Starting phenix.real_space_refine
on Fri Jan 17 08:22:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rnu_19395/01_2025/8rnu_19395.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rnu_19395/01_2025/8rnu_19395.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rnu_19395/01_2025/8rnu_19395.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rnu_19395/01_2025/8rnu_19395.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rnu_19395/01_2025/8rnu_19395.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rnu_19395/01_2025/8rnu_19395.cif"
  }
  resolution = 3.4
  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=   0.001 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    7044      2.51       5
     N    1692      2.21       5
     O    2064      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 10848
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 904
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 904
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 904
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 904
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 904
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 904
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 904
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 904
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 904
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 904
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 904
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 904
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 904
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
          Chain breaks: 1
  Time building chain proxies: 6.49, per 1000 atoms: 0.60
  Number of scatterers: 10848
  At special positions: 0
  Unit cell: (114.48, 110.24, 68.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    2064      8.00
     N    1692      7.00
     C    7044      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  52 " - pdb=" SG  CYS B 111 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  52 " - pdb=" SG  CYS F 111 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 111 " - pdb=" SG  CYS F  52 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 111 " - pdb=" SG  CYS D  52 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  52 " - pdb=" SG  CYS H 111 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 111 " - pdb=" SG  CYS H  52 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.69
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2592

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 16 sheets defined
      18.9% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 67 through 74
      removed outlier: 3.982A  pdb=" N   ASN A  74 " --> pdb=" O   GLU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 111
    Processing helix  chain 'K' and resid 67 through 72
      removed outlier: 4.230A  pdb=" N   LEU K  72 " --> pdb=" O   LEU K  69 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 100 through 103
    Processing helix  chain 'K' and resid 104 through 111
    Processing helix  chain 'E' and resid 67 through 72
    Processing helix  chain 'E' and resid 74 through 78
      removed outlier: 3.524A  pdb=" N   ALA E  77 " --> pdb=" O   ASN E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 104 through 111
    Processing helix  chain 'I' and resid 67 through 71
    Processing helix  chain 'I' and resid 74 through 78
    Processing helix  chain 'I' and resid 100 through 103
    Processing helix  chain 'I' and resid 104 through 111
    Processing helix  chain 'C' and resid 67 through 74
      removed outlier: 3.756A  pdb=" N   ASN C  74 " --> pdb=" O   GLU C  70 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 75 through 78
    Processing helix  chain 'C' and resid 104 through 111
    Processing helix  chain 'G' and resid 37 through 39
      No H-bonds generated for 'chain 'G' and resid 37 through 39'
    Processing helix  chain 'G' and resid 67 through 72
      removed outlier: 4.017A  pdb=" N   LEU G  72 " --> pdb=" O   LEU G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 100 through 103
    Processing helix  chain 'G' and resid 104 through 111
    Processing helix  chain 'B' and resid 67 through 72
    Processing helix  chain 'B' and resid 74 through 78
      removed outlier: 3.745A  pdb=" N   ALA B  77 " --> pdb=" O   ASN B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 111
    Processing helix  chain 'H' and resid 67 through 71
    Processing helix  chain 'H' and resid 73 through 78
      removed outlier: 4.539A  pdb=" N   ALA H  77 " --> pdb=" O   ILE H  73 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 100 through 103
    Processing helix  chain 'H' and resid 104 through 111
    Processing helix  chain 'D' and resid 67 through 74
      removed outlier: 3.888A  pdb=" N   ASN D  74 " --> pdb=" O   GLU D  70 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 75 through 78
    Processing helix  chain 'D' and resid 100 through 103
      removed outlier: 4.028A  pdb=" N   LEU D 103 " --> pdb=" O   ILE D 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 100 through 103'
    Processing helix  chain 'D' and resid 104 through 111
    Processing helix  chain 'J' and resid 67 through 71
    Processing helix  chain 'J' and resid 73 through 78
      removed outlier: 4.550A  pdb=" N   ALA J  77 " --> pdb=" O   ILE J  73 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLY J  78 " --> pdb=" O   ASN J  74 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 73 through 78'
    Processing helix  chain 'J' and resid 100 through 103
    Processing helix  chain 'J' and resid 104 through 111
    Processing helix  chain 'F' and resid 67 through 72
    Processing helix  chain 'F' and resid 74 through 78
    Processing helix  chain 'F' and resid 100 through 103
      removed outlier: 3.504A  pdb=" N   LEU F 103 " --> pdb=" O   ILE F 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 100 through 103'
    Processing helix  chain 'F' and resid 104 through 112
    Processing helix  chain 'L' and resid 37 through 39
      No H-bonds generated for 'chain 'L' and resid 37 through 39'
    Processing helix  chain 'L' and resid 67 through 71
      removed outlier: 3.602A  pdb=" N   GLU L  70 " --> pdb=" O   ASN L  67 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 100 through 103
    Processing helix  chain 'L' and resid 104 through 111
    Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 10
      removed outlier: 3.952A  pdb=" N   ASN A   6 " --> pdb=" O   SER A  19 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   VAL A  15 " --> pdb=" O   PHE A  10 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   TYR A  44 " --> pdb=" O   TYR A  53 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   TYR A  53 " --> pdb=" O   TYR A  44 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   CYS A  52 " --> pdb=" O   TYR B 117 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LYS B 118 " --> pdb=" O   ASP B  95 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   ASP B  95 " --> pdb=" O   LYS B 118 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96
      removed outlier: 3.799A  pdb=" N   ASP A  95 " --> pdb=" O   LYS A 118 " (cutoff:3.500A)
      removed outlier: 5.419A  pdb=" N   GLU A 115 " --> pdb=" O   CYS B  52 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   VAL B  54 " --> pdb=" O   GLU A 115 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   TYR A 117 " --> pdb=" O   VAL B  54 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ASP B  46 " --> pdb=" O   LYS B  51 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   VAL B  15 " --> pdb=" O   PHE B  10 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   PHE B  10 " --> pdb=" O   VAL B  15 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'K' and resid 6 through 9
      removed outlier: 3.529A  pdb=" N   LYS K   8 " --> pdb=" O   PHE K  17 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL K  34 " --> pdb=" O   ALA K  43 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ALA K  43 " --> pdb=" O   VAL K  34 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   ASP K  36 " --> pdb=" O   LEU K  41 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   LEU K  41 " --> pdb=" O   ASP K  36 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'K' and resid 95 through 97
      removed outlier: 3.740A  pdb=" N   THR K 116 " --> pdb=" O   ILE K  97 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 6 through 10
      removed outlier: 3.702A  pdb=" N   PHE E  10 " --> pdb=" O   VAL E  15 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   VAL E  15 " --> pdb=" O   PHE E  10 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 95 through 96
      removed outlier: 4.377A  pdb=" N   ASP E  95 " --> pdb=" O   LYS E 118 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LYS E 118 " --> pdb=" O   ASP E  95 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   GLU E 115 " --> pdb=" O   CYS F  52 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   VAL F  54 " --> pdb=" O   GLU E 115 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   TYR E 117 " --> pdb=" O   VAL F  54 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   VAL F  15 " --> pdb=" O   PHE F  10 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   PHE F  10 " --> pdb=" O   VAL F  15 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'I' and resid 16 through 19
      removed outlier: 3.525A  pdb=" N   ASN I  32 " --> pdb=" O   LEU I  45 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   LEU I  45 " --> pdb=" O   ASN I  32 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   VAL I  34 " --> pdb=" O   ALA I  43 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   ALA I  43 " --> pdb=" O   VAL I  34 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ASP I  36 " --> pdb=" O   LEU I  41 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   LEU I  41 " --> pdb=" O   ASP I  36 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR I  42 " --> pdb=" O   ILE I  55 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ILE I  55 " --> pdb=" O   THR I  42 " (cutoff:3.500A)
      removed outlier: 5.418A  pdb=" N   CYS I  52 " --> pdb=" O   TYR J 117 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   THR J 116 " --> pdb=" O   ILE J  97 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'I' and resid 95 through 96
      removed outlier: 3.846A  pdb=" N   LEU J  41 " --> pdb=" O   ASP J  36 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   ASP J  36 " --> pdb=" O   LEU J  41 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ALA J  43 " --> pdb=" O   VAL J  34 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL J  34 " --> pdb=" O   ALA J  43 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 8 through 10
      removed outlier: 3.732A  pdb=" N   PHE C  10 " --> pdb=" O   VAL C  15 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   VAL C  15 " --> pdb=" O   PHE C  10 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   VAL C  34 " --> pdb=" O   ALA C  43 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ALA C  43 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ASP C  36 " --> pdb=" O   LEU C  41 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LEU C  41 " --> pdb=" O   ASP C  36 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL C  54 " --> pdb=" O   TYR D 117 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ASP D  95 " --> pdb=" O   LYS D 118 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 8 through 10
      removed outlier: 3.732A  pdb=" N   PHE C  10 " --> pdb=" O   VAL C  15 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   VAL C  15 " --> pdb=" O   PHE C  10 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LYS C  51 " --> pdb=" O   ASP C  46 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL C  54 " --> pdb=" O   TYR D 117 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ASP D  95 " --> pdb=" O   LYS D 118 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 95 through 96
      removed outlier: 3.864A  pdb=" N   ASP C  95 " --> pdb=" O   LYS C 118 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   TYR C 117 " --> pdb=" O   VAL D  54 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   TYR D  44 " --> pdb=" O   TYR D  53 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   VAL D  15 " --> pdb=" O   PHE D  10 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ASN D   6 " --> pdb=" O   SER D  19 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'G' and resid 8 through 9
      removed outlier: 3.571A  pdb=" N   LYS G   8 " --> pdb=" O   PHE G  17 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LEU G  45 " --> pdb=" O   ASN G  32 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   VAL G  34 " --> pdb=" O   ALA G  43 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ALA G  43 " --> pdb=" O   VAL G  34 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ASP G  36 " --> pdb=" O   LEU G  41 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   LEU G  41 " --> pdb=" O   ASP G  36 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   CYS G  52 " --> pdb=" O   TYR H 117 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ASP H  95 " --> pdb=" O   LYS H 118 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'G' and resid 95 through 97
      removed outlier: 3.653A  pdb=" N   ASP G  95 " --> pdb=" O   LYS G 118 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   THR G 116 " --> pdb=" O   ILE G  97 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ASP H  36 " --> pdb=" O   LEU H  41 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ALA H  43 " --> pdb=" O   VAL H  34 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LYS H   8 " --> pdb=" O   PHE H  17 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 95 through 96
      removed outlier: 4.406A  pdb=" N   ASP F  95 " --> pdb=" O   LYS F 118 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 16 through 19
      removed outlier: 3.504A  pdb=" N   ASN L  32 " --> pdb=" O   LEU L  45 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   LEU L  45 " --> pdb=" O   ASN L  32 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   VAL L  34 " --> pdb=" O   ALA L  43 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ALA L  43 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   ASP L  36 " --> pdb=" O   LEU L  41 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU L  41 " --> pdb=" O   ASP L  36 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR L  42 " --> pdb=" O   ILE L  55 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE L  55 " --> pdb=" O   THR L  42 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 95 through 97
      removed outlier: 3.657A  pdb=" N   ASP L  95 " --> pdb=" O   LYS L 118 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   THR L 116 " --> pdb=" O   ILE L  97 " (cutoff:3.500A)

    301 hydrogen bonds defined for protein.
    711 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.71

  Time building geometry restraints manager: 3.15 seconds

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

  Histogram of bond lengths:
        0.89 -     1.07: 2
        1.07 -     1.26: 1897
        1.26 -     1.44: 2658
        1.44 -     1.63: 6430
        1.63 -     1.81: 77
  Bond restraints: 11064
  Sorted by residual:
  bond pdb=" CG  PRO I  64 "
       pdb=" CD  PRO I  64 "
    ideal  model  delta    sigma   weight residual
    1.503  0.886  0.617 3.40e-02 8.65e+02 3.30e+02
  bond pdb=" CG  PRO L  30 "
       pdb=" CD  PRO L  30 "
    ideal  model  delta    sigma   weight residual
    1.503  0.983  0.520 3.40e-02 8.65e+02 2.34e+02
  bond pdb=" CG  PRO E  21 "
       pdb=" CD  PRO E  21 "
    ideal  model  delta    sigma   weight residual
    1.503  1.164  0.339 3.40e-02 8.65e+02 9.96e+01
  bond pdb=" N   PRO I  64 "
       pdb=" CD  PRO I  64 "
    ideal  model  delta    sigma   weight residual
    1.473  1.576 -0.103 1.40e-02 5.10e+03 5.45e+01
  bond pdb=" N   PRO L  30 "
       pdb=" CD  PRO L  30 "
    ideal  model  delta    sigma   weight residual
    1.473  1.570 -0.097 1.40e-02 5.10e+03 4.78e+01
  ... (remaining 11059 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.38: 14962
        5.38 -    10.77: 45
       10.77 -    16.15: 8
       16.15 -    21.53: 7
       21.53 -    26.92: 2
  Bond angle restraints: 15024
  Sorted by residual:
  angle pdb=" N   PRO L  30 "
        pdb=" CD  PRO L  30 "
        pdb=" CG  PRO L  30 "
      ideal   model   delta    sigma   weight residual
     103.20   76.28   26.92 1.50e+00 4.44e-01 3.22e+02
  angle pdb=" N   PRO I  64 "
        pdb=" CD  PRO I  64 "
        pdb=" CG  PRO I  64 "
      ideal   model   delta    sigma   weight residual
     103.20   76.91   26.29 1.50e+00 4.44e-01 3.07e+02
  angle pdb=" CA  PRO K  30 "
        pdb=" N   PRO K  30 "
        pdb=" CD  PRO K  30 "
      ideal   model   delta    sigma   weight residual
     112.00   92.30   19.70 1.40e+00 5.10e-01 1.98e+02
  angle pdb=" CA  PRO E  21 "
        pdb=" N   PRO E  21 "
        pdb=" CD  PRO E  21 "
      ideal   model   delta    sigma   weight residual
     112.00   94.08   17.92 1.40e+00 5.10e-01 1.64e+02
  angle pdb=" N   PRO E  21 "
        pdb=" CD  PRO E  21 "
        pdb=" CG  PRO E  21 "
      ideal   model   delta    sigma   weight residual
     103.20   85.20   18.00 1.50e+00 4.44e-01 1.44e+02
  ... (remaining 15019 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.61: 5730
       17.61 -    35.23: 778
       35.23 -    52.84: 220
       52.84 -    70.45: 35
       70.45 -    88.07: 11
  Dihedral angle restraints: 6774
    sinusoidal: 2826
      harmonic: 3948
  Sorted by residual:
  dihedral pdb=" CA  PRO L  23 "
           pdb=" C   PRO L  23 "
           pdb=" N   GLU L  24 "
           pdb=" CA  GLU L  24 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.86  -33.14     0      5.00e+00 4.00e-02 4.39e+01
  dihedral pdb=" CA  PRO I  23 "
           pdb=" C   PRO I  23 "
           pdb=" N   GLU I  24 "
           pdb=" CA  GLU I  24 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -147.56  -32.44     0      5.00e+00 4.00e-02 4.21e+01
  dihedral pdb=" CA  ILE B 100 "
           pdb=" C   ILE B 100 "
           pdb=" N   ASP B 101 "
           pdb=" CA  ASP B 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.28  -31.72     0      5.00e+00 4.00e-02 4.02e+01
  ... (remaining 6771 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1410
       0.060 -    0.119: 307
       0.119 -    0.179: 45
       0.179 -    0.238: 1
       0.238 -    0.298: 1
  Chirality restraints: 1764
  Sorted by residual:
  chirality pdb=" CA  PRO I  64 "
            pdb=" N   PRO I  64 "
            pdb=" C   PRO I  64 "
            pdb=" CB  PRO I  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.42    0.30 2.00e-01 2.50e+01 2.22e+00
  chirality pdb=" CG  LEU I  72 "
            pdb=" CB  LEU I  72 "
            pdb=" CD1 LEU I  72 "
            pdb=" CD2 LEU I  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 8.29e-01
  chirality pdb=" CG  LEU K  71 "
            pdb=" CB  LEU K  71 "
            pdb=" CD1 LEU K  71 "
            pdb=" CD2 LEU K  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 7.69e-01
  ... (remaining 1761 not shown)

  Planarity restraints: 1920
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP K  29 "   -0.093 5.00e-02 4.00e+02   1.23e-01 2.44e+01
        pdb=" N   PRO K  30 "    0.212 5.00e-02 4.00e+02
        pdb=" CA  PRO K  30 "   -0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO K  30 "   -0.065 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL E  20 "    0.080 5.00e-02 4.00e+02   1.07e-01 1.82e+01
        pdb=" N   PRO E  21 "   -0.184 5.00e-02 4.00e+02
        pdb=" CA  PRO E  21 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO E  21 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET D  63 "    0.070 5.00e-02 4.00e+02   1.06e-01 1.79e+01
        pdb=" N   PRO D  64 "   -0.183 5.00e-02 4.00e+02
        pdb=" CA  PRO D  64 "    0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO D  64 "    0.056 5.00e-02 4.00e+02
  ... (remaining 1917 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 239
        2.66 -     3.22: 10477
        3.22 -     3.78: 17612
        3.78 -     4.34: 23571
        4.34 -     4.90: 36419
  Nonbonded interactions: 88318
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN K   1 "
            pdb=" O   VAL K  22 "
     model   vdw
     2.104 3.120
  nonbonded pdb=" OG  SER L  19 "
            pdb=" OD1 ASN L  32 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" ND2 ASN G  74 "
            pdb=" OG1 THR H   2 "
     model   vdw
     2.144 3.120
  nonbonded pdb=" O   ASP A  46 "
            pdb=" N   ASP A  50 "
     model   vdw
     2.163 3.120
  nonbonded pdb=" O   ASN C  38 "
            pdb=" NH2 ARG G  66 "
     model   vdw
     2.170 3.120
  ... (remaining 88313 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     25.940
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3017
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      :  0.010   0.617  11064  Z= 0.664
  Angle     :  1.036  26.917  15024  Z= 0.602
  Chirality :  0.050   0.298   1764
  Planarity :  0.009   0.123   1920
  Dihedral  : 17.191  88.067   4164
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 28.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.06 %
    Favored  : 89.94 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 21.31 %
    Favored  : 78.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -2.17 (0.22), residues: 1272
  helix: -0.79 (0.46), residues: 124
  sheet: -0.34 (0.27), residues: 358
  loop : -2.20 (0.20), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F 102 
 PHE   0.029   0.002   PHE J  25 
 TYR   0.009   0.001   TYR K 117 
 ARG   0.007   0.001   ARG G  66 

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 1.283 
Fit side-chains
REVERT: E   17 PHE cc_start: 0.4986 (t80) cc_final: 0.4681 (t80)
REVERT: I   99 ASN cc_start: 0.7568 (t0) cc_final: 0.7287 (t0)
REVERT: G   63 MET cc_start: 0.0841 (tmm) cc_final: 0.0368 (tmm)
REVERT: B   17 PHE cc_start: 0.3153 (t80) cc_final: 0.2603 (t80)
REVERT: F   63 MET cc_start: 0.2392 (tpt) cc_final: 0.0798 (tmm)
REVERT: F   72 LEU cc_start: 0.6307 (mt) cc_final: 0.5652 (pp)
  outliers start: 4
  outliers final: 1
  residues processed: 53
  average time/residue: 0.1700
  time to fit residues: 15.4094
Evaluate side-chains
  48 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 1.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue    7 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:   50.0000
   chunk 100 optimal weight:    6.9990
   chunk 55 optimal weight:    7.9990
   chunk 34 optimal weight:    5.9990
   chunk 67 optimal weight:   40.0000
   chunk 53 optimal weight:    4.9990
   chunk 103 optimal weight:   20.0000
   chunk 40 optimal weight:   20.0000
   chunk 62 optimal weight:   30.0000
   chunk 77 optimal weight:    7.9990
   chunk 119 optimal weight:   10.0000
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  32 ASN
A 112 HIS
** K  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  58 ASN
K 112 HIS
** I  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 112 HIS
** C   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  58 ASN
G 112 HIS
** B  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 112 HIS
J   6 ASN
J 112 HIS
L  32 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4946 r_free = 0.4946 target = 0.165049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4879 r_free = 0.4879 target = 0.151617 restraints weight = 36270.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.4892 rms_B_bonded: 5.20
r_work (final): 0.4892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3174
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079  11064  Z= 0.294
  Angle     :  0.768  10.819  15024  Z= 0.404
  Chirality :  0.051   0.167   1764
  Planarity :  0.008   0.082   1920
  Dihedral  :  7.128  34.137   1406
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 24.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.38 %
    Favored  : 89.62 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 20.83 %
    Favored  : 75.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -2.16 (0.22), residues: 1272
  helix: -1.49 (0.40), residues: 134
  sheet: -0.03 (0.28), residues: 342
  loop : -2.20 (0.21), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS F 102 
 PHE   0.022   0.002   PHE H  17 
 TYR   0.010   0.001   TYR E 108 
 ARG   0.008   0.001   ARG B  66 

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 50
  time to evaluate  : 1.380 
Fit side-chains
REVERT: A   50 ASP cc_start: 0.3385 (OUTLIER) cc_final: 0.2421 (m-30)
REVERT: A  102 HIS cc_start: -0.3015 (OUTLIER) cc_final: -0.3701 (t-170)
REVERT: E   21 PRO cc_start: 0.4539 (Cg_exo) cc_final: 0.3503 (Cg_endo)
REVERT: E   50 ASP cc_start: 0.4453 (OUTLIER) cc_final: 0.2032 (m-30)
REVERT: C   50 ASP cc_start: 0.5924 (OUTLIER) cc_final: 0.5493 (m-30)
REVERT: C  102 HIS cc_start: -0.4040 (OUTLIER) cc_final: -0.4576 (t70)
REVERT: G   63 MET cc_start: 0.1659 (tmm) cc_final: 0.1029 (tmm)
REVERT: B   81 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7609 (mm)
REVERT: J   63 MET cc_start: 0.0554 (OUTLIER) cc_final: 0.0350 (ppp)
REVERT: F   45 LEU cc_start: -0.2322 (OUTLIER) cc_final: -0.6120 (pt)
REVERT: F   63 MET cc_start: 0.3003 (tpt) cc_final: 0.0997 (tmm)
REVERT: F   72 LEU cc_start: 0.6781 (mt) cc_final: 0.6160 (pp)
  outliers start: 45
  outliers final: 16
  residues processed: 91
  average time/residue: 0.1686
  time to fit residues: 25.0332
Evaluate side-chains
  70 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 46
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 PHE
Chi-restraints excluded: chain A residue   50 ASP
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain K residue   22 VAL
Chi-restraints excluded: chain E residue   27 ASP
Chi-restraints excluded: chain E residue   50 ASP
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain I residue   22 VAL
Chi-restraints excluded: chain I residue   25 PHE
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   50 ASP
Chi-restraints excluded: chain C residue  102 HIS
Chi-restraints excluded: chain G residue    7 ILE
Chi-restraints excluded: chain B residue   25 PHE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  102 HIS
Chi-restraints excluded: chain H residue   22 VAL
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain J residue   18 ILE
Chi-restraints excluded: chain J residue   63 MET
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain F residue   45 LEU
Chi-restraints excluded: chain L residue   22 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 130 optimal weight:    8.9990
   chunk 17 optimal weight:    0.9980
   chunk 37 optimal weight:    8.9990
   chunk 15 optimal weight:   10.0000
   chunk 13 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 76 optimal weight:   30.0000
   chunk 23 optimal weight:    8.9990
   chunk 90 optimal weight:    0.6980
   chunk 115 optimal weight:    5.9990
   chunk 91 optimal weight:   10.0000
   overall best weight:    3.3386

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

Flipped N/Q/H residues before XYZ refinement:
** K  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  38 ASN
K 102 HIS
E 112 HIS
** I  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 ASN
** B  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  32 ASN
J  74 ASN
F   6 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4931 r_free = 0.4931 target = 0.164793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4895 r_free = 0.4895 target = 0.150751 restraints weight = 51094.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.4884 rms_B_bonded: 7.23
r_work (final): 0.4884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3115
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  11064  Z= 0.210
  Angle     :  0.637   9.256  15024  Z= 0.335
  Chirality :  0.049   0.151   1764
  Planarity :  0.007   0.074   1920
  Dihedral  :  6.594  30.212   1406
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 18.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 20.03 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -2.02 (0.23), residues: 1272
  helix: -1.60 (0.38), residues: 140
  sheet: -0.04 (0.27), residues: 362
  loop : -2.05 (0.22), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H 112 
 PHE   0.026   0.001   PHE J  25 
 TYR   0.007   0.001   TYR E  53 
 ARG   0.004   0.001   ARG D 109 

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 49
  time to evaluate  : 1.224 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.2739 (OUTLIER) cc_final: 0.1901 (m-30)
REVERT: A  102 HIS cc_start: -0.3063 (OUTLIER) cc_final: -0.3604 (t70)
REVERT: K   91 MET cc_start: 0.0758 (pmm) cc_final: 0.0136 (mmp)
REVERT: E   21 PRO cc_start: 0.5124 (Cg_exo) cc_final: 0.4160 (Cg_endo)
REVERT: E   27 ASP cc_start: 0.1474 (OUTLIER) cc_final: -0.0372 (p0)
REVERT: I   99 ASN cc_start: 0.8527 (t0) cc_final: 0.8291 (t0)
REVERT: C  102 HIS cc_start: -0.4116 (OUTLIER) cc_final: -0.4482 (t70)
REVERT: G   63 MET cc_start: 0.1384 (tmm) cc_final: 0.0863 (tmm)
REVERT: B   50 ASP cc_start: 0.5142 (OUTLIER) cc_final: 0.4886 (m-30)
REVERT: B   81 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7596 (mm)
REVERT: H   19 SER cc_start: 0.8300 (OUTLIER) cc_final: 0.8047 (p)
REVERT: D   50 ASP cc_start: 0.3378 (OUTLIER) cc_final: 0.2151 (m-30)
REVERT: D  101 ASP cc_start: 0.3311 (OUTLIER) cc_final: 0.2636 (m-30)
REVERT: J   63 MET cc_start: 0.1334 (ppp) cc_final: 0.0888 (ppp)
REVERT: J  102 HIS cc_start: -0.0176 (OUTLIER) cc_final: -0.3722 (t70)
REVERT: F   63 MET cc_start: 0.2689 (tpt) cc_final: 0.1362 (tmm)
REVERT: F   72 LEU cc_start: 0.6574 (mt) cc_final: 0.5978 (pp)
REVERT: L   63 MET cc_start: 0.0607 (tmm) cc_final: -0.0534 (tpt)
  outliers start: 57
  outliers final: 24
  residues processed: 103
  average time/residue: 0.1852
  time to fit residues: 29.7891
Evaluate side-chains
  82 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 48
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 PHE
Chi-restraints excluded: chain A residue   50 ASP
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain K residue   25 PHE
Chi-restraints excluded: chain E residue   27 ASP
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  114 LYS
Chi-restraints excluded: chain I residue   22 VAL
Chi-restraints excluded: chain I residue   25 PHE
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue  102 HIS
Chi-restraints excluded: chain G residue    7 ILE
Chi-restraints excluded: chain G residue   22 VAL
Chi-restraints excluded: chain B residue   25 PHE
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   50 ASP
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  102 HIS
Chi-restraints excluded: chain B residue  109 ARG
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   91 MET
Chi-restraints excluded: chain D residue   50 ASP
Chi-restraints excluded: chain D residue  101 ASP
Chi-restraints excluded: chain J residue   18 ILE
Chi-restraints excluded: chain J residue   25 PHE
Chi-restraints excluded: chain J residue  102 HIS
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain F residue  102 HIS
Chi-restraints excluded: chain L residue    7 ILE
Chi-restraints excluded: chain L residue   17 PHE
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   25 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 30 optimal weight:   30.0000
   chunk 90 optimal weight:   20.0000
   chunk 78 optimal weight:    9.9990
   chunk 105 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   chunk 73 optimal weight:   20.0000
   chunk 13 optimal weight:    2.9990
   chunk 46 optimal weight:    9.9990
   chunk 48 optimal weight:   20.0000
   chunk 111 optimal weight:   40.0000
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  32 ASN
** K   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 ASN
B  74 ASN
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4949 r_free = 0.4949 target = 0.172694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4903 r_free = 0.4903 target = 0.152299 restraints weight = 38615.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.4868 rms_B_bonded: 8.06
r_work (final): 0.4868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2896
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076  11064  Z= 0.257
  Angle     :  0.691   9.456  15024  Z= 0.365
  Chirality :  0.050   0.158   1764
  Planarity :  0.007   0.068   1920
  Dihedral  :  6.755  30.394   1406
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 23.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.91 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 20.99 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -2.06 (0.23), residues: 1272
  helix: -1.48 (0.40), residues: 126
  sheet: -0.31 (0.27), residues: 374
  loop : -1.99 (0.22), residues: 772

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F 102 
 PHE   0.023   0.002   PHE J  25 
 TYR   0.010   0.001   TYR E 108 
 ARG   0.007   0.001   ARG I  66 

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 46
  time to evaluate  : 1.261 
Fit side-chains
REVERT: A   50 ASP cc_start: 0.3060 (OUTLIER) cc_final: 0.1911 (m-30)
REVERT: A  102 HIS cc_start: -0.1481 (OUTLIER) cc_final: -0.2939 (t70)
REVERT: K   91 MET cc_start: 0.1411 (pmm) cc_final: -0.0077 (mmp)
REVERT: E   21 PRO cc_start: 0.4036 (Cg_exo) cc_final: 0.3480 (Cg_endo)
REVERT: E   27 ASP cc_start: 0.0737 (OUTLIER) cc_final: -0.0713 (p0)
REVERT: E   50 ASP cc_start: 0.4038 (OUTLIER) cc_final: 0.2017 (m-30)
REVERT: I   99 ASN cc_start: 0.8179 (t0) cc_final: 0.7968 (t0)
REVERT: C  102 HIS cc_start: -0.2739 (OUTLIER) cc_final: -0.3840 (t70)
REVERT: G   63 MET cc_start: 0.1819 (tmm) cc_final: 0.1535 (tmm)
REVERT: G  102 HIS cc_start: -0.1631 (OUTLIER) cc_final: -0.3460 (t70)
REVERT: D   63 MET cc_start: 0.2846 (tpp) cc_final: 0.2591 (tpp)
REVERT: J   63 MET cc_start: -0.0334 (ppp) cc_final: -0.0850 (ppp)
REVERT: J  102 HIS cc_start: -0.0090 (OUTLIER) cc_final: -0.3729 (t70)
REVERT: F   17 PHE cc_start: 0.1467 (m-80) cc_final: 0.1153 (m-80)
REVERT: F   45 LEU cc_start: -0.1776 (OUTLIER) cc_final: -0.5533 (pt)
REVERT: F   63 MET cc_start: 0.1524 (tpt) cc_final: 0.0709 (tmm)
REVERT: F   72 LEU cc_start: 0.6165 (mt) cc_final: 0.5739 (pp)
  outliers start: 56
  outliers final: 31
  residues processed: 99
  average time/residue: 0.1728
  time to fit residues: 27.6010
Evaluate side-chains
  85 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 46
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 PHE
Chi-restraints excluded: chain A residue   50 ASP
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain K residue    7 ILE
Chi-restraints excluded: chain K residue   25 PHE
Chi-restraints excluded: chain E residue   27 ASP
Chi-restraints excluded: chain E residue   50 ASP
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  114 LYS
Chi-restraints excluded: chain I residue   22 VAL
Chi-restraints excluded: chain I residue   25 PHE
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   61 ILE
Chi-restraints excluded: chain C residue  102 HIS
Chi-restraints excluded: chain G residue    7 ILE
Chi-restraints excluded: chain G residue   22 VAL
Chi-restraints excluded: chain G residue   68 LEU
Chi-restraints excluded: chain G residue  102 HIS
Chi-restraints excluded: chain B residue   25 PHE
Chi-restraints excluded: chain B residue  102 HIS
Chi-restraints excluded: chain H residue    7 ILE
Chi-restraints excluded: chain H residue   22 VAL
Chi-restraints excluded: chain H residue   91 MET
Chi-restraints excluded: chain D residue   50 ASP
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain J residue    7 ILE
Chi-restraints excluded: chain J residue   25 PHE
Chi-restraints excluded: chain J residue  102 HIS
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain F residue   45 LEU
Chi-restraints excluded: chain F residue  102 HIS
Chi-restraints excluded: chain L residue    2 THR
Chi-restraints excluded: chain L residue    7 ILE
Chi-restraints excluded: chain L residue   17 PHE
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   25 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 30 optimal weight:   30.0000
   chunk 15 optimal weight:   10.0000
   chunk 72 optimal weight:    0.0370
   chunk 54 optimal weight:    9.9990
   chunk 120 optimal weight:   30.0000
   chunk 102 optimal weight:    0.4980
   chunk 61 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 31 optimal weight:   10.0000
   chunk 51 optimal weight:   50.0000
   chunk 131 optimal weight:    3.9990
   overall best weight:    3.9064

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

Flipped N/Q/H residues before XYZ refinement:
** A   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4950 r_free = 0.4950 target = 0.172821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4899 r_free = 0.4899 target = 0.152232 restraints weight = 37642.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.4871 rms_B_bonded: 7.92
r_work (final): 0.4871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2874
moved from start:          0.2971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  11064  Z= 0.212
  Angle     :  0.629  10.357  15024  Z= 0.331
  Chirality :  0.048   0.211   1764
  Planarity :  0.007   0.069   1920
  Dihedral  :  6.493  27.958   1406
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 20.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.36 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 21.23 %
    Favored  : 74.12 %
  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: -2.09 (0.23), residues: 1272
  helix: -1.42 (0.40), residues: 140
  sheet: -0.33 (0.27), residues: 374
  loop : -2.02 (0.22), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H 112 
 PHE   0.027   0.001   PHE J  25 
 TYR   0.007   0.001   TYR B 108 
 ARG   0.004   0.001   ARG B  66 

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 50
  time to evaluate  : 1.438 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.3264 (OUTLIER) cc_final: 0.2400 (m-30)
REVERT: A  102 HIS cc_start: -0.2032 (OUTLIER) cc_final: -0.3138 (t70)
REVERT: K   91 MET cc_start: 0.1360 (pmm) cc_final: 0.0389 (mmp)
REVERT: E   21 PRO cc_start: 0.3980 (Cg_exo) cc_final: 0.3447 (Cg_endo)
REVERT: E   27 ASP cc_start: 0.0309 (OUTLIER) cc_final: -0.0614 (p0)
REVERT: E   50 ASP cc_start: 0.4331 (OUTLIER) cc_final: 0.2602 (m-30)
REVERT: C  102 HIS cc_start: -0.2997 (OUTLIER) cc_final: -0.3684 (t70)
REVERT: G   63 MET cc_start: 0.1196 (tmm) cc_final: 0.0880 (tmm)
REVERT: G  102 HIS cc_start: -0.1816 (OUTLIER) cc_final: -0.3738 (t70)
REVERT: J   63 MET cc_start: -0.0359 (ppp) cc_final: -0.0778 (ppp)
REVERT: J  102 HIS cc_start: -0.0171 (OUTLIER) cc_final: -0.3772 (t70)
REVERT: F   17 PHE cc_start: 0.1441 (m-80) cc_final: 0.1165 (m-80)
REVERT: F   63 MET cc_start: 0.1575 (tpt) cc_final: 0.0746 (tmm)
REVERT: L   63 MET cc_start: 0.0150 (tmm) cc_final: -0.0728 (tpt)
REVERT: L  102 HIS cc_start: 0.1190 (OUTLIER) cc_final: -0.0623 (t70)
  outliers start: 58
  outliers final: 32
  residues processed: 104
  average time/residue: 0.1744
  time to fit residues: 29.7383
Evaluate side-chains
  90 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 50
  time to evaluate  : 1.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 PHE
Chi-restraints excluded: chain A residue   50 ASP
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain K residue    7 ILE
Chi-restraints excluded: chain K residue   22 VAL
Chi-restraints excluded: chain K residue   25 PHE
Chi-restraints excluded: chain E residue   27 ASP
Chi-restraints excluded: chain E residue   50 ASP
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  114 LYS
Chi-restraints excluded: chain I residue   22 VAL
Chi-restraints excluded: chain I residue   25 PHE
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  102 HIS
Chi-restraints excluded: chain G residue    7 ILE
Chi-restraints excluded: chain G residue   22 VAL
Chi-restraints excluded: chain G residue  102 HIS
Chi-restraints excluded: chain B residue   25 PHE
Chi-restraints excluded: chain B residue  102 HIS
Chi-restraints excluded: chain H residue   22 VAL
Chi-restraints excluded: chain H residue   91 MET
Chi-restraints excluded: chain D residue   50 ASP
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain J residue    7 ILE
Chi-restraints excluded: chain J residue   18 ILE
Chi-restraints excluded: chain J residue   25 PHE
Chi-restraints excluded: chain J residue  102 HIS
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain F residue  102 HIS
Chi-restraints excluded: chain L residue    7 ILE
Chi-restraints excluded: chain L residue   17 PHE
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   25 PHE
Chi-restraints excluded: chain L residue   79 THR
Chi-restraints excluded: chain L residue  102 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 83 optimal weight:    0.0070
   chunk 62 optimal weight:   20.0000
   chunk 1 optimal weight:   20.0000
   chunk 125 optimal weight:   20.0000
   chunk 112 optimal weight:    0.0270
   chunk 16 optimal weight:   20.0000
   chunk 81 optimal weight:   50.0000
   chunk 15 optimal weight:    6.9990
   chunk 54 optimal weight:   20.0000
   chunk 128 optimal weight:    9.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    5.4064

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

Flipped N/Q/H residues before XYZ refinement:
** A   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  38 ASN
** C   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 102 HIS
L   6 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4939 r_free = 0.4939 target = 0.172601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.4896 r_free = 0.4896 target = 0.151515 restraints weight = 38968.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.4869 rms_B_bonded: 7.99
r_work (final): 0.4869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3133
moved from start:          0.3503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  11064  Z= 0.242
  Angle     :  0.675  10.299  15024  Z= 0.354
  Chirality :  0.050   0.225   1764
  Planarity :  0.007   0.067   1920
  Dihedral  :  6.611  28.924   1406
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 23.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.22 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 21.31 %
    Favored  : 74.36 %
  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: -2.12 (0.23), residues: 1272
  helix: -1.35 (0.43), residues: 128
  sheet: -0.41 (0.27), residues: 374
  loop : -2.02 (0.22), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H 112 
 PHE   0.027   0.002   PHE J  25 
 TYR   0.009   0.001   TYR E 108 
 ARG   0.005   0.001   ARG B  66 

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 53
  time to evaluate  : 1.179 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.3284 (OUTLIER) cc_final: 0.2242 (m-30)
REVERT: A  102 HIS cc_start: -0.2145 (OUTLIER) cc_final: -0.3366 (t70)
REVERT: K  102 HIS cc_start: -0.1410 (OUTLIER) cc_final: -0.4130 (t70)
REVERT: E   21 PRO cc_start: 0.4559 (Cg_exo) cc_final: 0.3946 (Cg_endo)
REVERT: E   27 ASP cc_start: 0.0940 (OUTLIER) cc_final: -0.0074 (p0)
REVERT: C  102 HIS cc_start: -0.3486 (OUTLIER) cc_final: -0.4129 (t70)
REVERT: G   63 MET cc_start: 0.2495 (tmm) cc_final: 0.1956 (tmm)
REVERT: G  102 HIS cc_start: -0.1735 (OUTLIER) cc_final: -0.3934 (t70)
REVERT: D   91 MET cc_start: 0.1026 (mpp) cc_final: 0.0385 (mpp)
REVERT: J   63 MET cc_start: 0.0770 (ppp) cc_final: 0.0024 (ppp)
REVERT: J  102 HIS cc_start: -0.1316 (OUTLIER) cc_final: -0.4301 (t70)
REVERT: F   17 PHE cc_start: 0.2162 (m-80) cc_final: 0.1958 (m-80)
REVERT: F   63 MET cc_start: 0.1927 (tpt) cc_final: 0.1058 (tmm)
REVERT: L  102 HIS cc_start: 0.1266 (OUTLIER) cc_final: -0.0619 (t70)
  outliers start: 54
  outliers final: 36
  residues processed: 102
  average time/residue: 0.1598
  time to fit residues: 26.4917
Evaluate side-chains
  95 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 51
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 PHE
Chi-restraints excluded: chain A residue   50 ASP
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain K residue    7 ILE
Chi-restraints excluded: chain K residue   22 VAL
Chi-restraints excluded: chain K residue   25 PHE
Chi-restraints excluded: chain K residue  102 HIS
Chi-restraints excluded: chain E residue   27 ASP
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  114 LYS
Chi-restraints excluded: chain I residue   22 VAL
Chi-restraints excluded: chain I residue   25 PHE
Chi-restraints excluded: chain I residue   72 LEU
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  102 HIS
Chi-restraints excluded: chain G residue    7 ILE
Chi-restraints excluded: chain G residue   22 VAL
Chi-restraints excluded: chain G residue  102 HIS
Chi-restraints excluded: chain B residue   25 PHE
Chi-restraints excluded: chain B residue  102 HIS
Chi-restraints excluded: chain H residue   22 VAL
Chi-restraints excluded: chain H residue   63 MET
Chi-restraints excluded: chain D residue    4 GLU
Chi-restraints excluded: chain D residue   50 ASP
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain J residue    7 ILE
Chi-restraints excluded: chain J residue   18 ILE
Chi-restraints excluded: chain J residue   25 PHE
Chi-restraints excluded: chain J residue  102 HIS
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain F residue  102 HIS
Chi-restraints excluded: chain L residue    2 THR
Chi-restraints excluded: chain L residue    7 ILE
Chi-restraints excluded: chain L residue   17 PHE
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   25 PHE
Chi-restraints excluded: chain L residue   79 THR
Chi-restraints excluded: chain L residue  102 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 102 optimal weight:   30.0000
   chunk 61 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 123 optimal weight:    0.0970
   chunk 14 optimal weight:   10.0000
   chunk 76 optimal weight:    8.9990
   chunk 82 optimal weight:    8.9990
   chunk 35 optimal weight:    3.9990
   chunk 125 optimal weight:    9.9990
   chunk 92 optimal weight:    6.9990
   chunk 78 optimal weight:    8.9990
   overall best weight:    4.4186

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

Flipped N/Q/H residues before XYZ refinement:
** A   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 112 HIS
** K   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   6 ASN
** C   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  74 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4945 r_free = 0.4945 target = 0.172772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4891 r_free = 0.4891 target = 0.151434 restraints weight = 38635.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.4863 rms_B_bonded: 8.22
r_work (final): 0.4863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2949
moved from start:          0.3693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  11064  Z= 0.221
  Angle     :  0.671  13.313  15024  Z= 0.343
  Chirality :  0.049   0.212   1764
  Planarity :  0.007   0.070   1920
  Dihedral  :  6.510  27.704   1406
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 22.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.59 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 22.36 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.09 (0.23), residues: 1272
  helix: -1.28 (0.43), residues: 128
  sheet: -0.39 (0.27), residues: 374
  loop : -2.01 (0.22), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.001   HIS F 102 
 PHE   0.027   0.001   PHE J  25 
 TYR   0.009   0.001   TYR F  80 
 ARG   0.005   0.001   ARG B  66 

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 53
  time to evaluate  : 1.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.3240 (OUTLIER) cc_final: 0.2205 (m-30)
REVERT: A  102 HIS cc_start: -0.2255 (OUTLIER) cc_final: -0.3404 (t70)
REVERT: K  102 HIS cc_start: -0.0814 (OUTLIER) cc_final: -0.3872 (t70)
REVERT: E   21 PRO cc_start: 0.4215 (Cg_exo) cc_final: 0.3758 (Cg_endo)
REVERT: E   27 ASP cc_start: -0.0128 (OUTLIER) cc_final: -0.0485 (p0)
REVERT: C  102 HIS cc_start: -0.3204 (OUTLIER) cc_final: -0.3883 (t70)
REVERT: G   63 MET cc_start: 0.1680 (tmm) cc_final: 0.1169 (tmm)
REVERT: G  102 HIS cc_start: -0.1857 (OUTLIER) cc_final: -0.3951 (t70)
REVERT: B   17 PHE cc_start: 0.3176 (t80) cc_final: 0.2349 (t80)
REVERT: J   18 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8968 (tp)
REVERT: J   63 MET cc_start: -0.0533 (ppp) cc_final: -0.1068 (ppp)
REVERT: J  102 HIS cc_start: -0.0744 (OUTLIER) cc_final: -0.4028 (t70)
REVERT: F   63 MET cc_start: 0.1486 (tpt) cc_final: 0.0720 (tmm)
REVERT: F  100 ILE cc_start: 0.0796 (OUTLIER) cc_final: 0.0588 (mp)
REVERT: L   10 PHE cc_start: 0.1879 (m-80) cc_final: 0.1250 (m-80)
REVERT: L  102 HIS cc_start: 0.1231 (OUTLIER) cc_final: -0.0630 (t70)
  outliers start: 51
  outliers final: 31
  residues processed: 100
  average time/residue: 0.1670
  time to fit residues: 27.1376
Evaluate side-chains
  92 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 51
  time to evaluate  : 1.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 PHE
Chi-restraints excluded: chain A residue   50 ASP
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain K residue    7 ILE
Chi-restraints excluded: chain K residue   22 VAL
Chi-restraints excluded: chain K residue   25 PHE
Chi-restraints excluded: chain K residue  102 HIS
Chi-restraints excluded: chain E residue   27 ASP
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  114 LYS
Chi-restraints excluded: chain I residue   22 VAL
Chi-restraints excluded: chain I residue   25 PHE
Chi-restraints excluded: chain I residue   75 ILE
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  102 HIS
Chi-restraints excluded: chain G residue    7 ILE
Chi-restraints excluded: chain G residue   22 VAL
Chi-restraints excluded: chain G residue  102 HIS
Chi-restraints excluded: chain B residue   25 PHE
Chi-restraints excluded: chain H residue   22 VAL
Chi-restraints excluded: chain H residue   63 MET
Chi-restraints excluded: chain D residue   50 ASP
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain J residue   18 ILE
Chi-restraints excluded: chain J residue   25 PHE
Chi-restraints excluded: chain J residue  102 HIS
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain F residue  100 ILE
Chi-restraints excluded: chain F residue  102 HIS
Chi-restraints excluded: chain L residue    2 THR
Chi-restraints excluded: chain L residue    7 ILE
Chi-restraints excluded: chain L residue   17 PHE
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   24 GLU
Chi-restraints excluded: chain L residue   25 PHE
Chi-restraints excluded: chain L residue   79 THR
Chi-restraints excluded: chain L residue  102 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 46 optimal weight:    0.1980
   chunk 38 optimal weight:    5.9990
   chunk 76 optimal weight:    7.9990
   chunk 66 optimal weight:   20.0000
   chunk 81 optimal weight:   50.0000
   chunk 23 optimal weight:   40.0000
   chunk 99 optimal weight:    7.9990
   chunk 96 optimal weight:   20.0000
   chunk 69 optimal weight:   40.0000
   chunk 34 optimal weight:    8.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    5.0388

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

Flipped N/Q/H residues before XYZ refinement:
** A   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 112 HIS
** K   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   1 GLN
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 102 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4959 r_free = 0.4959 target = 0.179445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4906 r_free = 0.4906 target = 0.165904 restraints weight = 45451.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.4898 rms_B_bonded: 5.48
r_work (final): 0.4898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3102
moved from start:          0.4063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  11064  Z= 0.230
  Angle     :  0.667  13.059  15024  Z= 0.345
  Chirality :  0.049   0.207   1764
  Planarity :  0.007   0.069   1920
  Dihedral  :  6.507  28.463   1406
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 23.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.30 %
    Favored  : 89.70 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 22.20 %
    Favored  : 73.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.23), residues: 1272
  helix: -1.28 (0.42), residues: 128
  sheet: -0.40 (0.27), residues: 374
  loop : -2.03 (0.22), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H  35 
 PHE   0.027   0.001   PHE J  25 
 TYR   0.009   0.001   TYR F  80 
 ARG   0.004   0.001   ARG B  66 

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 51
  time to evaluate  : 1.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.3123 (OUTLIER) cc_final: 0.1765 (m-30)
REVERT: A  102 HIS cc_start: -0.2597 (OUTLIER) cc_final: -0.3690 (t70)
REVERT: E   21 PRO cc_start: 0.5108 (Cg_exo) cc_final: 0.4335 (Cg_endo)
REVERT: E   27 ASP cc_start: 0.1030 (OUTLIER) cc_final: 0.0218 (p0)
REVERT: C  102 HIS cc_start: -0.4511 (OUTLIER) cc_final: -0.4790 (t70)
REVERT: G   63 MET cc_start: 0.1278 (tmm) cc_final: 0.0868 (tmm)
REVERT: B   17 PHE cc_start: 0.3593 (t80) cc_final: 0.2664 (t80)
REVERT: D   91 MET cc_start: 0.0006 (mpp) cc_final: -0.0409 (mpp)
REVERT: D  100 ILE cc_start: 0.3923 (OUTLIER) cc_final: 0.3690 (mt)
REVERT: J   18 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8977 (tp)
REVERT: J   63 MET cc_start: -0.0281 (ppp) cc_final: -0.0792 (ppp)
REVERT: J  102 HIS cc_start: -0.0429 (OUTLIER) cc_final: -0.3834 (t70)
REVERT: F   63 MET cc_start: 0.1841 (tpt) cc_final: 0.0921 (tmm)
REVERT: L  102 HIS cc_start: 0.1651 (OUTLIER) cc_final: -0.0559 (t70)
  outliers start: 50
  outliers final: 33
  residues processed: 97
  average time/residue: 0.1672
  time to fit residues: 26.4735
Evaluate side-chains
  91 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 50
  time to evaluate  : 1.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 PHE
Chi-restraints excluded: chain A residue   50 ASP
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain K residue    7 ILE
Chi-restraints excluded: chain K residue   22 VAL
Chi-restraints excluded: chain K residue   25 PHE
Chi-restraints excluded: chain E residue   27 ASP
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  114 LYS
Chi-restraints excluded: chain I residue   22 VAL
Chi-restraints excluded: chain I residue   25 PHE
Chi-restraints excluded: chain I residue   72 LEU
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  102 HIS
Chi-restraints excluded: chain G residue    7 ILE
Chi-restraints excluded: chain G residue   22 VAL
Chi-restraints excluded: chain B residue   25 PHE
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain H residue   22 VAL
Chi-restraints excluded: chain H residue   63 MET
Chi-restraints excluded: chain D residue   50 ASP
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain D residue  117 TYR
Chi-restraints excluded: chain J residue   18 ILE
Chi-restraints excluded: chain J residue   25 PHE
Chi-restraints excluded: chain J residue  102 HIS
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain F residue  102 HIS
Chi-restraints excluded: chain L residue    2 THR
Chi-restraints excluded: chain L residue    7 ILE
Chi-restraints excluded: chain L residue   17 PHE
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   24 GLU
Chi-restraints excluded: chain L residue   25 PHE
Chi-restraints excluded: chain L residue   79 THR
Chi-restraints excluded: chain L residue  102 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 104 optimal weight:    9.9990
   chunk 65 optimal weight:   20.0000
   chunk 55 optimal weight:    3.9990
   chunk 48 optimal weight:   20.0000
   chunk 86 optimal weight:   20.0000
   chunk 46 optimal weight:    8.9990
   chunk 95 optimal weight:    8.9990
   chunk 101 optimal weight:    2.9990
   chunk 15 optimal weight:   40.0000
   chunk 53 optimal weight:    0.0270
   overall best weight:    5.0046

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

Flipped N/Q/H residues before XYZ refinement:
** A   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 112 HIS
** K   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  35 HIS
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4925 r_free = 0.4925 target = 0.171884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.4877 r_free = 0.4877 target = 0.151349 restraints weight = 38219.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.4856 rms_B_bonded: 8.43
r_work (final): 0.4856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3099
moved from start:          0.4276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  11064  Z= 0.232
  Angle     :  0.677  12.662  15024  Z= 0.348
  Chirality :  0.049   0.205   1764
  Planarity :  0.007   0.071   1920
  Dihedral  :  6.501  28.695   1406
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 23.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.83 %
    Favored  : 90.17 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 22.44 %
    Favored  : 73.88 %
  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 (0.23), residues: 1272
  helix: -1.24 (0.43), residues: 128
  sheet: -0.45 (0.26), residues: 374
  loop : -2.01 (0.22), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS F 102 
 PHE   0.026   0.001   PHE J  25 
 TYR   0.009   0.001   TYR F  80 
 ARG   0.005   0.001   ARG B  66 

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 48
  time to evaluate  : 1.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.3083 (OUTLIER) cc_final: 0.1892 (m-30)
REVERT: A  102 HIS cc_start: -0.2643 (OUTLIER) cc_final: -0.3719 (t70)
REVERT: K  102 HIS cc_start: -0.0738 (OUTLIER) cc_final: -0.3837 (t70)
REVERT: E   21 PRO cc_start: 0.4854 (Cg_exo) cc_final: 0.4221 (Cg_endo)
REVERT: E   27 ASP cc_start: 0.0785 (OUTLIER) cc_final: 0.0116 (p0)
REVERT: I   63 MET cc_start: 0.2206 (tmm) cc_final: 0.1760 (tmm)
REVERT: C  102 HIS cc_start: -0.3281 (OUTLIER) cc_final: -0.4010 (t70)
REVERT: G   63 MET cc_start: 0.1911 (tmm) cc_final: 0.1395 (tmm)
REVERT: G  102 HIS cc_start: -0.1476 (OUTLIER) cc_final: -0.3847 (t70)
REVERT: B   17 PHE cc_start: 0.3368 (t80) cc_final: 0.2558 (t80)
REVERT: D  100 ILE cc_start: 0.3878 (OUTLIER) cc_final: 0.3490 (mt)
REVERT: J   18 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8919 (tp)
REVERT: J   63 MET cc_start: 0.0388 (ppp) cc_final: -0.0148 (ppp)
REVERT: J  102 HIS cc_start: -0.0508 (OUTLIER) cc_final: -0.3926 (t70)
REVERT: F   63 MET cc_start: 0.1359 (tpt) cc_final: 0.0593 (tmm)
REVERT: L  102 HIS cc_start: 0.1193 (OUTLIER) cc_final: -0.0938 (t70)
  outliers start: 46
  outliers final: 32
  residues processed: 91
  average time/residue: 0.1873
  time to fit residues: 27.7067
Evaluate side-chains
  89 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 47
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 PHE
Chi-restraints excluded: chain A residue   50 ASP
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain K residue    7 ILE
Chi-restraints excluded: chain K residue   22 VAL
Chi-restraints excluded: chain K residue   25 PHE
Chi-restraints excluded: chain K residue   91 MET
Chi-restraints excluded: chain K residue  102 HIS
Chi-restraints excluded: chain E residue   27 ASP
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  114 LYS
Chi-restraints excluded: chain I residue   22 VAL
Chi-restraints excluded: chain I residue   25 PHE
Chi-restraints excluded: chain I residue   72 LEU
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain C residue  102 HIS
Chi-restraints excluded: chain G residue    7 ILE
Chi-restraints excluded: chain G residue   22 VAL
Chi-restraints excluded: chain G residue  102 HIS
Chi-restraints excluded: chain B residue   25 PHE
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  101 ASP
Chi-restraints excluded: chain H residue   22 VAL
Chi-restraints excluded: chain H residue   63 MET
Chi-restraints excluded: chain D residue   50 ASP
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain D residue  117 TYR
Chi-restraints excluded: chain J residue   18 ILE
Chi-restraints excluded: chain J residue   25 PHE
Chi-restraints excluded: chain J residue  102 HIS
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain L residue    2 THR
Chi-restraints excluded: chain L residue   17 PHE
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   25 PHE
Chi-restraints excluded: chain L residue   79 THR
Chi-restraints excluded: chain L residue  102 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 130 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0670
   chunk 23 optimal weight:    9.9990
   chunk 114 optimal weight:    8.9990
   chunk 28 optimal weight:   50.0000
   chunk 118 optimal weight:   20.0000
   chunk 126 optimal weight:   50.0000
   chunk 65 optimal weight:   40.0000
   chunk 34 optimal weight:    0.0970
   chunk 95 optimal weight:    6.9990
   chunk 124 optimal weight:    6.9990
   overall best weight:    3.8322

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

Flipped N/Q/H residues before XYZ refinement:
** A   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 112 HIS
K   1 GLN
** K  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 102 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5000 r_free = 0.5000 target = 0.167988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4822 r_free = 0.4822 target = 0.149534 restraints weight = 58936.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.4762 rms_B_bonded: 9.41
r_work (final): 0.4762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3809
moved from start:          0.4551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  11064  Z= 0.213
  Angle     :  0.648  12.543  15024  Z= 0.333
  Chirality :  0.048   0.199   1764
  Planarity :  0.007   0.071   1920
  Dihedral  :  6.280  28.112   1406
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 19.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 22.28 %
    Favored  : 74.44 %
  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: -2.05 (0.23), residues: 1272
  helix: -1.17 (0.42), residues: 132
  sheet: -0.21 (0.27), residues: 359
  loop : -2.06 (0.22), residues: 781

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS H  35 
 PHE   0.026   0.001   PHE J  25 
 TYR   0.009   0.001   TYR F  80 
 ARG   0.006   0.001   ARG K  66 

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 49
  time to evaluate  : 1.171 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 ASP cc_start: 0.3233 (OUTLIER) cc_final: 0.2005 (m-30)
REVERT: A  102 HIS cc_start: -0.3171 (OUTLIER) cc_final: -0.3900 (t70)
REVERT: K  102 HIS cc_start: -0.3094 (OUTLIER) cc_final: -0.4830 (t70)
REVERT: E   21 PRO cc_start: 0.4975 (Cg_exo) cc_final: 0.4607 (Cg_endo)
REVERT: E   27 ASP cc_start: 0.0262 (OUTLIER) cc_final: -0.0123 (p0)
REVERT: I   63 MET cc_start: 0.0651 (tmm) cc_final: 0.0219 (tmm)
REVERT: G   63 MET cc_start: 0.1115 (tmm) cc_final: 0.0728 (tmm)
REVERT: G  102 HIS cc_start: -0.1290 (OUTLIER) cc_final: -0.3722 (t70)
REVERT: B   17 PHE cc_start: 0.4126 (t80) cc_final: 0.3149 (t80)
REVERT: H   63 MET cc_start: 0.0710 (OUTLIER) cc_final: 0.0086 (tmm)
REVERT: D   91 MET cc_start: 0.0737 (mpp) cc_final: 0.0528 (mpp)
REVERT: D  100 ILE cc_start: 0.4251 (OUTLIER) cc_final: 0.3848 (mt)
REVERT: J   18 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8958 (tp)
REVERT: J   63 MET cc_start: -0.0733 (ppp) cc_final: -0.1022 (ppp)
REVERT: F   63 MET cc_start: 0.2269 (tpt) cc_final: 0.1572 (tmm)
REVERT: L   10 PHE cc_start: 0.2197 (m-80) cc_final: 0.1673 (m-80)
REVERT: L   63 MET cc_start: 0.0499 (tmm) cc_final: 0.0260 (tmm)
REVERT: L  102 HIS cc_start: 0.1374 (OUTLIER) cc_final: -0.0663 (t70)
  outliers start: 41
  outliers final: 29
  residues processed: 87
  average time/residue: 0.1677
  time to fit residues: 23.8315
Evaluate side-chains
  86 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 48
  time to evaluate  : 1.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 PHE
Chi-restraints excluded: chain A residue   50 ASP
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain K residue    7 ILE
Chi-restraints excluded: chain K residue   22 VAL
Chi-restraints excluded: chain K residue   25 PHE
Chi-restraints excluded: chain K residue  102 HIS
Chi-restraints excluded: chain E residue   27 ASP
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue  100 ILE
Chi-restraints excluded: chain E residue  114 LYS
Chi-restraints excluded: chain I residue   22 VAL
Chi-restraints excluded: chain I residue   25 PHE
Chi-restraints excluded: chain I residue   72 LEU
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  100 ILE
Chi-restraints excluded: chain G residue    7 ILE
Chi-restraints excluded: chain G residue   22 VAL
Chi-restraints excluded: chain G residue  102 HIS
Chi-restraints excluded: chain B residue   25 PHE
Chi-restraints excluded: chain B residue  101 ASP
Chi-restraints excluded: chain H residue   22 VAL
Chi-restraints excluded: chain H residue   63 MET
Chi-restraints excluded: chain D residue   50 ASP
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  114 LYS
Chi-restraints excluded: chain D residue  117 TYR
Chi-restraints excluded: chain J residue   18 ILE
Chi-restraints excluded: chain J residue   25 PHE
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain F residue  102 HIS
Chi-restraints excluded: chain L residue   17 PHE
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   25 PHE
Chi-restraints excluded: chain L residue   79 THR
Chi-restraints excluded: chain L residue  102 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 115 optimal weight:    8.9990
   chunk 32 optimal weight:    5.9990
   chunk 84 optimal weight:    9.9990
   chunk 113 optimal weight:    5.9990
   chunk 120 optimal weight:    9.9990
   chunk 107 optimal weight:   50.0000
   chunk 94 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   chunk 122 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 59 optimal weight:   40.0000
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  99 ASN
G  99 ASN
** B  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 102 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5122 r_free = 0.5122 target = 0.172284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4873 r_free = 0.4873 target = 0.154537 restraints weight = 61578.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.4736 rms_B_bonded: 9.23
r_work (final): 0.4736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3888
moved from start:          0.4798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  11064  Z= 0.248
  Angle     :  0.701  15.225  15024  Z= 0.359
  Chirality :  0.049   0.207   1764
  Planarity :  0.007   0.071   1920
  Dihedral  :  6.497  29.438   1406
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 24.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.22 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 22.12 %
    Favored  : 74.60 %
  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: -2.07 (0.23), residues: 1272
  helix: -1.14 (0.43), residues: 126
  sheet: -0.12 (0.28), residues: 343
  loop : -2.11 (0.22), residues: 803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS H  35 
 PHE   0.023   0.002   PHE J  25 
 TYR   0.011   0.001   TYR E 108 
 ARG   0.004   0.001   ARG B  66 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4895.40 seconds
wall clock time: 89 minutes 6.65 seconds (5346.65 seconds total)