU C  57 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   LYS D  58 " --> pdb=" O   GLU C  57 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   THR C  59 " --> pdb=" O   LYS D  58 " (cutoff:3.500A)
      removed outlier: 5.767A  pdb=" N   GLU C  46 " --> pdb=" O   GLY F  47 " (cutoff:3.500A)
      removed outlier: 8.783A  pdb=" N   VAL F  49 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   VAL C  48 " --> pdb=" O   VAL F  49 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   GLY F  51 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 8.702A  pdb=" N   HIS C  50 " --> pdb=" O   GLY F  51 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   ALA F  53 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 9.108A  pdb=" N   VAL C  52 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
      removed outlier: 10.426A  pdb=" N   VAL F  55 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 8.923A  pdb=" N   THR C  54 " --> pdb=" O   VAL F  55 " (cutoff:3.500A)
      removed outlier: 10.087A  pdb=" N   GLU F  57 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 9.056A  pdb=" N   ALA C  56 " --> pdb=" O   GLU F  57 " (cutoff:3.500A)
      removed outlier: 9.630A  pdb=" N   THR F  59 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   LYS C  58 " --> pdb=" O   THR F  59 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   GLU F  61 " --> pdb=" O   LYS C  58 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   LYS C  60 " --> pdb=" O   GLU F  61 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   VAL F  63 " --> pdb=" O   LYS C  60 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   GLN C  62 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   ASN F  65 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   THR C  64 " --> pdb=" O   ASN F  65 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 69 through 82
      removed outlier: 6.912A  pdb=" N   VAL D  70 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL C  71 " --> pdb=" O   VAL D  70 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   THR D  72 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   GLY C  73 " --> pdb=" O   THR D  72 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   VAL C  77 " --> pdb=" O   ALA D  76 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   ALA D  78 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   GLN C  79 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   LYS D  80 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   THR C  81 " --> pdb=" O   LYS D  80 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   VAL D  82 " --> pdb=" O   THR C  81 " (cutoff:3.500A)
      removed outlier: 9.147A  pdb=" N   VAL C  70 " --> pdb=" O   VAL F  71 " (cutoff:3.500A)
      removed outlier: 10.233A  pdb=" N   GLY F  73 " --> pdb=" O   VAL C  70 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   THR C  72 " --> pdb=" O   GLY F  73 " (cutoff:3.500A)
      removed outlier: 9.127A  pdb=" N   THR F  75 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   VAL C  74 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   VAL F  77 " --> pdb=" O   VAL C  74 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   ALA C  76 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 10.155A  pdb=" N   GLN F  79 " --> pdb=" O   ALA C  76 " (cutoff:3.500A)
      removed outlier: 8.736A  pdb=" N   ALA C  78 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
      removed outlier: 10.588A  pdb=" N   THR F  81 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 9.047A  pdb=" N   LYS C  80 " --> pdb=" O   THR F  81 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 86 through 92
      removed outlier: 8.927A  pdb=" N   GLY C  86 " --> pdb=" O   SER D  87 " (cutoff:3.500A)
      removed outlier: 9.529A  pdb=" N   ALA D  89 " --> pdb=" O   GLY C  86 " (cutoff:3.500A)
      removed outlier: 5.914A  pdb=" N   ILE C  88 " --> pdb=" O   ALA D  89 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   ALA D  91 " --> pdb=" O   ILE C  88 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ALA C  90 " --> pdb=" O   ALA D  91 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   SER C  87 " --> pdb=" O   GLY F  86 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   ILE F  88 " --> pdb=" O   SER C  87 " (cutoff:3.500A)

    44 hydrogen bonds defined for protein.
    132 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: 0.61

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.23 -     1.37: 850
        1.37 -     1.51: 864
        1.51 -     1.66: 922
        1.66 -     1.80: 2
        1.80 -     1.94: 2
  Bond restraints: 2640
  Sorted by residual:
  bond pdb=" C16 1KI C 201 "
       pdb=" S27 1KI C 201 "
    ideal  model  delta    sigma   weight residual
    1.770  1.668  0.102 2.00e-02 2.50e+03 2.60e+01
  bond pdb=" C18 1KI A 201 "
       pdb=" C19 1KI A 201 "
    ideal  model  delta    sigma   weight residual
    1.454  1.555 -0.101 2.00e-02 2.50e+03 2.57e+01
  bond pdb=" C16 1KI A 201 "
       pdb=" S27 1KI A 201 "
    ideal  model  delta    sigma   weight residual
    1.770  1.669  0.101 2.00e-02 2.50e+03 2.56e+01
  bond pdb=" C18 1KI C 201 "
       pdb=" C19 1KI C 201 "
    ideal  model  delta    sigma   weight residual
    1.454  1.554 -0.100 2.00e-02 2.50e+03 2.52e+01
  bond pdb=" C16 1KI A 201 "
       pdb=" N15 1KI A 201 "
    ideal  model  delta    sigma   weight residual
    1.303  1.396 -0.093 2.00e-02 2.50e+03 2.18e+01
  ... (remaining 2635 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.61: 3568
        4.61 -     9.23: 10
        9.23 -    13.84: 0
       13.84 -    18.46: 0
       18.46 -    23.07: 2
  Bond angle restraints: 3580
  Sorted by residual:
  angle pdb=" C17 1KI C 201 "
        pdb=" C18 1KI C 201 "
        pdb=" C19 1KI C 201 "
      ideal   model   delta    sigma   weight residual
     126.82  103.75   23.07 3.00e+00 1.11e-01 5.91e+01
  angle pdb=" C17 1KI A 201 "
        pdb=" C18 1KI A 201 "
        pdb=" C19 1KI A 201 "
      ideal   model   delta    sigma   weight residual
     126.82  103.76   23.06 3.00e+00 1.11e-01 5.91e+01
  angle pdb=" C13 1KI C 201 "
        pdb=" S27 1KI C 201 "
        pdb=" C16 1KI C 201 "
      ideal   model   delta    sigma   weight residual
      89.32   98.45   -9.13 3.00e+00 1.11e-01 9.27e+00
  angle pdb=" C13 1KI A 201 "
        pdb=" S27 1KI A 201 "
        pdb=" C16 1KI A 201 "
      ideal   model   delta    sigma   weight residual
      89.32   98.44   -9.12 3.00e+00 1.11e-01 9.25e+00
  angle pdb=" C05 1KI A 201 "
        pdb=" N04 1KI A 201 "
        pdb=" C11 1KI A 201 "
      ideal   model   delta    sigma   weight residual
     112.35  119.89   -7.54 3.00e+00 1.11e-01 6.32e+00
  ... (remaining 3575 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.30: 1449
       16.30 -    32.60: 53
       32.60 -    48.90: 17
       48.90 -    65.20: 7
       65.20 -    81.50: 6
  Dihedral angle restraints: 1532
    sinusoidal: 518
      harmonic: 1014
  Sorted by residual:
  dihedral pdb=" CB  GLU D  46 "
           pdb=" CG  GLU D  46 "
           pdb=" CD  GLU D  46 "
           pdb=" OE1 GLU D  46 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   81.50  -81.50     1      3.00e+01 1.11e-03 9.09e+00
  dihedral pdb=" CB  GLU C  46 "
           pdb=" CG  GLU C  46 "
           pdb=" CD  GLU C  46 "
           pdb=" OE1 GLU C  46 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   81.47  -81.47     1      3.00e+01 1.11e-03 9.09e+00
  dihedral pdb=" CB  GLU F  46 "
           pdb=" CG  GLU F  46 "
           pdb=" CD  GLU F  46 "
           pdb=" OE1 GLU F  46 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   81.40  -81.40     1      3.00e+01 1.11e-03 9.07e+00
  ... (remaining 1529 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 158
       0.025 -    0.049: 182
       0.049 -    0.074: 41
       0.074 -    0.099: 18
       0.099 -    0.123: 63
  Chirality restraints: 462
  Sorted by residual:
  chirality pdb=" CA  VAL F  49 "
            pdb=" N   VAL F  49 "
            pdb=" C   VAL F  49 "
            pdb=" CB  VAL F  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.80e-01
  chirality pdb=" CA  VAL E  49 "
            pdb=" N   VAL E  49 "
            pdb=" C   VAL E  49 "
            pdb=" CB  VAL E  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.79e-01
  chirality pdb=" CA  VAL D  49 "
            pdb=" N   VAL D  49 "
            pdb=" C   VAL D  49 "
            pdb=" CB  VAL D  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.77e-01
  ... (remaining 459 not shown)

  Planarity restraints: 440
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A  50 "    0.005 2.00e-02 2.50e+03   5.43e-03 4.42e-01
        pdb=" CG  HIS A  50 "   -0.012 2.00e-02 2.50e+03
        pdb=" ND1 HIS A  50 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 HIS A  50 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 HIS A  50 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE2 HIS A  50 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B  50 "    0.005 2.00e-02 2.50e+03   5.32e-03 4.25e-01
        pdb=" CG  HIS B  50 "   -0.011 2.00e-02 2.50e+03
        pdb=" ND1 HIS B  50 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 HIS B  50 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 HIS B  50 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE2 HIS B  50 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS E  50 "    0.005 2.00e-02 2.50e+03   5.15e-03 3.98e-01
        pdb=" CG  HIS E  50 "   -0.011 2.00e-02 2.50e+03
        pdb=" ND1 HIS E  50 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 HIS E  50 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 HIS E  50 "    0.000 2.00e-02 2.50e+03
        pdb=" NE2 HIS E  50 "    0.002 2.00e-02 2.50e+03
  ... (remaining 437 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 810
        2.87 -     3.38: 2137
        3.38 -     3.88: 4309
        3.88 -     4.39: 4351
        4.39 -     4.90: 9013
  Nonbonded interactions: 20620
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A  46 "
            pdb=" NZ  LYS E  80 "
     model   vdw
     2.361 3.120
  nonbonded pdb=" NZ  LYS A  80 "
            pdb=" OE1 GLU B  46 "
     model   vdw
     2.366 3.120
  nonbonded pdb=" OE1 GLU C  46 "
            pdb=" NZ  LYS F  80 "
     model   vdw
     2.377 3.120
  nonbonded pdb=" NZ  LYS C  80 "
            pdb=" OE1 GLU D  46 "
     model   vdw
     2.378 3.120
  nonbonded pdb=" OE1 GLU A  83 "
            pdb=" F10 1KI A 201 "
     model   vdw
     2.458 2.990
  ... (remaining 20615 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 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}

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:                  0.010
  Normalize map: mean=0, sd=1:             2.790
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     16.660
  Find NCS groups from input model:        0.060
  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:13.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
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      :  0.008   0.102   2640  Z= 0.410
  Angle     :  0.859  23.070   3580  Z= 0.370
  Chirality :  0.053   0.123    462
  Planarity :  0.002   0.005    440
  Dihedral  : 12.788  81.499    896
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.83 (0.39), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.15 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS A  50 
 PHE   0.006   0.002   PHE D  94 
 TYR   0.003   0.001   TYR B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19712 (   44)
  hydrogen bonds       : angle       9.07459 (  132)
  covalent geometry    : bond        0.00839 ( 2640)
  covalent geometry    : angle       0.85945 ( 3580)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.7566 (p90) cc_final: 0.7054 (p90)
REVERT: B   46 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7513 (mt-10)
REVERT: C   38 LEU cc_start: 0.8809 (tp) cc_final: 0.8583 (tm)
REVERT: C   46 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7327 (mt-10)
REVERT: C   94 PHE cc_start: 0.7546 (p90) cc_final: 0.6798 (p90)
REVERT: D   94 PHE cc_start: 0.7724 (p90) cc_final: 0.7503 (p90)
REVERT: E   38 LEU cc_start: 0.8894 (tp) cc_final: 0.8670 (tm)
REVERT: E   94 PHE cc_start: 0.7910 (p90) cc_final: 0.7489 (p90)
REVERT: F   94 PHE cc_start: 0.7880 (p90) cc_final: 0.7603 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 1.4572
  time to fit residues: 106.8554
Evaluate side-chains
  59 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 14 optimal weight:    8.9990
   chunk 28 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 17 optimal weight:    9.9990
   chunk 21 optimal weight:    7.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
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 = 0.4165 r_free = 0.4165 target = 0.144904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.110407 restraints weight = 15445.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 3.75
r_work: 0.3505 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3503
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3503
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   2640  Z= 0.279
  Angle     :  0.877  13.177   3580  Z= 0.421
  Chirality :  0.060   0.143    462
  Planarity :  0.003   0.020    440
  Dihedral  :  6.656  51.828    398
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 13.26 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.40), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.04 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.004   HIS A  50 
 PHE   0.009   0.002   PHE F  94 
 TYR   0.007   0.002   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04878 (   44)
  hydrogen bonds       : angle       7.25719 (  132)
  covalent geometry    : bond        0.00621 ( 2640)
  covalent geometry    : angle       0.87676 ( 3580)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.7496 (p90) cc_final: 0.6943 (p90)
REVERT: C   94 PHE cc_start: 0.7491 (p90) cc_final: 0.6760 (p90)
REVERT: E   38 LEU cc_start: 0.8898 (tp) cc_final: 0.8650 (tm)
REVERT: E   94 PHE cc_start: 0.7875 (p90) cc_final: 0.7483 (p90)
REVERT: F   44 THR cc_start: 0.8744 (m) cc_final: 0.8201 (p)
  outliers start: 3
  outliers final: 0
  residues processed: 64
  average time/residue: 1.2556
  time to fit residues: 82.1352
Evaluate side-chains
  62 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 8 optimal weight:    0.0270
   chunk 30 optimal weight:    7.9990
   chunk 24 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 5 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9980
   overall best weight:    0.7842

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.153137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.118100 restraints weight = 16174.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 3.99
r_work: 0.3629 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3624
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3624 r_free = 0.3624    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3624 r_free = 0.3624    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3624
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   2640  Z= 0.098
  Angle     :  0.674  10.123   3580  Z= 0.304
  Chirality :  0.052   0.123    462
  Planarity :  0.002   0.014    440
  Dihedral  :  4.997  39.259    398
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 17.05 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.42), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B  50 
 PHE   0.007   0.002   PHE D  94 
 TYR   0.006   0.002   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02344 (   44)
  hydrogen bonds       : angle       6.38043 (  132)
  covalent geometry    : bond        0.00202 ( 2640)
  covalent geometry    : angle       0.67355 ( 3580)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.7511 (p90) cc_final: 0.6998 (p90)
REVERT: C   94 PHE cc_start: 0.7465 (p90) cc_final: 0.6749 (p90)
REVERT: D   44 THR cc_start: 0.8341 (m) cc_final: 0.8047 (p)
REVERT: D   94 PHE cc_start: 0.7500 (p90) cc_final: 0.7105 (p90)
REVERT: E   38 LEU cc_start: 0.8897 (tp) cc_final: 0.8636 (tm)
REVERT: E   44 THR cc_start: 0.8618 (m) cc_final: 0.8241 (p)
REVERT: F   44 THR cc_start: 0.8754 (m) cc_final: 0.8334 (p)
  outliers start: 3
  outliers final: 0
  residues processed: 61
  average time/residue: 1.0696
  time to fit residues: 66.9402
Evaluate side-chains
  60 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 29 optimal weight:   20.0000
   chunk 19 optimal weight:    4.9990
   chunk 17 optimal weight:   20.0000
   chunk 25 optimal weight:    0.7980
   chunk 3 optimal weight:    7.9990
   chunk 27 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 7 optimal weight:    8.9990
   overall best weight:    3.2986

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN
D  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.147653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.113065 restraints weight = 14659.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 3.76
r_work: 0.3547 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3543
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3543 r_free = 0.3543    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3543 r_free = 0.3543    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3543
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   2640  Z= 0.198
  Angle     :  0.790  11.959   3580  Z= 0.369
  Chirality :  0.056   0.134    462
  Planarity :  0.002   0.013    440
  Dihedral  :  5.656  42.553    398
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.29 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.42 (0.41), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS A  50 
 PHE   0.010   0.002   PHE B  94 
 TYR   0.006   0.001   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03735 (   44)
  hydrogen bonds       : angle       6.78828 (  132)
  covalent geometry    : bond        0.00435 ( 2640)
  covalent geometry    : angle       0.79004 ( 3580)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.7518 (p90) cc_final: 0.6999 (p90)
REVERT: C   94 PHE cc_start: 0.7468 (p90) cc_final: 0.6714 (p90)
REVERT: D   44 THR cc_start: 0.8497 (m) cc_final: 0.8185 (p)
REVERT: D   94 PHE cc_start: 0.7547 (p90) cc_final: 0.7098 (p90)
REVERT: E   38 LEU cc_start: 0.8888 (tp) cc_final: 0.8648 (tm)
REVERT: E   44 THR cc_start: 0.8563 (m) cc_final: 0.8060 (p)
REVERT: F   44 THR cc_start: 0.8681 (m) cc_final: 0.8152 (p)
  outliers start: 6
  outliers final: 1
  residues processed: 61
  average time/residue: 1.0835
  time to fit residues: 67.8409
Evaluate side-chains
  59 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   38 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 2 optimal weight:    8.9990
   chunk 16 optimal weight:    0.7980
   chunk 35 optimal weight:    9.9990
   chunk 17 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.151091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.115676 restraints weight = 19548.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 4.18
r_work: 0.3589 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3587
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3587 r_free = 0.3587    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3587 r_free = 0.3587    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3587
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   2640  Z= 0.115
  Angle     :  0.688  10.444   3580  Z= 0.311
  Chirality :  0.053   0.126    462
  Planarity :  0.002   0.012    440
  Dihedral  :  4.962  42.938    398
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 18.18 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.43), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.67 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS A  50 
 PHE   0.010   0.002   PHE E  94 
 TYR   0.005   0.001   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02681 (   44)
  hydrogen bonds       : angle       6.36296 (  132)
  covalent geometry    : bond        0.00241 ( 2640)
  covalent geometry    : angle       0.68767 ( 3580)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.7462 (p90) cc_final: 0.6957 (p90)
REVERT: C   94 PHE cc_start: 0.7441 (p90) cc_final: 0.6776 (p90)
REVERT: D   44 THR cc_start: 0.8442 (m) cc_final: 0.8154 (p)
REVERT: D   94 PHE cc_start: 0.7464 (p90) cc_final: 0.7017 (p90)
REVERT: E   38 LEU cc_start: 0.8908 (tp) cc_final: 0.8652 (tm)
REVERT: E   44 THR cc_start: 0.8624 (m) cc_final: 0.8190 (p)
REVERT: F   44 THR cc_start: 0.8705 (m) cc_final: 0.8252 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 57
  average time/residue: 1.1012
  time to fit residues: 64.3889
Evaluate side-chains
  58 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   38 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 20 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 7 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 29 optimal weight:    9.9990
   chunk 16 optimal weight:    0.7980
   chunk 11 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 35 optimal weight:    9.9990
   overall best weight:    3.7386

-------------------------------------------------------------------------------
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 = 0.4184 r_free = 0.4184 target = 0.146625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.111760 restraints weight = 16844.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 3.92
r_work: 0.3525 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3522
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3522 r_free = 0.3522    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3522 r_free = 0.3522    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3522
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   2640  Z= 0.223
  Angle     :  0.815  12.346   3580  Z= 0.382
  Chirality :  0.057   0.136    462
  Planarity :  0.002   0.011    440
  Dihedral  :  5.584  40.851    398
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 17.80 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.42), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.81 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.004   HIS A  50 
 PHE   0.012   0.002   PHE B  94 
 TYR   0.005   0.001   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03934 (   44)
  hydrogen bonds       : angle       6.82269 (  132)
  covalent geometry    : bond        0.00496 ( 2640)
  covalent geometry    : angle       0.81484 ( 3580)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.7517 (p90) cc_final: 0.7049 (p90)
REVERT: C   94 PHE cc_start: 0.7450 (p90) cc_final: 0.6812 (p90)
REVERT: D   44 THR cc_start: 0.8545 (m) cc_final: 0.8213 (p)
REVERT: D   94 PHE cc_start: 0.7474 (p90) cc_final: 0.7074 (p90)
REVERT: E   38 LEU cc_start: 0.8896 (tp) cc_final: 0.8655 (tm)
REVERT: E   44 THR cc_start: 0.8599 (m) cc_final: 0.8072 (p)
REVERT: F   44 THR cc_start: 0.8676 (m) cc_final: 0.8149 (p)
  outliers start: 4
  outliers final: 1
  residues processed: 62
  average time/residue: 1.1833
  time to fit residues: 75.1744
Evaluate side-chains
  59 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   38 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 10 optimal weight:    0.0050
   chunk 22 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 6 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 30 optimal weight:    7.9990
   overall best weight:    2.6002

-------------------------------------------------------------------------------
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 = 0.4210 r_free = 0.4210 target = 0.148441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.113541 restraints weight = 16485.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 3.91
r_work: 0.3559 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3555
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3555 r_free = 0.3555    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3555
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   2640  Z= 0.166
  Angle     :  0.766  11.601   3580  Z= 0.351
  Chirality :  0.055   0.131    462
  Planarity :  0.002   0.011    440
  Dihedral  :  5.340  43.430    398
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 19.32 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.31 (0.42), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS A  50 
 PHE   0.012   0.002   PHE E  94 
 TYR   0.004   0.001   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03352 (   44)
  hydrogen bonds       : angle       6.61584 (  132)
  covalent geometry    : bond        0.00361 ( 2640)
  covalent geometry    : angle       0.76586 ( 3580)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.7496 (p90) cc_final: 0.7041 (p90)
REVERT: C   94 PHE cc_start: 0.7438 (p90) cc_final: 0.6817 (p90)
REVERT: D   44 THR cc_start: 0.8514 (m) cc_final: 0.8187 (p)
REVERT: D   94 PHE cc_start: 0.7478 (p90) cc_final: 0.7022 (p90)
REVERT: E   38 LEU cc_start: 0.8879 (tp) cc_final: 0.8644 (tm)
REVERT: E   44 THR cc_start: 0.8603 (m) cc_final: 0.8143 (p)
REVERT: F   44 THR cc_start: 0.8669 (m) cc_final: 0.8166 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 61
  average time/residue: 1.0059
  time to fit residues: 63.0350
Evaluate side-chains
  62 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 26 optimal weight:    0.6980
   chunk 5 optimal weight:    9.9990
   chunk 10 optimal weight:    0.0470
   chunk 27 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 1 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    2.1484

-------------------------------------------------------------------------------
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 = 0.4228 r_free = 0.4228 target = 0.149592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.114576 restraints weight = 16741.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 3.97
r_work: 0.3575 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3573
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3573 r_free = 0.3573    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3573 r_free = 0.3573    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3573
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2640  Z= 0.145
  Angle     :  0.734  11.003   3580  Z= 0.335
  Chirality :  0.054   0.128    462
  Planarity :  0.002   0.010    440
  Dihedral  :  5.294  45.225    398
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 19.32 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.42), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS A  50 
 PHE   0.013   0.002   PHE B  94 
 TYR   0.004   0.001   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03104 (   44)
  hydrogen bonds       : angle       6.46687 (  132)
  covalent geometry    : bond        0.00312 ( 2640)
  covalent geometry    : angle       0.73356 ( 3580)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.7462 (p90) cc_final: 0.6940 (p90)
REVERT: B   58 LYS cc_start: 0.8576 (mttp) cc_final: 0.8375 (mttp)
REVERT: C   94 PHE cc_start: 0.7427 (p90) cc_final: 0.6810 (p90)
REVERT: D   44 THR cc_start: 0.8508 (m) cc_final: 0.8162 (p)
REVERT: D   94 PHE cc_start: 0.7487 (p90) cc_final: 0.7030 (p90)
REVERT: E   38 LEU cc_start: 0.8878 (tp) cc_final: 0.8645 (tm)
REVERT: E   44 THR cc_start: 0.8596 (m) cc_final: 0.8150 (p)
REVERT: F   44 THR cc_start: 0.8682 (m) cc_final: 0.8174 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 63
  average time/residue: 1.1215
  time to fit residues: 72.4130
Evaluate side-chains
  62 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 8 optimal weight:    0.7980
   chunk 30 optimal weight:    0.1980
   chunk 3 optimal weight:    6.9990
   chunk 14 optimal weight:    6.9990
   chunk 28 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 34 optimal weight:    0.7980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.4280 r_free = 0.4280 target = 0.153014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.117794 restraints weight = 17306.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3807 rms_B_bonded: 4.08
r_work: 0.3628 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3628
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3628 r_free = 0.3628    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3628 r_free = 0.3628    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3628
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   2640  Z= 0.103
  Angle     :  0.667   9.474   3580  Z= 0.303
  Chirality :  0.053   0.126    462
  Planarity :  0.002   0.011    440
  Dihedral  :  4.933  43.989    398
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 18.94 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.43), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.55 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.003   HIS A  50 
 PHE   0.011   0.002   PHE E  94 
 TYR   0.004   0.001   TYR E  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02521 (   44)
  hydrogen bonds       : angle       6.06120 (  132)
  covalent geometry    : bond        0.00218 ( 2640)
  covalent geometry    : angle       0.66682 ( 3580)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.7424 (p90) cc_final: 0.6926 (p90)
REVERT: C   94 PHE cc_start: 0.7433 (p90) cc_final: 0.6835 (p90)
REVERT: D   44 THR cc_start: 0.8414 (m) cc_final: 0.8109 (p)
REVERT: D   94 PHE cc_start: 0.7475 (p90) cc_final: 0.7080 (p90)
REVERT: E   38 LEU cc_start: 0.8884 (tp) cc_final: 0.8635 (tm)
REVERT: E   44 THR cc_start: 0.8625 (m) cc_final: 0.8213 (p)
REVERT: F   44 THR cc_start: 0.8730 (m) cc_final: 0.8294 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 61
  average time/residue: 1.1329
  time to fit residues: 70.8004
Evaluate side-chains
  61 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   38 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 25 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 24 optimal weight:    0.0270
   chunk 20 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:   20.0000
   chunk 14 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    2.2046

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.150091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.114898 restraints weight = 16184.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 3.96
r_work: 0.3581 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3580
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3580 r_free = 0.3580    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3580 r_free = 0.3580    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3580
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2640  Z= 0.149
  Angle     :  0.737  10.544   3580  Z= 0.340
  Chirality :  0.054   0.127    462
  Planarity :  0.002   0.013    440
  Dihedral  :  5.290  45.337    398
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.45 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.43), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.60 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS A  50 
 PHE   0.015   0.002   PHE B  94 
 TYR   0.003   0.001   TYR E  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03012 (   44)
  hydrogen bonds       : angle       6.34695 (  132)
  covalent geometry    : bond        0.00328 ( 2640)
  covalent geometry    : angle       0.73654 ( 3580)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A   94 PHE cc_start: 0.7454 (p90) cc_final: 0.6935 (p90)
REVERT: B   38 LEU cc_start: 0.8865 (tp) cc_final: 0.8652 (tp)
REVERT: C   94 PHE cc_start: 0.7446 (p90) cc_final: 0.6831 (p90)
REVERT: D   44 THR cc_start: 0.8500 (m) cc_final: 0.8197 (p)
REVERT: D   94 PHE cc_start: 0.7502 (p90) cc_final: 0.7094 (p90)
REVERT: E   38 LEU cc_start: 0.8910 (tp) cc_final: 0.8659 (tm)
REVERT: E   44 THR cc_start: 0.8599 (m) cc_final: 0.8144 (p)
REVERT: F   44 THR cc_start: 0.8664 (m) cc_final: 0.8156 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 1.1486
  time to fit residues: 72.9551
Evaluate side-chains
  62 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 28 optimal weight:    7.9990
   chunk 31 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 3 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.150077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.114626 restraints weight = 19869.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3751 rms_B_bonded: 4.16
r_work: 0.3574 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3571
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.2184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2640  Z= 0.149
  Angle     :  0.743  10.733   3580  Z= 0.342
  Chirality :  0.054   0.128    462
  Planarity :  0.002   0.013    440
  Dihedral  :  5.245  45.597    398
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.08 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.43), residues: 372
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.60 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS A  50 
 PHE   0.012   0.002   PHE E  94 
 TYR   0.004   0.001   TYR E  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03096 (   44)
  hydrogen bonds       : angle       6.32388 (  132)
  covalent geometry    : bond        0.00327 ( 2640)
  covalent geometry    : angle       0.74254 ( 3580)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2830.27 seconds
wall clock time: 49 minutes 17.87 seconds (2957.87 seconds total)