Starting phenix.real_space_refine
on Wed Jul 30 04:18:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6teb_10479/07_2025/6teb_10479.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6teb_10479/07_2025/6teb_10479.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6teb_10479/07_2025/6teb_10479.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6teb_10479/07_2025/6teb_10479.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6teb_10479/07_2025/6teb_10479.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6teb_10479/07_2025/6teb_10479.cif"
  }
  resolution = 4.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    7662      2.51       5
     N    2166      2.21       5
     O    2328      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 75 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12168
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 972
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 3, 'TRANS': 126}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 972
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 3, 'TRANS': 126}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1056
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 1056
          Classifications: {'peptide': 134}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 124}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 1056
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 1056
          Classifications: {'peptide': 134}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 124}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "E"
      Number of atoms: 972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 972
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 3, 'TRANS': 126}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 972
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 3, 'TRANS': 126}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 1056
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 1056
          Classifications: {'peptide': 134}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 124}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "H"
      Number of atoms: 1056
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 1056
          Classifications: {'peptide': 134}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 124}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "I"
      Number of atoms: 972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 972
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 3, 'TRANS': 126}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 972
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 3, 'TRANS': 126}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 1056
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 1056
          Classifications: {'peptide': 134}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 124}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "L"
      Number of atoms: 1056
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 134, 1056
          Classifications: {'peptide': 134}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 124}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
  Time building chain proxies: 7.77, per 1000 atoms: 0.64
  Number of scatterers: 12168
  At special positions: 0
  Unit cell: (106.3, 106.3, 90.355, 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      12     16.00
     O    2328      8.00
     N    2166      7.00
     C    7662      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.78
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2832

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 21 sheets defined
      10.2% alpha, 23.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 73 through 85
      removed outlier: 3.560A  pdb=" N   ALA A  79 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ARG A  80 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 85
      removed outlier: 3.560A  pdb=" N   ALA B  79 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ARG B  80 " --> pdb=" O   ASP B  76 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 68
      removed outlier: 3.576A  pdb=" N   VAL D  59 " --> pdb=" O   SER D  55 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLU D  60 " --> pdb=" O   LEU D  56 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ARG D  61 " --> pdb=" O   ASP D  57 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ALA D  64 " --> pdb=" O   GLU D  60 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   PHE D  65 " --> pdb=" O   ARG D  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 68
      removed outlier: 3.570A  pdb=" N   VAL C  59 " --> pdb=" O   SER C  55 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLU C  60 " --> pdb=" O   LEU C  56 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ARG C  61 " --> pdb=" O   ASP C  57 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ALA C  64 " --> pdb=" O   GLU C  60 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   PHE C  65 " --> pdb=" O   ARG C  61 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE C  66 " --> pdb=" O   LEU C  62 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 73 through 85
      removed outlier: 3.560A  pdb=" N   ALA E  79 " --> pdb=" O   THR E  75 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ARG E  80 " --> pdb=" O   ASP E  76 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 73 through 85
      removed outlier: 3.560A  pdb=" N   ALA F  79 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ARG F  80 " --> pdb=" O   ASP F  76 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 55 through 68
      removed outlier: 3.575A  pdb=" N   VAL G  59 " --> pdb=" O   SER G  55 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLU G  60 " --> pdb=" O   LEU G  56 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ARG G  61 " --> pdb=" O   ASP G  57 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ALA G  64 " --> pdb=" O   GLU G  60 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   PHE G  65 " --> pdb=" O   ARG G  61 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 68
      removed outlier: 3.571A  pdb=" N   VAL H  59 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLU H  60 " --> pdb=" O   LEU H  56 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ARG H  61 " --> pdb=" O   ASP H  57 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ALA H  64 " --> pdb=" O   GLU H  60 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   PHE H  65 " --> pdb=" O   ARG H  61 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE H  66 " --> pdb=" O   LEU H  62 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 73 through 85
      removed outlier: 3.560A  pdb=" N   ALA I  79 " --> pdb=" O   THR I  75 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ARG I  80 " --> pdb=" O   ASP I  76 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 73 through 85
      removed outlier: 3.560A  pdb=" N   ALA J  79 " --> pdb=" O   THR J  75 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ARG J  80 " --> pdb=" O   ASP J  76 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 55 through 68
      removed outlier: 3.576A  pdb=" N   VAL K  59 " --> pdb=" O   SER K  55 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   GLU K  60 " --> pdb=" O   LEU K  56 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ARG K  61 " --> pdb=" O   ASP K  57 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ALA K  64 " --> pdb=" O   GLU K  60 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   PHE K  65 " --> pdb=" O   ARG K  61 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 55 through 68
      removed outlier: 3.570A  pdb=" N   VAL L  59 " --> pdb=" O   SER L  55 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLU L  60 " --> pdb=" O   LEU L  56 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ARG L  61 " --> pdb=" O   ASP L  57 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ALA L  64 " --> pdb=" O   GLU L  60 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   PHE L  65 " --> pdb=" O   ARG L  61 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE L  66 " --> pdb=" O   LEU L  62 " (cutoff:3.500A)
    Processing sheet with id=1, first strand: chain 'A' and resid 22 through 23
      removed outlier: 5.685A  pdb=" N   ILE A 107 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   ALA A 127 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   ALA A  62 " --> pdb=" O   SER A 128 " (cutoff:3.500A)
    Processing sheet with id=2, first strand: chain 'A' and resid 22 through 23
      removed outlier: 6.077A  pdb=" N   THR A 108 " --> pdb=" O   ALA B  36 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ILE A 110 " --> pdb=" O   PHE B  34 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   ALA B  62 " --> pdb=" O   SER B 128 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   ALA B 127 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 5.685A  pdb=" N   ILE B 107 " --> pdb=" O   ALA B 127 " (cutoff:3.500A)
    Processing sheet with id=3, first strand: chain 'D' and resid 25 through 26
      removed outlier: 3.609A  pdb=" N   GLU D  25 " --> pdb=" O   ASN D  37 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ASN D  37 " --> pdb=" O   GLU D  25 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=3
    Processing sheet with id=4, first strand: chain 'D' and resid 52 through 54
      removed outlier: 3.942A  pdb=" N   GLY D  52 " --> pdb=" O   LEU D 200 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU D 200 " --> pdb=" O   GLY D  52 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ARG D  54 " --> pdb=" O   GLY D 198 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   ALA D 197 " --> pdb=" O   GLN D 193 " (cutoff:3.500A)
    Processing sheet with id=5, first strand: chain 'D' and resid 158 through 159
    Processing sheet with id=6, first strand: chain 'C' and resid 52 through 54
      removed outlier: 3.944A  pdb=" N   GLY C  52 " --> pdb=" O   LEU C 200 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LEU C 200 " --> pdb=" O   GLY C  52 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ARG C  54 " --> pdb=" O   GLY C 198 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   ALA C 197 " --> pdb=" O   GLN C 193 " (cutoff:3.500A)
    Processing sheet with id=7, first strand: chain 'C' and resid 158 through 159
    Processing sheet with id=8, first strand: chain 'E' and resid 22 through 23
      removed outlier: 5.686A  pdb=" N   ILE E 107 " --> pdb=" O   ALA E 127 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   ALA E 127 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   ALA E  62 " --> pdb=" O   SER E 128 " (cutoff:3.500A)
    Processing sheet with id=9, first strand: chain 'E' and resid 22 through 23
      removed outlier: 6.077A  pdb=" N   THR E 108 " --> pdb=" O   ALA F  36 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ILE E 110 " --> pdb=" O   PHE F  34 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   ALA F  62 " --> pdb=" O   SER F 128 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   ALA F 127 " --> pdb=" O   ILE F 107 " (cutoff:3.500A)
      removed outlier: 5.685A  pdb=" N   ILE F 107 " --> pdb=" O   ALA F 127 " (cutoff:3.500A)
    Processing sheet with id=10, first strand: chain 'G' and resid 25 through 26
      removed outlier: 3.609A  pdb=" N   GLU G  25 " --> pdb=" O   ASN G  37 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ASN G  37 " --> pdb=" O   GLU G  25 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=10
    Processing sheet with id=11, first strand: chain 'G' and resid 52 through 54
      removed outlier: 3.942A  pdb=" N   GLY G  52 " --> pdb=" O   LEU G 200 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU G 200 " --> pdb=" O   GLY G  52 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG G  54 " --> pdb=" O   GLY G 198 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   ALA G 197 " --> pdb=" O   GLN G 193 " (cutoff:3.500A)
    Processing sheet with id=12, first strand: chain 'G' and resid 158 through 159
    Processing sheet with id=13, first strand: chain 'H' and resid 52 through 54
      removed outlier: 3.944A  pdb=" N   GLY H  52 " --> pdb=" O   LEU H 200 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LEU H 200 " --> pdb=" O   GLY H  52 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ARG H  54 " --> pdb=" O   GLY H 198 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   ALA H 197 " --> pdb=" O   GLN H 193 " (cutoff:3.500A)
    Processing sheet with id=14, first strand: chain 'H' and resid 158 through 159
    Processing sheet with id=15, first strand: chain 'I' and resid 22 through 23
      removed outlier: 5.685A  pdb=" N   ILE I 107 " --> pdb=" O   ALA I 127 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   ALA I 127 " --> pdb=" O   ILE I 107 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   ALA I  62 " --> pdb=" O   SER I 128 " (cutoff:3.500A)
    Processing sheet with id=16, first strand: chain 'I' and resid 22 through 23
      removed outlier: 6.076A  pdb=" N   THR I 108 " --> pdb=" O   ALA J  36 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ILE I 110 " --> pdb=" O   PHE J  34 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   ALA J  62 " --> pdb=" O   SER J 128 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   ALA J 127 " --> pdb=" O   ILE J 107 " (cutoff:3.500A)
      removed outlier: 5.685A  pdb=" N   ILE J 107 " --> pdb=" O   ALA J 127 " (cutoff:3.500A)
    Processing sheet with id=17, first strand: chain 'K' and resid 25 through 26
      removed outlier: 3.609A  pdb=" N   GLU K  25 " --> pdb=" O   ASN K  37 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ASN K  37 " --> pdb=" O   GLU K  25 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=17
    Processing sheet with id=18, first strand: chain 'K' and resid 52 through 54
      removed outlier: 3.943A  pdb=" N   GLY K  52 " --> pdb=" O   LEU K 200 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU K 200 " --> pdb=" O   GLY K  52 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ARG K  54 " --> pdb=" O   GLY K 198 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   ALA K 197 " --> pdb=" O   GLN K 193 " (cutoff:3.500A)
    Processing sheet with id=19, first strand: chain 'K' and resid 158 through 159
    Processing sheet with id=20, first strand: chain 'L' and resid 52 through 54
      removed outlier: 3.944A  pdb=" N   GLY L  52 " --> pdb=" O   LEU L 200 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   LEU L 200 " --> pdb=" O   GLY L  52 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ARG L  54 " --> pdb=" O   GLY L 198 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   ALA L 197 " --> pdb=" O   GLN L 193 " (cutoff:3.500A)
    Processing sheet with id=21, first strand: chain 'L' and resid 158 through 159

    303 hydrogen bonds defined for protein.
    801 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: 3.29

  Time building geometry restraints manager: 3.35 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4166
        1.34 -     1.45: 1982
        1.45 -     1.57: 6260
        1.57 -     1.68: 0
        1.68 -     1.80: 24
  Bond restraints: 12432
  Sorted by residual:
  bond pdb=" N   THR L 185 "
       pdb=" CA  THR L 185 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.036 1.21e-02 6.83e+03 8.69e+00
  bond pdb=" N   THR C 185 "
       pdb=" CA  THR C 185 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.035 1.21e-02 6.83e+03 8.58e+00
  bond pdb=" N   THR H 185 "
       pdb=" CA  THR H 185 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.035 1.21e-02 6.83e+03 8.52e+00
  bond pdb=" N   VAL L 192 "
       pdb=" CA  VAL L 192 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.24e-02 6.50e+03 8.09e+00
  bond pdb=" N   THR G 185 "
       pdb=" CA  THR G 185 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.034 1.21e-02 6.83e+03 8.08e+00
  ... (remaining 12427 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.06: 16356
        3.06 -     6.12: 411
        6.12 -     9.17: 39
        9.17 -    12.23: 12
       12.23 -    15.29: 6
  Bond angle restraints: 16824
  Sorted by residual:
  angle pdb=" C   ILE F 107 "
        pdb=" N   THR F 108 "
        pdb=" CA  THR F 108 "
      ideal   model   delta    sigma   weight residual
     121.54  130.18   -8.64 1.91e+00 2.74e-01 2.05e+01
  angle pdb=" C   ILE I 107 "
        pdb=" N   THR I 108 "
        pdb=" CA  THR I 108 "
      ideal   model   delta    sigma   weight residual
     121.54  130.18   -8.64 1.91e+00 2.74e-01 2.04e+01
  angle pdb=" C   ILE A 107 "
        pdb=" N   THR A 108 "
        pdb=" CA  THR A 108 "
      ideal   model   delta    sigma   weight residual
     121.54  130.16   -8.62 1.91e+00 2.74e-01 2.04e+01
  angle pdb=" C   ILE J 107 "
        pdb=" N   THR J 108 "
        pdb=" CA  THR J 108 "
      ideal   model   delta    sigma   weight residual
     121.54  130.15   -8.61 1.91e+00 2.74e-01 2.03e+01
  angle pdb=" C   ILE B 107 "
        pdb=" N   THR B 108 "
        pdb=" CA  THR B 108 "
      ideal   model   delta    sigma   weight residual
     121.54  130.14   -8.60 1.91e+00 2.74e-01 2.03e+01
  ... (remaining 16819 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.47: 6423
       15.47 -    30.95: 645
       30.95 -    46.42: 159
       46.42 -    61.90: 9
       61.90 -    77.37: 18
  Dihedral angle restraints: 7254
    sinusoidal: 2844
      harmonic: 4410
  Sorted by residual:
  dihedral pdb=" CA  GLN D  72 "
           pdb=" C   GLN D  72 "
           pdb=" N   LEU D  73 "
           pdb=" CA  LEU D  73 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.96  -28.04     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CA  GLN K  72 "
           pdb=" C   GLN K  72 "
           pdb=" N   LEU K  73 "
           pdb=" CA  LEU K  73 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.96  -28.04     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CA  GLN G  72 "
           pdb=" C   GLN G  72 "
           pdb=" N   LEU G  73 "
           pdb=" CA  LEU G  73 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.96  -28.04     0      5.00e+00 4.00e-02 3.15e+01
  ... (remaining 7251 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 1520
       0.091 -    0.182: 247
       0.182 -    0.273: 21
       0.273 -    0.364: 0
       0.364 -    0.455: 12
  Chirality restraints: 1800
  Sorted by residual:
  chirality pdb=" CB  THR A  42 "
            pdb=" CA  THR A  42 "
            pdb=" OG1 THR A  42 "
            pdb=" CG2 THR A  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.10    0.46 2.00e-01 2.50e+01 5.19e+00
  chirality pdb=" CB  THR I  42 "
            pdb=" CA  THR I  42 "
            pdb=" OG1 THR I  42 "
            pdb=" CG2 THR I  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.10    0.46 2.00e-01 2.50e+01 5.18e+00
  chirality pdb=" CB  THR E  42 "
            pdb=" CA  THR E  42 "
            pdb=" OG1 THR E  42 "
            pdb=" CG2 THR E  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.10    0.45 2.00e-01 2.50e+01 5.16e+00
  ... (remaining 1797 not shown)

  Planarity restraints: 2262
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO K 165 "    0.054 5.00e-02 4.00e+02   8.28e-02 1.10e+01
        pdb=" N   PRO K 166 "   -0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO K 166 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO K 166 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO D 165 "    0.054 5.00e-02 4.00e+02   8.28e-02 1.10e+01
        pdb=" N   PRO D 166 "   -0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO D 166 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO D 166 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO G 165 "    0.054 5.00e-02 4.00e+02   8.28e-02 1.10e+01
        pdb=" N   PRO G 166 "   -0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO G 166 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO G 166 "    0.046 5.00e-02 4.00e+02
  ... (remaining 2259 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 3648
        2.81 -     3.33: 11956
        3.33 -     3.85: 21151
        3.85 -     4.38: 24087
        4.38 -     4.90: 40105
  Nonbonded interactions: 100947
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU C  34 "
            pdb=" NH1 ARG G 182 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" OE2 GLU H  34 "
            pdb=" NH1 ARG K 182 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" NH1 ARG D 182 "
            pdb=" OE2 GLU L  34 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" N   ASP K 184 "
            pdb=" O   PRO K 204 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" N   ASP G 184 "
            pdb=" O   PRO G 204 "
     model   vdw
     2.295 3.120
  ... (remaining 100942 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 'E'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'H'
  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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.980
  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:          0.470
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     29.850
  Find NCS groups from input model:        0.480
  Set up NCS constraints:                  0.070
  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:             0.010
  Load rotamer database and sin/cos tables:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
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      :  0.007   0.057  12432  Z= 0.331
  Angle     :  1.138  15.287  16824  Z= 0.618
  Chirality :  0.073   0.455   1800
  Planarity :  0.008   0.083   2262
  Dihedral  : 13.672  77.369   4422
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 20.47
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 16.73 %
    Favored  : 83.07 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  9.62 %
    Favored  : 89.18 %
  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: -5.28 (0.16), residues: 1536
  helix: -3.58 (0.29), residues: 174
  sheet: -2.92 (0.20), residues: 462
  loop : -3.98 (0.15), residues: 900

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP K  81 
 HIS   0.006   0.001   HIS C  74 
 PHE   0.029   0.003   PHE H  76 
 TYR   0.008   0.002   TYR F 122 
 ARG   0.007   0.001   ARG J  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.28409 (  285)
  hydrogen bonds       : angle      10.76406 (  801)
  covalent geometry    : bond        0.00654 (12432)
  covalent geometry    : angle       1.13773 (16824)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  657 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 642
  time to evaluate  : 1.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 ASN cc_start: 0.7749 (t0) cc_final: 0.7520 (t0)
REVERT: A    9 LEU cc_start: 0.7887 (pp) cc_final: 0.7631 (pp)
REVERT: A   11 ILE cc_start: 0.8565 (pt) cc_final: 0.8175 (mp)
REVERT: A   24 ILE cc_start: 0.8985 (pt) cc_final: 0.8452 (tp)
REVERT: A   92 GLN cc_start: 0.8839 (tt0) cc_final: 0.8501 (tt0)
REVERT: A   93 VAL cc_start: 0.8806 (t) cc_final: 0.8604 (p)
REVERT: A  111 ASP cc_start: 0.8477 (p0) cc_final: 0.7770 (p0)
REVERT: A  124 LEU cc_start: 0.8849 (tt) cc_final: 0.8451 (tp)
REVERT: B    9 LEU cc_start: 0.8382 (pp) cc_final: 0.8083 (pt)
REVERT: B   24 ILE cc_start: 0.8751 (pt) cc_final: 0.7901 (tp)
REVERT: B   43 SER cc_start: 0.7755 (p) cc_final: 0.6658 (t)
REVERT: B   71 LYS cc_start: 0.8643 (mtmt) cc_final: 0.8365 (mtmt)
REVERT: B   85 ASP cc_start: 0.8801 (m-30) cc_final: 0.8113 (t0)
REVERT: B   91 PHE cc_start: 0.8565 (m-80) cc_final: 0.8242 (m-10)
REVERT: B   92 GLN cc_start: 0.8856 (tt0) cc_final: 0.8640 (tt0)
REVERT: B  124 LEU cc_start: 0.8916 (tt) cc_final: 0.8073 (tt)
REVERT: D   57 ASP cc_start: 0.8641 (t0) cc_final: 0.7946 (t0)
REVERT: D   66 PHE cc_start: 0.9250 (t80) cc_final: 0.8944 (t80)
REVERT: D  207 GLU cc_start: 0.7832 (pp20) cc_final: 0.7569 (pp20)
REVERT: C   37 ASN cc_start: 0.8670 (t0) cc_final: 0.7788 (t0)
REVERT: C  208 VAL cc_start: 0.8755 (t) cc_final: 0.8496 (t)
REVERT: E    9 LEU cc_start: 0.8024 (pp) cc_final: 0.7796 (pt)
REVERT: E   11 ILE cc_start: 0.8663 (pt) cc_final: 0.8385 (mp)
REVERT: E   24 ILE cc_start: 0.9031 (pt) cc_final: 0.8323 (tp)
REVERT: E   92 GLN cc_start: 0.8821 (tt0) cc_final: 0.7443 (tt0)
REVERT: E  100 ILE cc_start: 0.8046 (pt) cc_final: 0.7792 (pt)
REVERT: E  102 GLN cc_start: 0.7609 (tp-100) cc_final: 0.7313 (tp40)
REVERT: E  111 ASP cc_start: 0.8645 (p0) cc_final: 0.8311 (p0)
REVERT: E  124 LEU cc_start: 0.8907 (tt) cc_final: 0.8485 (tp)
REVERT: F    4 GLN cc_start: 0.7087 (mm-40) cc_final: 0.6839 (mp10)
REVERT: F    9 LEU cc_start: 0.8179 (pp) cc_final: 0.7848 (pt)
REVERT: F   24 ILE cc_start: 0.8729 (pt) cc_final: 0.7939 (tp)
REVERT: F   42 THR cc_start: 0.9172 (t) cc_final: 0.8941 (m)
REVERT: F   43 SER cc_start: 0.7806 (p) cc_final: 0.6740 (t)
REVERT: F   71 LYS cc_start: 0.8678 (mtmt) cc_final: 0.8235 (mtpp)
REVERT: F   77 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8327 (tp30)
REVERT: F   80 ARG cc_start: 0.8652 (tmm160) cc_final: 0.8299 (tmm160)
REVERT: F   85 ASP cc_start: 0.8621 (m-30) cc_final: 0.8175 (t0)
REVERT: F   91 PHE cc_start: 0.8534 (m-80) cc_final: 0.8079 (m-10)
REVERT: F   92 GLN cc_start: 0.8681 (tt0) cc_final: 0.8390 (tt0)
REVERT: F  124 LEU cc_start: 0.9121 (tt) cc_final: 0.8746 (tp)
REVERT: G   66 PHE cc_start: 0.9222 (t80) cc_final: 0.8848 (t80)
REVERT: G  207 GLU cc_start: 0.7829 (pp20) cc_final: 0.7624 (pp20)
REVERT: H   37 ASN cc_start: 0.8726 (t0) cc_final: 0.8219 (t0)
REVERT: I    9 LEU cc_start: 0.7889 (pp) cc_final: 0.7633 (pt)
REVERT: I   11 ILE cc_start: 0.8618 (pt) cc_final: 0.8296 (mp)
REVERT: I   24 ILE cc_start: 0.9003 (pt) cc_final: 0.8252 (tp)
REVERT: I   81 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8234 (tp40)
REVERT: I   85 ASP cc_start: 0.9045 (m-30) cc_final: 0.8324 (m-30)
REVERT: I   92 GLN cc_start: 0.8810 (tt0) cc_final: 0.7431 (tt0)
REVERT: I  102 GLN cc_start: 0.7511 (tp-100) cc_final: 0.7018 (tp40)
REVERT: I  111 ASP cc_start: 0.8464 (p0) cc_final: 0.7797 (p0)
REVERT: I  124 LEU cc_start: 0.8854 (tt) cc_final: 0.8322 (tp)
REVERT: J    8 ASP cc_start: 0.7849 (m-30) cc_final: 0.7572 (t70)
REVERT: J    9 LEU cc_start: 0.8083 (pp) cc_final: 0.7535 (pp)
REVERT: J   24 ILE cc_start: 0.8733 (pt) cc_final: 0.7897 (tp)
REVERT: J   43 SER cc_start: 0.7769 (p) cc_final: 0.6946 (t)
REVERT: J   71 LYS cc_start: 0.8519 (mtmt) cc_final: 0.8130 (mtpp)
REVERT: J   77 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8216 (tp30)
REVERT: J   80 ARG cc_start: 0.8632 (tmm160) cc_final: 0.8386 (tmm160)
REVERT: J   85 ASP cc_start: 0.8780 (m-30) cc_final: 0.8295 (t0)
REVERT: J   91 PHE cc_start: 0.8502 (m-80) cc_final: 0.7952 (m-10)
REVERT: J   92 GLN cc_start: 0.8817 (tt0) cc_final: 0.8441 (tt0)
REVERT: K   66 PHE cc_start: 0.9298 (t80) cc_final: 0.8980 (t80)
REVERT: L   37 ASN cc_start: 0.8629 (t0) cc_final: 0.8005 (t0)
REVERT: L   66 PHE cc_start: 0.9199 (t80) cc_final: 0.8908 (t80)
  outliers start: 15
  outliers final: 1
  residues processed: 653
  average time/residue: 0.2595
  time to fit residues: 233.3234
Evaluate side-chains
  441 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 440
  time to evaluate  : 1.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    3.9990
   chunk 118 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 79 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 122 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   chunk 141 optimal weight:    2.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A  20 GLN
** B  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  72 GLN
C  72 GLN
E  20 GLN
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  20 GLN
** F  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  72 GLN
H  72 GLN
I  20 GLN
** I  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  20 GLN
** J  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  72 GLN
** L  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.103385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.090126 restraints weight = 41731.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.092139 restraints weight = 24172.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.093457 restraints weight = 16016.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.4653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  12432  Z= 0.249
  Angle     :  0.881  10.243  16824  Z= 0.465
  Chirality :  0.053   0.190   1800
  Planarity :  0.010   0.128   2262
  Dihedral  :  7.674  30.502   1698
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 23.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.37 %
    Favored  : 87.63 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  6.41 %
    Favored  : 92.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.39 %
    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: -4.57 (0.18), residues: 1536
  helix: -3.07 (0.30), residues: 180
  sheet: -2.37 (0.28), residues: 318
  loop : -3.49 (0.15), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.004   TRP G  78 
 HIS   0.009   0.002   HIS L  74 
 PHE   0.023   0.003   PHE K 195 
 TYR   0.014   0.003   TYR B 112 
 ARG   0.008   0.001   ARG I  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04419 (  285)
  hydrogen bonds       : angle       7.09285 (  801)
  covalent geometry    : bond        0.00547 (12432)
  covalent geometry    : angle       0.88125 (16824)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  546 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 536
  time to evaluate  : 1.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 VAL cc_start: 0.9228 (t) cc_final: 0.8974 (p)
REVERT: A   81 GLN cc_start: 0.9069 (tp40) cc_final: 0.8277 (tp40)
REVERT: A   85 ASP cc_start: 0.8943 (m-30) cc_final: 0.8260 (m-30)
REVERT: B   77 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8841 (tp30)
REVERT: D   57 ASP cc_start: 0.8538 (t0) cc_final: 0.8227 (t0)
REVERT: D   58 ASP cc_start: 0.7390 (m-30) cc_final: 0.6692 (m-30)
REVERT: D  187 ARG cc_start: 0.8163 (ptp90) cc_final: 0.7778 (ptp-110)
REVERT: C   37 ASN cc_start: 0.8434 (t0) cc_final: 0.7830 (t0)
REVERT: C   60 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7475 (pt0)
REVERT: E   81 GLN cc_start: 0.9006 (tp40) cc_final: 0.7982 (tp40)
REVERT: E   85 ASP cc_start: 0.8915 (m-30) cc_final: 0.8422 (m-30)
REVERT: E   92 GLN cc_start: 0.8475 (tt0) cc_final: 0.8098 (tt0)
REVERT: E  100 ILE cc_start: 0.8070 (pt) cc_final: 0.7748 (pt)
REVERT: E  102 GLN cc_start: 0.8265 (tp-100) cc_final: 0.7554 (mm110)
REVERT: E  111 ASP cc_start: 0.8328 (p0) cc_final: 0.7883 (p0)
REVERT: F   71 LYS cc_start: 0.8896 (mtmt) cc_final: 0.8479 (mtpp)
REVERT: F   82 ILE cc_start: 0.9419 (tp) cc_final: 0.9215 (tp)
REVERT: F   85 ASP cc_start: 0.8776 (m-30) cc_final: 0.8154 (m-30)
REVERT: F   88 VAL cc_start: 0.8937 (m) cc_final: 0.8724 (p)
REVERT: G   56 LEU cc_start: 0.9360 (mm) cc_final: 0.9147 (mm)
REVERT: H   11 ASN cc_start: 0.8505 (t0) cc_final: 0.8149 (t0)
REVERT: H   37 ASN cc_start: 0.8379 (t0) cc_final: 0.7752 (t0)
REVERT: H   60 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7529 (pt0)
REVERT: H  187 ARG cc_start: 0.8519 (ptp90) cc_final: 0.8184 (ptp90)
REVERT: I   78 ARG cc_start: 0.8675 (tpt-90) cc_final: 0.8413 (tpt-90)
REVERT: I  102 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7881 (mm110)
REVERT: I  106 MET cc_start: 0.7612 (ptp) cc_final: 0.7272 (ptp)
REVERT: I  111 ASP cc_start: 0.8299 (p0) cc_final: 0.7990 (p0)
REVERT: J   35 ASN cc_start: 0.9171 (m-40) cc_final: 0.8773 (m-40)
REVERT: J   98 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.6802 (m-10)
REVERT: L   37 ASN cc_start: 0.8409 (t0) cc_final: 0.8113 (t0)
REVERT: L  193 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8223 (pt0)
  outliers start: 10
  outliers final: 0
  residues processed: 545
  average time/residue: 0.2544
  time to fit residues: 192.9243
Evaluate side-chains
  401 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 400
  time to evaluate  : 1.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   chunk 43 optimal weight:    4.9990
   chunk 113 optimal weight:    0.8980
   chunk 155 optimal weight:    1.9990
   chunk 70 optimal weight:    9.9990
   chunk 97 optimal weight:    0.9980
   chunk 129 optimal weight:    6.9990
   chunk 114 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A  20 GLN
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 116 HIS
B  20 GLN
** B  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 116 HIS
** D  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 167 GLN
** C  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  20 GLN
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 116 HIS
F  20 GLN
** F  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 116 HIS
G 167 GLN
I  20 GLN
** I  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 102 GLN
I 116 HIS
J  20 GLN
** J  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 116 HIS
K 193 GLN
** L  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.100129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.086578 restraints weight = 42651.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.088457 restraints weight = 25061.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.089759 restraints weight = 16863.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.6007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  12432  Z= 0.223
  Angle     :  0.841   8.732  16824  Z= 0.444
  Chirality :  0.052   0.197   1800
  Planarity :  0.008   0.074   2262
  Dihedral  :  7.390  31.335   1698
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 24.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.35 %
    Favored  : 86.65 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  8.81 %
    Favored  : 90.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    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: -4.39 (0.18), residues: 1536
  helix: -2.69 (0.30), residues: 180
  sheet: -2.53 (0.22), residues: 402
  loop : -3.29 (0.17), residues: 954

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP L  78 
 HIS   0.009   0.002   HIS L  74 
 PHE   0.044   0.003   PHE C 195 
 TYR   0.024   0.002   TYR G  47 
 ARG   0.010   0.001   ARG A  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04413 (  285)
  hydrogen bonds       : angle       6.63210 (  801)
  covalent geometry    : bond        0.00497 (12432)
  covalent geometry    : angle       0.84072 (16824)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  504 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 496
  time to evaluate  : 1.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 VAL cc_start: 0.9370 (t) cc_final: 0.9143 (p)
REVERT: A   53 LEU cc_start: 0.9209 (mm) cc_final: 0.8994 (mp)
REVERT: A   81 GLN cc_start: 0.9110 (tp40) cc_final: 0.8388 (tp40)
REVERT: A   85 ASP cc_start: 0.9054 (m-30) cc_final: 0.8418 (m-30)
REVERT: B   77 GLU cc_start: 0.9178 (tm-30) cc_final: 0.8952 (tp30)
REVERT: B   82 ILE cc_start: 0.9422 (tp) cc_final: 0.8642 (pt)
REVERT: D  187 ARG cc_start: 0.8088 (ptp90) cc_final: 0.7854 (ptp-170)
REVERT: C   60 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7909 (pt0)
REVERT: E    5 ASN cc_start: 0.8317 (t0) cc_final: 0.8102 (t0)
REVERT: E   81 GLN cc_start: 0.9042 (tp40) cc_final: 0.8285 (tp40)
REVERT: E   92 GLN cc_start: 0.8484 (tt0) cc_final: 0.8181 (tt0)
REVERT: E  102 GLN cc_start: 0.8328 (tp-100) cc_final: 0.7718 (mm110)
REVERT: F   71 LYS cc_start: 0.8960 (mtmt) cc_final: 0.8514 (mtpp)
REVERT: F   82 ILE cc_start: 0.9399 (tp) cc_final: 0.8985 (tp)
REVERT: F   85 ASP cc_start: 0.8752 (m-30) cc_final: 0.8328 (t0)
REVERT: H   37 ASN cc_start: 0.7966 (t0) cc_final: 0.7750 (t0)
REVERT: H   60 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7700 (pt0)
REVERT: H   67 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7253 (tm-30)
REVERT: H  186 ASP cc_start: 0.7887 (p0) cc_final: 0.7630 (p0)
REVERT: I   92 GLN cc_start: 0.8275 (tt0) cc_final: 0.7038 (tt0)
REVERT: I  102 GLN cc_start: 0.8510 (tp40) cc_final: 0.7859 (tp40)
REVERT: J   35 ASN cc_start: 0.9193 (m-40) cc_final: 0.8687 (m-40)
REVERT: K   54 ARG cc_start: 0.7239 (pmt170) cc_final: 0.6990 (pmt-80)
REVERT: L   21 GLU cc_start: 0.7649 (mt-10) cc_final: 0.6290 (mt-10)
REVERT: L   67 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7358 (tm-30)
  outliers start: 8
  outliers final: 1
  residues processed: 503
  average time/residue: 0.2295
  time to fit residues: 164.3801
Evaluate side-chains
  384 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 383
  time to evaluate  : 1.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 73 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 134 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0470
   chunk 122 optimal weight:    2.9990
   chunk 85 optimal weight:    0.5980
   chunk 124 optimal weight:    0.5980
   chunk 93 optimal weight:    4.9990
   overall best weight:    1.8482

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

Flipped N/Q/H residues before XYZ refinement:
A  20 GLN
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  20 GLN
** B  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 193 GLN
** C  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  20 GLN
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  20 GLN
** F  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 167 GLN
I  20 GLN
** I  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  20 GLN
** J  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 167 GLN
K 193 GLN
** L  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.098507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.082984 restraints weight = 40382.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.085161 restraints weight = 23049.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.086647 restraints weight = 15294.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.6613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  12432  Z= 0.212
  Angle     :  0.848   8.837  16824  Z= 0.445
  Chirality :  0.053   0.208   1800
  Planarity :  0.007   0.065   2262
  Dihedral  :  7.345  29.551   1698
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 22.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.09 %
    Favored  : 86.91 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  6.89 %
    Favored  : 92.39 %
  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: -4.31 (0.18), residues: 1536
  helix: -2.52 (0.31), residues: 186
  sheet: -2.51 (0.23), residues: 402
  loop : -3.24 (0.17), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C  78 
 HIS   0.008   0.002   HIS C  74 
 PHE   0.038   0.003   PHE D  76 
 TYR   0.013   0.002   TYR E 122 
 ARG   0.009   0.001   ARG C  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04247 (  285)
  hydrogen bonds       : angle       6.50705 (  801)
  covalent geometry    : bond        0.00473 (12432)
  covalent geometry    : angle       0.84770 (16824)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  491 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 482
  time to evaluate  : 1.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 ASN cc_start: 0.9205 (m-40) cc_final: 0.8532 (p0)
REVERT: A   41 VAL cc_start: 0.9235 (t) cc_final: 0.9009 (p)
REVERT: A   82 ILE cc_start: 0.9253 (tp) cc_final: 0.8955 (tp)
REVERT: A   85 ASP cc_start: 0.9015 (m-30) cc_final: 0.8541 (m-30)
REVERT: B   77 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8880 (tp30)
REVERT: B   85 ASP cc_start: 0.8784 (t0) cc_final: 0.8414 (t0)
REVERT: B  111 ASP cc_start: 0.8794 (p0) cc_final: 0.8296 (p0)
REVERT: D   23 ARG cc_start: 0.7458 (tpp-160) cc_final: 0.7253 (tpp-160)
REVERT: D   57 ASP cc_start: 0.8805 (t0) cc_final: 0.8349 (t0)
REVERT: D   58 ASP cc_start: 0.8133 (m-30) cc_final: 0.7773 (m-30)
REVERT: C   53 LEU cc_start: 0.7612 (mt) cc_final: 0.6528 (mt)
REVERT: C   60 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7539 (mt-10)
REVERT: C  193 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8453 (mp10)
REVERT: E   31 ARG cc_start: 0.8260 (ttt90) cc_final: 0.7936 (tpt-90)
REVERT: E   35 ASN cc_start: 0.8992 (m-40) cc_final: 0.8670 (p0)
REVERT: E   81 GLN cc_start: 0.9248 (tp40) cc_final: 0.8825 (tp40)
REVERT: E  102 GLN cc_start: 0.8510 (tp-100) cc_final: 0.8048 (mm110)
REVERT: F   71 LYS cc_start: 0.8946 (mtmt) cc_final: 0.8458 (mtpp)
REVERT: F   80 ARG cc_start: 0.9117 (tmm160) cc_final: 0.8453 (tmm160)
REVERT: F   85 ASP cc_start: 0.8922 (m-30) cc_final: 0.8509 (t0)
REVERT: G    8 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7526 (m-80)
REVERT: G   69 ARG cc_start: 0.7217 (ptp90) cc_final: 0.6991 (ptp90)
REVERT: H   69 ARG cc_start: 0.7103 (ptp90) cc_final: 0.6836 (ptp90)
REVERT: H  186 ASP cc_start: 0.8189 (p0) cc_final: 0.7554 (p0)
REVERT: I   78 ARG cc_start: 0.8760 (tpt-90) cc_final: 0.8517 (tpt-90)
REVERT: I   85 ASP cc_start: 0.9197 (m-30) cc_final: 0.8860 (m-30)
REVERT: J   35 ASN cc_start: 0.9283 (m-40) cc_final: 0.8955 (m110)
REVERT: J   77 GLU cc_start: 0.8880 (tp30) cc_final: 0.8370 (tp30)
REVERT: J   80 ARG cc_start: 0.8551 (tmm160) cc_final: 0.7446 (tmm160)
REVERT: J   82 ILE cc_start: 0.9243 (tp) cc_final: 0.8764 (tp)
REVERT: J  107 ILE cc_start: 0.9543 (tt) cc_final: 0.9205 (tt)
REVERT: J  111 ASP cc_start: 0.8866 (p0) cc_final: 0.8327 (p0)
REVERT: L    8 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8175 (m-80)
REVERT: L   53 LEU cc_start: 0.7342 (mt) cc_final: 0.6111 (mt)
REVERT: L   57 ASP cc_start: 0.9001 (t0) cc_final: 0.8655 (t0)
  outliers start: 9
  outliers final: 0
  residues processed: 490
  average time/residue: 0.2544
  time to fit residues: 175.3091
Evaluate side-chains
  354 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 352
  time to evaluate  : 1.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 137 optimal weight:    6.9990
   chunk 98 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 116 optimal weight:    0.0060
   chunk 40 optimal weight:    4.9990
   chunk 151 optimal weight:    2.9990
   chunk 88 optimal weight:    0.6980
   chunk 145 optimal weight:    4.9990
   chunk 124 optimal weight:    1.9990
   overall best weight:    1.1402

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

Flipped N/Q/H residues before XYZ refinement:
A  20 GLN
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  20 GLN
** B  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 193 GLN
E  20 GLN
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  20 GLN
** F  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 167 GLN
I  20 GLN
** I  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  20 GLN
** J  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  72 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.102008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.087885 restraints weight = 41711.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.089921 restraints weight = 24812.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.091301 restraints weight = 16669.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.6920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12432  Z= 0.174
  Angle     :  0.842   8.958  16824  Z= 0.438
  Chirality :  0.052   0.204   1800
  Planarity :  0.007   0.060   2262
  Dihedral  :  7.155  29.056   1698
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 22.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.35 %
    Favored  : 86.65 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  4.17 %
    Favored  : 95.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.14 (0.18), residues: 1536
  helix: -2.20 (0.32), residues: 180
  sheet: -2.26 (0.25), residues: 366
  loop : -3.24 (0.17), residues: 990

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP L  78 
 HIS   0.008   0.002   HIS L  74 
 PHE   0.031   0.002   PHE D  76 
 TYR   0.011   0.002   TYR E 122 
 ARG   0.011   0.001   ARG C  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04242 (  285)
  hydrogen bonds       : angle       6.24078 (  801)
  covalent geometry    : bond        0.00395 (12432)
  covalent geometry    : angle       0.84234 (16824)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  463 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 456
  time to evaluate  : 1.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 ASN cc_start: 0.9028 (m-40) cc_final: 0.8545 (p0)
REVERT: A  107 ILE cc_start: 0.9374 (tt) cc_final: 0.9145 (tt)
REVERT: A  111 ASP cc_start: 0.8366 (p0) cc_final: 0.7879 (p0)
REVERT: B  111 ASP cc_start: 0.8692 (p0) cc_final: 0.8153 (p0)
REVERT: D  193 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8145 (pm20)
REVERT: C   56 LEU cc_start: 0.9345 (mm) cc_final: 0.9069 (mm)
REVERT: C   60 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7358 (mt-10)
REVERT: E   35 ASN cc_start: 0.8857 (m-40) cc_final: 0.8650 (p0)
REVERT: E   81 GLN cc_start: 0.9036 (tp40) cc_final: 0.8369 (tp40)
REVERT: E   85 ASP cc_start: 0.8869 (m-30) cc_final: 0.8607 (m-30)
REVERT: E  102 GLN cc_start: 0.8606 (tp-100) cc_final: 0.8202 (mm110)
REVERT: F   71 LYS cc_start: 0.9031 (mtmt) cc_final: 0.8522 (mtpp)
REVERT: F   87 GLU cc_start: 0.8036 (pm20) cc_final: 0.7751 (pm20)
REVERT: G   69 ARG cc_start: 0.7196 (ptp90) cc_final: 0.6837 (ptp90)
REVERT: G  193 GLN cc_start: 0.8633 (mp10) cc_final: 0.8335 (pt0)
REVERT: H   69 ARG cc_start: 0.7108 (ptp90) cc_final: 0.6710 (ptp90)
REVERT: H  186 ASP cc_start: 0.8126 (p0) cc_final: 0.7200 (p0)
REVERT: I   78 ARG cc_start: 0.8650 (tpt-90) cc_final: 0.8377 (tpt-90)
REVERT: I   92 GLN cc_start: 0.8204 (tt0) cc_final: 0.6825 (tt0)
REVERT: I  100 ILE cc_start: 0.8090 (pt) cc_final: 0.7606 (pt)
REVERT: I  102 GLN cc_start: 0.8505 (tp40) cc_final: 0.7825 (tp40)
REVERT: J   35 ASN cc_start: 0.9170 (m-40) cc_final: 0.8489 (m-40)
REVERT: J   80 ARG cc_start: 0.8310 (tmm160) cc_final: 0.7703 (ttp80)
REVERT: J   82 ILE cc_start: 0.9159 (tp) cc_final: 0.8835 (tp)
REVERT: J  107 ILE cc_start: 0.9416 (tt) cc_final: 0.9072 (tt)
REVERT: L   57 ASP cc_start: 0.8807 (t0) cc_final: 0.8482 (t0)
  outliers start: 7
  outliers final: 0
  residues processed: 462
  average time/residue: 0.2247
  time to fit residues: 149.2895
Evaluate side-chains
  353 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 352
  time to evaluate  : 1.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 83 optimal weight:    0.5980
   chunk 10 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 52 optimal weight:   10.0000
   chunk 80 optimal weight:    2.9990
   chunk 155 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
A  20 GLN
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  20 GLN
** B  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  20 GLN
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  20 GLN
** F  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  20 GLN
I  92 GLN
J  20 GLN
** J  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.100143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.086427 restraints weight = 42925.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.088309 restraints weight = 25811.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.089540 restraints weight = 17497.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.7250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12432  Z= 0.218
  Angle     :  0.868   8.651  16824  Z= 0.454
  Chirality :  0.053   0.209   1800
  Planarity :  0.007   0.062   2262
  Dihedral  :  7.251  34.632   1698
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 24.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.71 %
    Favored  : 85.29 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  4.41 %
    Favored  : 95.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.39 %
    Twisted General : 0.07 %

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: -4.08 (0.18), residues: 1536
  helix: -2.25 (0.32), residues: 186
  sheet: -2.44 (0.25), residues: 360
  loop : -3.08 (0.17), residues: 990

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP H  78 
 HIS   0.008   0.002   HIS C  74 
 PHE   0.041   0.003   PHE K  76 
 TYR   0.015   0.002   TYR C  47 
 ARG   0.004   0.001   ARG L  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04252 (  285)
  hydrogen bonds       : angle       6.22188 (  801)
  covalent geometry    : bond        0.00492 (12432)
  covalent geometry    : angle       0.86779 (16824)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  437 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 431
  time to evaluate  : 1.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 ASN cc_start: 0.8978 (m-40) cc_final: 0.8640 (p0)
REVERT: A  111 ASP cc_start: 0.8340 (p0) cc_final: 0.8120 (p0)
REVERT: B   77 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8848 (tp30)
REVERT: B  111 ASP cc_start: 0.8672 (p0) cc_final: 0.8291 (p0)
REVERT: C    6 VAL cc_start: 0.7471 (p) cc_final: 0.7182 (t)
REVERT: C   60 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7353 (mt-10)
REVERT: C  193 GLN cc_start: 0.8444 (mp10) cc_final: 0.8198 (pt0)
REVERT: E    5 ASN cc_start: 0.8279 (t0) cc_final: 0.8073 (t0)
REVERT: E   81 GLN cc_start: 0.9049 (tp40) cc_final: 0.8504 (tp40)
REVERT: E   82 ILE cc_start: 0.9213 (tp) cc_final: 0.8888 (tp)
REVERT: E   85 ASP cc_start: 0.9075 (m-30) cc_final: 0.8654 (m-30)
REVERT: F   71 LYS cc_start: 0.9048 (mtmt) cc_final: 0.8534 (mtpp)
REVERT: I   82 ILE cc_start: 0.9350 (pt) cc_final: 0.8754 (pt)
REVERT: I   85 ASP cc_start: 0.8953 (m-30) cc_final: 0.8668 (m-30)
REVERT: I  100 ILE cc_start: 0.8175 (pt) cc_final: 0.7923 (pt)
REVERT: I  102 GLN cc_start: 0.8541 (tp40) cc_final: 0.8247 (tp40)
REVERT: J   35 ASN cc_start: 0.8965 (m-40) cc_final: 0.8737 (m-40)
REVERT: J   82 ILE cc_start: 0.9164 (tp) cc_final: 0.8859 (tp)
REVERT: J  107 ILE cc_start: 0.9424 (tt) cc_final: 0.9125 (tt)
REVERT: J  132 LEU cc_start: 0.8370 (mt) cc_final: 0.8157 (mt)
REVERT: L   57 ASP cc_start: 0.8760 (t0) cc_final: 0.8395 (t0)
REVERT: L   67 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7428 (tm-30)
REVERT: L   69 ARG cc_start: 0.7292 (ptp90) cc_final: 0.6852 (ptp90)
  outliers start: 6
  outliers final: 0
  residues processed: 437
  average time/residue: 0.2332
  time to fit residues: 147.1394
Evaluate side-chains
  350 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 350
  time to evaluate  : 1.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 87 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 40 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 29 optimal weight:    0.2980
   chunk 33 optimal weight:    4.9990
   chunk 151 optimal weight:    4.9990
   chunk 121 optimal weight:    8.9990
   chunk 133 optimal weight:    0.0970
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A  20 GLN
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  20 GLN
** B  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  11 ASN
C  74 HIS
E  20 GLN
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  20 GLN
** F  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 193 GLN
H  11 ASN
I  20 GLN
J  20 GLN
** J  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.100135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.085742 restraints weight = 42957.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.087722 restraints weight = 25027.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.089143 restraints weight = 16714.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.7434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12432  Z= 0.202
  Angle     :  0.893  10.346  16824  Z= 0.462
  Chirality :  0.054   0.219   1800
  Planarity :  0.007   0.072   2262
  Dihedral  :  7.085  32.806   1698
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 24.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.61 %
    Favored  : 86.39 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  3.69 %
    Favored  : 95.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.39 %
    Twisted General : 0.07 %

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: -4.13 (0.18), residues: 1536
  helix: -2.19 (0.33), residues: 186
  sheet: -2.20 (0.27), residues: 294
  loop : -3.24 (0.16), residues: 1056

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP K  78 
 HIS   0.008   0.002   HIS H  74 
 PHE   0.039   0.002   PHE H  76 
 TYR   0.013   0.002   TYR C  47 
 ARG   0.008   0.001   ARG J  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04317 (  285)
  hydrogen bonds       : angle       6.11291 (  801)
  covalent geometry    : bond        0.00457 (12432)
  covalent geometry    : angle       0.89331 (16824)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  438 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 432
  time to evaluate  : 1.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 ASN cc_start: 0.8936 (m-40) cc_final: 0.8588 (p0)
REVERT: B  111 ASP cc_start: 0.8687 (p0) cc_final: 0.8236 (p0)
REVERT: C    6 VAL cc_start: 0.7226 (p) cc_final: 0.6996 (t)
REVERT: C   60 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7314 (mt-10)
REVERT: C  193 GLN cc_start: 0.8553 (mp10) cc_final: 0.8311 (pm20)
REVERT: C  202 GLN cc_start: 0.8533 (pm20) cc_final: 0.8242 (pm20)
REVERT: E   31 ARG cc_start: 0.8205 (ttt90) cc_final: 0.7718 (tpt-90)
REVERT: E   34 PHE cc_start: 0.9200 (m-10) cc_final: 0.8975 (m-10)
REVERT: E   81 GLN cc_start: 0.9037 (tp40) cc_final: 0.8477 (tp40)
REVERT: E   85 ASP cc_start: 0.9073 (m-30) cc_final: 0.8783 (m-30)
REVERT: E  132 LEU cc_start: 0.8555 (mm) cc_final: 0.8274 (mt)
REVERT: F   71 LYS cc_start: 0.9047 (mtmt) cc_final: 0.8522 (mtpp)
REVERT: F   85 ASP cc_start: 0.8838 (t0) cc_final: 0.8545 (t0)
REVERT: G   69 ARG cc_start: 0.7367 (ptp90) cc_final: 0.6576 (ptp90)
REVERT: I   82 ILE cc_start: 0.9465 (pt) cc_final: 0.9256 (pt)
REVERT: I   85 ASP cc_start: 0.9082 (m-30) cc_final: 0.8703 (m-30)
REVERT: I   92 GLN cc_start: 0.7910 (tt0) cc_final: 0.6654 (tt0)
REVERT: I  100 ILE cc_start: 0.7961 (pt) cc_final: 0.7306 (pt)
REVERT: I  102 GLN cc_start: 0.8711 (tp40) cc_final: 0.7984 (tp40)
REVERT: J   82 ILE cc_start: 0.9129 (tp) cc_final: 0.8766 (tp)
REVERT: J  107 ILE cc_start: 0.9347 (tt) cc_final: 0.9098 (tt)
REVERT: J  111 ASP cc_start: 0.8658 (p0) cc_final: 0.8164 (p0)
REVERT: L   69 ARG cc_start: 0.7240 (ptp90) cc_final: 0.6874 (ptp90)
  outliers start: 6
  outliers final: 0
  residues processed: 438
  average time/residue: 0.2282
  time to fit residues: 144.6131
Evaluate side-chains
  351 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 351
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 114 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 143 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 90 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 125 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 112 optimal weight:    6.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
A  20 GLN
** A  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  20 GLN
** B  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  20 GLN
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  20 GLN
** F  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  20 GLN
J  20 GLN
** J  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.100055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.086133 restraints weight = 42534.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.088109 restraints weight = 24621.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.089495 restraints weight = 16421.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.7662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  12432  Z= 0.199
  Angle     :  0.903  11.652  16824  Z= 0.465
  Chirality :  0.055   0.235   1800
  Planarity :  0.007   0.086   2262
  Dihedral  :  7.073  31.010   1698
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 23.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.93 %
    Favored  : 86.07 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  1.76 %
    Favored  : 97.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.39 %
    Twisted General : 0.07 %

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: -3.97 (0.18), residues: 1536
  helix: -1.66 (0.38), residues: 150
  sheet: -2.03 (0.23), residues: 366
  loop : -3.23 (0.17), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP L  78 
 HIS   0.008   0.002   HIS L  74 
 PHE   0.040   0.002   PHE G  76 
 TYR   0.013   0.002   TYR C  47 
 ARG   0.008   0.001   ARG H  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04223 (  285)
  hydrogen bonds       : angle       6.07704 (  801)
  covalent geometry    : bond        0.00455 (12432)
  covalent geometry    : angle       0.90267 (16824)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  434 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 428
  time to evaluate  : 1.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 ASN cc_start: 0.8885 (m-40) cc_final: 0.8622 (p0)
REVERT: A  132 LEU cc_start: 0.8307 (mm) cc_final: 0.7953 (mt)
REVERT: B   63 SER cc_start: 0.9452 (m) cc_final: 0.8956 (p)
REVERT: B   77 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8823 (tp30)
REVERT: B   85 ASP cc_start: 0.8825 (t0) cc_final: 0.8161 (t0)
REVERT: C    6 VAL cc_start: 0.7133 (p) cc_final: 0.6887 (t)
REVERT: C   60 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7382 (mt-10)
REVERT: C  202 GLN cc_start: 0.8510 (pm20) cc_final: 0.8235 (pm20)
REVERT: E   81 GLN cc_start: 0.9004 (tp40) cc_final: 0.8478 (tp40)
REVERT: E   82 ILE cc_start: 0.9452 (tp) cc_final: 0.9152 (tp)
REVERT: E  132 LEU cc_start: 0.8536 (mm) cc_final: 0.8236 (mt)
REVERT: F   52 GLU cc_start: 0.7470 (mp0) cc_final: 0.7267 (mp0)
REVERT: F   71 LYS cc_start: 0.9059 (mtmt) cc_final: 0.8560 (mtpp)
REVERT: H  193 GLN cc_start: 0.8429 (mp10) cc_final: 0.8183 (pt0)
REVERT: I   82 ILE cc_start: 0.9418 (pt) cc_final: 0.9187 (pt)
REVERT: I   85 ASP cc_start: 0.9003 (m-30) cc_final: 0.8683 (m-30)
REVERT: I   92 GLN cc_start: 0.7825 (tt0) cc_final: 0.6480 (tt0)
REVERT: I  100 ILE cc_start: 0.8027 (pt) cc_final: 0.7489 (pt)
REVERT: I  102 GLN cc_start: 0.8723 (tp40) cc_final: 0.8150 (tp40)
REVERT: J   82 ILE cc_start: 0.9120 (tp) cc_final: 0.8802 (tp)
REVERT: J   92 GLN cc_start: 0.8216 (tt0) cc_final: 0.7818 (tt0)
REVERT: J  102 GLN cc_start: 0.8768 (tp40) cc_final: 0.7166 (tp40)
REVERT: K   56 LEU cc_start: 0.9305 (mm) cc_final: 0.8988 (mm)
REVERT: L   67 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7371 (tm-30)
REVERT: L  193 GLN cc_start: 0.8451 (mp10) cc_final: 0.8225 (pt0)
  outliers start: 6
  outliers final: 0
  residues processed: 434
  average time/residue: 0.2451
  time to fit residues: 154.9695
Evaluate side-chains
  348 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 348
  time to evaluate  : 1.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 83 optimal weight:    0.9990
   chunk 120 optimal weight:    1.9990
   chunk 144 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 75 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 63 optimal weight:    7.9990
   chunk 153 optimal weight:    0.9980
   chunk 139 optimal weight:    1.9990
   chunk 90 optimal weight:    0.7980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A  20 GLN
B  20 GLN
B  92 GLN
C  11 ASN
E  20 GLN
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  20 GLN
** F  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  20 GLN
J  20 GLN
** J  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.101233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.087088 restraints weight = 42313.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.089064 restraints weight = 25052.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.090457 restraints weight = 16902.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.7780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12432  Z= 0.188
  Angle     :  0.928  14.260  16824  Z= 0.473
  Chirality :  0.055   0.227   1800
  Planarity :  0.007   0.069   2262
  Dihedral  :  6.964  30.709   1698
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 24.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.87 %
    Favored  : 86.13 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  0.96 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.39 %
    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: -3.96 (0.18), residues: 1536
  helix: -1.72 (0.38), residues: 150
  sheet: -2.09 (0.23), residues: 372
  loop : -3.19 (0.17), residues: 1014

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP G  78 
 HIS   0.008   0.002   HIS H  74 
 PHE   0.037   0.002   PHE K  76 
 TYR   0.014   0.002   TYR C  47 
 ARG   0.008   0.001   ARG A  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03980 (  285)
  hydrogen bonds       : angle       5.98810 (  801)
  covalent geometry    : bond        0.00426 (12432)
  covalent geometry    : angle       0.92789 (16824)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  433 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 427
  time to evaluate  : 1.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 ASN cc_start: 0.8873 (m-40) cc_final: 0.8643 (p0)
REVERT: A  132 LEU cc_start: 0.8272 (mm) cc_final: 0.7860 (mt)
REVERT: B   63 SER cc_start: 0.9427 (m) cc_final: 0.8936 (p)
REVERT: B   85 ASP cc_start: 0.8850 (t0) cc_final: 0.8133 (t0)
REVERT: C   60 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7255 (mt-10)
REVERT: C  202 GLN cc_start: 0.8473 (pm20) cc_final: 0.8232 (pm20)
REVERT: E    5 ASN cc_start: 0.8173 (t0) cc_final: 0.7973 (t0)
REVERT: E   82 ILE cc_start: 0.9379 (tp) cc_final: 0.8633 (tp)
REVERT: E  102 GLN cc_start: 0.8586 (mm110) cc_final: 0.8271 (mm110)
REVERT: E  132 LEU cc_start: 0.8514 (mm) cc_final: 0.8121 (mt)
REVERT: F   52 GLU cc_start: 0.7439 (mp0) cc_final: 0.7204 (mp0)
REVERT: G   57 ASP cc_start: 0.8773 (t0) cc_final: 0.8541 (t0)
REVERT: G   69 ARG cc_start: 0.7284 (ptp90) cc_final: 0.6628 (ptp90)
REVERT: I   30 THR cc_start: 0.9082 (m) cc_final: 0.8859 (t)
REVERT: I   85 ASP cc_start: 0.8956 (m-30) cc_final: 0.8656 (m-30)
REVERT: I   92 GLN cc_start: 0.7915 (tt0) cc_final: 0.7272 (tt0)
REVERT: I  102 GLN cc_start: 0.8758 (tp40) cc_final: 0.7350 (tp40)
REVERT: J   82 ILE cc_start: 0.9163 (tp) cc_final: 0.8883 (tp)
REVERT: K   63 ILE cc_start: 0.9670 (pt) cc_final: 0.9339 (mt)
REVERT: L   11 ASN cc_start: 0.8775 (t0) cc_final: 0.8188 (t0)
REVERT: L   56 LEU cc_start: 0.9408 (mm) cc_final: 0.9173 (mm)
REVERT: L   69 ARG cc_start: 0.7361 (ptp90) cc_final: 0.6555 (ptp90)
REVERT: L  193 GLN cc_start: 0.8459 (mp10) cc_final: 0.8140 (pt0)
  outliers start: 6
  outliers final: 0
  residues processed: 433
  average time/residue: 0.2218
  time to fit residues: 138.4457
Evaluate side-chains
  348 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 348
  time to evaluate  : 1.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 3 optimal weight:    0.2980
   chunk 146 optimal weight:    0.0070
   chunk 2 optimal weight:    6.9990
   chunk 41 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9980
   chunk 98 optimal weight:    5.9990
   chunk 131 optimal weight:    0.7980
   chunk 104 optimal weight:    8.9990
   chunk 118 optimal weight:    0.9980
   chunk 119 optimal weight:    1.9990
   chunk 121 optimal weight:    2.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
A  20 GLN
B  20 GLN
B  92 GLN
** D  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  11 ASN
E  20 GLN
E  92 GLN
F  20 GLN
** F  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  20 GLN
J  20 GLN
** J  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.104206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.090258 restraints weight = 42052.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.092307 restraints weight = 24513.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.093727 restraints weight = 16448.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.7991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12432  Z= 0.162
  Angle     :  0.924  16.236  16824  Z= 0.468
  Chirality :  0.054   0.245   1800
  Planarity :  0.007   0.064   2262
  Dihedral  :  6.706  30.432   1698
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 21.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.17 %
    Favored  : 87.83 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  0.40 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.39 %
    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: -3.86 (0.18), residues: 1536
  helix: -1.55 (0.39), residues: 150
  sheet: -1.96 (0.23), residues: 372
  loop : -3.17 (0.16), residues: 1014

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP D  40 
 HIS   0.007   0.001   HIS L  74 
 PHE   0.036   0.002   PHE K  76 
 TYR   0.011   0.002   TYR C  47 
 ARG   0.009   0.001   ARG G  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03986 (  285)
  hydrogen bonds       : angle       5.80978 (  801)
  covalent geometry    : bond        0.00363 (12432)
  covalent geometry    : angle       0.92362 (16824)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  432 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 426
  time to evaluate  : 1.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 LEU cc_start: 0.8249 (mm) cc_final: 0.7608 (mt)
REVERT: B   63 SER cc_start: 0.9424 (m) cc_final: 0.8924 (p)
REVERT: B   85 ASP cc_start: 0.8797 (t0) cc_final: 0.8086 (t0)
REVERT: C   56 LEU cc_start: 0.9287 (mm) cc_final: 0.9081 (mm)
REVERT: C   60 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7245 (mt-10)
REVERT: C  202 GLN cc_start: 0.8598 (pm20) cc_final: 0.8338 (pm20)
REVERT: E   85 ASP cc_start: 0.9100 (m-30) cc_final: 0.8860 (m-30)
REVERT: E  132 LEU cc_start: 0.8465 (mm) cc_final: 0.8119 (mt)
REVERT: F   92 GLN cc_start: 0.7730 (tt0) cc_final: 0.7425 (tm-30)
REVERT: G   11 ASN cc_start: 0.7992 (t0) cc_final: 0.7732 (t0)
REVERT: G   69 ARG cc_start: 0.7180 (ptp90) cc_final: 0.6606 (ptp90)
REVERT: H   25 GLU cc_start: 0.8417 (pm20) cc_final: 0.8198 (pm20)
REVERT: H   69 ARG cc_start: 0.7091 (ptp90) cc_final: 0.5983 (ptp90)
REVERT: I   92 GLN cc_start: 0.7655 (tt0) cc_final: 0.6292 (tt0)
REVERT: I  100 ILE cc_start: 0.7848 (pt) cc_final: 0.7169 (pt)
REVERT: I  102 GLN cc_start: 0.8679 (tp40) cc_final: 0.7993 (tp40)
REVERT: J   63 SER cc_start: 0.9359 (m) cc_final: 0.8933 (p)
REVERT: J   82 ILE cc_start: 0.9102 (tp) cc_final: 0.8868 (tp)
REVERT: J   92 GLN cc_start: 0.8101 (tt0) cc_final: 0.7848 (tt0)
REVERT: J  102 GLN cc_start: 0.8814 (tp40) cc_final: 0.7196 (tp40)
REVERT: L   11 ASN cc_start: 0.8763 (t0) cc_final: 0.8191 (t0)
REVERT: L   56 LEU cc_start: 0.9378 (mm) cc_final: 0.9152 (mm)
REVERT: L  193 GLN cc_start: 0.8447 (mp10) cc_final: 0.7997 (pm20)
  outliers start: 6
  outliers final: 0
  residues processed: 432
  average time/residue: 0.2206
  time to fit residues: 138.3670
Evaluate side-chains
  349 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 349
  time to evaluate  : 1.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 60 optimal weight:    0.0980
   chunk 16 optimal weight:    9.9990
   chunk 67 optimal weight:    0.9980
   chunk 113 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 128 optimal weight:    1.9990
   chunk 107 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9980
   chunk 127 optimal weight:    5.9990
   chunk 138 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
A  20 GLN
B  20 GLN
B  92 GLN
D   4 HIS
** D  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  20 GLN
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  20 GLN
** F  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 196 GLN
I  20 GLN
J  20 GLN
** J  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.101198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.086957 restraints weight = 42394.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.088915 restraints weight = 25136.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.090234 restraints weight = 16977.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.8080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  12432  Z= 0.204
  Angle     :  0.933  16.197  16824  Z= 0.479
  Chirality :  0.054   0.227   1800
  Planarity :  0.007   0.073   2262
  Dihedral  :  6.828  30.258   1698
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 24.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.15 %
    Favored  : 86.85 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  0.88 %
    Favored  : 98.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.39 %
    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: -3.88 (0.18), residues: 1536
  helix: -1.57 (0.40), residues: 150
  sheet: -1.95 (0.23), residues: 366
  loop : -3.19 (0.17), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D  40 
 HIS   0.008   0.002   HIS H  74 
 PHE   0.055   0.003   PHE D  76 
 TYR   0.012   0.002   TYR C  47 
 ARG   0.008   0.001   ARG A  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04068 (  285)
  hydrogen bonds       : angle       6.06144 (  801)
  covalent geometry    : bond        0.00465 (12432)
  covalent geometry    : angle       0.93279 (16824)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4368.20 seconds
wall clock time: 76 minutes 6.63 seconds (4566.63 seconds total)