Starting phenix.real_space_refine
on Wed Mar  4 07:53:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6teb_10479/03_2026/6teb_10479.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6teb_10479/03_2026/6teb_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6teb_10479/03_2026/6teb_10479.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6teb_10479/03_2026/6teb_10479.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6teb_10479/03_2026/6teb_10479.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6teb_10479/03_2026/6teb_10479.map"
  }
  resolution = 4.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.79, per 1000 atoms: 0.23
  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: 0.85
  Conformation dependent library (CDL) restraints added in 553.7 milliseconds
  

  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: 0.39
  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: 1.74

  Time building geometry restraints manager: 1.11 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: 0.02
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:             1.810
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.460
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.020
-------------------------------------------------------------------------------
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 : 20.55
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.007   0.001   ARG J  60 
 TYR   0.008   0.002   TYR F 122 
 PHE   0.029   0.003   PHE H  76 
 TRP   0.016   0.002   TRP K  81 
 HIS   0.006   0.001   HIS C  74 

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

*********************** 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  : 0.313 
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: 0.7521 (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: 0.8174 (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: 0.8476 (p0) cc_final: 0.7769 (p0)
REVERT: A  124 LEU cc_start: 0.8849 (tt) cc_final: 0.8452 (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: 0.8564 (m-80) cc_final: 0.8241 (m-10)
REVERT: B   92 GLN cc_start: 0.8856 (tt0) cc_final: 0.8640 (tt0)
REVERT: B  124 LEU cc_start: 0.8917 (tt) cc_final: 0.8074 (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: 0.7833 (pp20) cc_final: 0.7569 (pp20)
REVERT: C   37 ASN cc_start: 0.8671 (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: 0.8664 (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: 0.8745 (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: 0.8295 (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: 0.8465 (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: 0.9297 (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: 0.1140
  time to fit residues: 103.9638
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  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    0.8980
   chunk 149 optimal weight:    3.9990
   overall best weight:    1.7786

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

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

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.105224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.092089 restraints weight = 41995.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.094153 restraints weight = 24423.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.095462 restraints weight = 16190.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.096405 restraints weight = 11874.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.096996 restraints weight = 9372.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.4415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  12432  Z= 0.217
  Angle     :  0.861  11.103  16824  Z= 0.450
  Chirality :  0.054   0.182   1800
  Planarity :  0.009   0.107   2262
  Dihedral  :  7.631  29.897   1698
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 21.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.04 %
    Favored  : 87.96 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  6.41 %
    Favored  : 92.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.61 (0.17), residues: 1536
  helix: -2.98 (0.31), residues: 180
  sheet: -2.45 (0.26), residues: 348
  loop : -3.53 (0.15), residues: 1008

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  61 
 TYR   0.015   0.003   TYR F 112 
 PHE   0.023   0.002   PHE K 195 
 TRP   0.027   0.003   TRP G  78 
 HIS   0.009   0.002   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 (12432)
  covalent geometry    : angle       0.86051 (16824)
  hydrogen bonds       : bond        0.04598 (  285)
  hydrogen bonds       : angle       7.22339 (  801)

*********************** 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
  533 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 525
  time to evaluate  : 0.451 
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   41 VAL cc_start: 0.9206 (t) cc_final: 0.8981 (p)
REVERT: A   81 GLN cc_start: 0.9029 (tp40) cc_final: 0.8141 (tp40)
REVERT: A   85 ASP cc_start: 0.8943 (m-30) cc_final: 0.8243 (m-30)
REVERT: B   82 ILE cc_start: 0.9294 (tp) cc_final: 0.8966 (tp)
REVERT: B   85 ASP cc_start: 0.8808 (m-30) cc_final: 0.8171 (m-30)
REVERT: D   57 ASP cc_start: 0.8490 (t0) cc_final: 0.8042 (t0)
REVERT: C   37 ASN cc_start: 0.8471 (t0) cc_final: 0.8069 (t0)
REVERT: C   60 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7479 (pt0)
REVERT: E   81 GLN cc_start: 0.8960 (tp40) cc_final: 0.7957 (tp40)
REVERT: E   92 GLN cc_start: 0.8414 (tt0) cc_final: 0.8135 (tt0)
REVERT: E  100 ILE cc_start: 0.7882 (pt) cc_final: 0.7601 (pt)
REVERT: E  102 GLN cc_start: 0.8224 (tp-100) cc_final: 0.7519 (mm110)
REVERT: E  111 ASP cc_start: 0.8234 (p0) cc_final: 0.7965 (p0)
REVERT: F   82 ILE cc_start: 0.9428 (tp) cc_final: 0.8910 (tp)
REVERT: F   85 ASP cc_start: 0.8610 (m-30) cc_final: 0.8252 (m-30)
REVERT: G   56 LEU cc_start: 0.9369 (mm) cc_final: 0.9118 (mm)
REVERT: G   57 ASP cc_start: 0.8503 (t70) cc_final: 0.8284 (t0)
REVERT: H   11 ASN cc_start: 0.8436 (t0) cc_final: 0.8101 (t0)
REVERT: H   37 ASN cc_start: 0.8418 (t0) cc_final: 0.7787 (t0)
REVERT: H   60 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7473 (pt0)
REVERT: H  187 ARG cc_start: 0.8482 (ptp90) cc_final: 0.8212 (ptp90)
REVERT: I   78 ARG cc_start: 0.8644 (tpt-90) cc_final: 0.8370 (tpt-90)
REVERT: I   92 GLN cc_start: 0.8087 (tt0) cc_final: 0.6960 (tt0)
REVERT: I  100 ILE cc_start: 0.7773 (pt) cc_final: 0.7094 (pt)
REVERT: I  102 GLN cc_start: 0.8133 (tp-100) cc_final: 0.7247 (tp40)
REVERT: I  106 MET cc_start: 0.7702 (ptp) cc_final: 0.7440 (ptp)
REVERT: I  111 ASP cc_start: 0.8203 (p0) cc_final: 0.7966 (p0)
REVERT: J    5 ASN cc_start: 0.8224 (t0) cc_final: 0.8014 (t0)
REVERT: J   35 ASN cc_start: 0.9143 (m-40) cc_final: 0.8775 (m-40)
REVERT: J   82 ILE cc_start: 0.9412 (tp) cc_final: 0.8632 (tp)
REVERT: J   85 ASP cc_start: 0.8575 (m-30) cc_final: 0.8305 (t0)
REVERT: J   98 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6405 (m-10)
REVERT: J  124 LEU cc_start: 0.9146 (tt) cc_final: 0.8797 (tt)
REVERT: L   37 ASN cc_start: 0.8334 (t0) cc_final: 0.8087 (t0)
REVERT: L  193 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8204 (pt0)
  outliers start: 8
  outliers final: 0
  residues processed: 532
  average time/residue: 0.1074
  time to fit residues: 80.5001
Evaluate side-chains
  396 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 395
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 129 optimal weight:   10.0000
   chunk 7 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 92 optimal weight:    7.9990
   chunk 117 optimal weight:    0.9980
   chunk 126 optimal weight:    1.9990
   chunk 141 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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**
B 116 HIS
** D  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  20 GLN
E  92 GLN
E 102 GLN
E 116 HIS
F  20 GLN
** F  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 116 HIS
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**
J 116 HIS
** L  72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.099460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.086094 restraints weight = 43080.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.088017 restraints weight = 25380.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.089256 restraints weight = 16980.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.090150 restraints weight = 12585.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.090667 restraints weight = 9989.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.6023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  12432  Z= 0.243
  Angle     :  0.864   8.337  16824  Z= 0.461
  Chirality :  0.053   0.223   1800
  Planarity :  0.008   0.074   2262
  Dihedral  :  7.539  31.683   1698
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 24.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.00 %
    Favored  : 86.00 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  8.89 %
    Favored  : 90.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.11 (0.19), residues: 1536
  helix: -2.10 (0.36), residues: 144
  sheet: -2.48 (0.21), residues: 438
  loop : -3.10 (0.18), residues: 954

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  60 
 TYR   0.014   0.002   TYR I 112 
 PHE   0.051   0.003   PHE C 195 
 TRP   0.029   0.003   TRP L  78 
 HIS   0.008   0.002   HIS H  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00529 (12432)
  covalent geometry    : angle       0.86383 (16824)
  hydrogen bonds       : bond        0.04470 (  285)
  hydrogen bonds       : angle       6.68338 (  801)

*********************** 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
  496 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 487
  time to evaluate  : 0.472 
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   81 GLN cc_start: 0.9036 (tp40) cc_final: 0.8329 (tp40)
REVERT: A   85 ASP cc_start: 0.8991 (m-30) cc_final: 0.8358 (m-30)
REVERT: B   51 ARG cc_start: 0.8572 (ttp80) cc_final: 0.8280 (ttp80)
REVERT: B   82 ILE cc_start: 0.9298 (tp) cc_final: 0.8728 (tp)
REVERT: B   85 ASP cc_start: 0.8915 (m-30) cc_final: 0.8453 (t0)
REVERT: C   37 ASN cc_start: 0.8423 (t0) cc_final: 0.8207 (t0)
REVERT: C   60 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7636 (pt0)
REVERT: E   35 ASN cc_start: 0.8957 (m-40) cc_final: 0.8600 (p0)
REVERT: E   81 GLN cc_start: 0.9024 (tp40) cc_final: 0.8297 (tp40)
REVERT: E   85 ASP cc_start: 0.8903 (m-30) cc_final: 0.8385 (m-30)
REVERT: E  102 GLN cc_start: 0.8306 (tp40) cc_final: 0.7981 (tp40)
REVERT: F   82 ILE cc_start: 0.9377 (tp) cc_final: 0.8940 (tp)
REVERT: F   85 ASP cc_start: 0.8668 (m-30) cc_final: 0.8278 (t0)
REVERT: F  111 ASP cc_start: 0.8282 (p0) cc_final: 0.7872 (p0)
REVERT: G   57 ASP cc_start: 0.8465 (t70) cc_final: 0.8195 (t0)
REVERT: G  167 GLN cc_start: 0.6958 (tp-100) cc_final: 0.6597 (mm-40)
REVERT: H   37 ASN cc_start: 0.8027 (t0) cc_final: 0.7785 (t0)
REVERT: H   60 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7746 (pt0)
REVERT: I   92 GLN cc_start: 0.8281 (tt0) cc_final: 0.7569 (tt0)
REVERT: I  100 ILE cc_start: 0.7722 (pt) cc_final: 0.7241 (pt)
REVERT: I  102 GLN cc_start: 0.8200 (tp-100) cc_final: 0.7784 (tp40)
REVERT: J   35 ASN cc_start: 0.9083 (m-40) cc_final: 0.8585 (m-40)
REVERT: J   82 ILE cc_start: 0.9250 (tp) cc_final: 0.9000 (tp)
REVERT: J   85 ASP cc_start: 0.8768 (m-30) cc_final: 0.8078 (m-30)
REVERT: J  111 ASP cc_start: 0.8119 (p0) cc_final: 0.7841 (p0)
REVERT: J  124 LEU cc_start: 0.9089 (tt) cc_final: 0.8546 (tt)
REVERT: L   67 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7332 (tm-30)
  outliers start: 9
  outliers final: 0
  residues processed: 495
  average time/residue: 0.1044
  time to fit residues: 74.9526
Evaluate side-chains
  376 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 376
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 57 optimal weight:    8.9990
   chunk 75 optimal weight:    0.9990
   chunk 131 optimal weight:    3.9990
   chunk 3 optimal weight:    7.9990
   chunk 148 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 0 optimal weight:    0.7980
   chunk 30 optimal weight:    7.9990
   chunk 97 optimal weight:    2.9990
   chunk 80 optimal weight:    0.5980
   chunk 90 optimal weight:    2.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 ** 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**
F  20 GLN
** F  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 193 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**
L  72 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.101181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.088115 restraints weight = 42554.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.089953 restraints weight = 25325.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.091202 restraints weight = 17166.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.092101 restraints weight = 12786.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.092700 restraints weight = 10194.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.6568

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= 0.180
  Angle     :  0.823   8.674  16824  Z= 0.428
  Chirality :  0.052   0.189   1800
  Planarity :  0.007   0.062   2262
  Dihedral  :  7.231  33.677   1698
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 21.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.24 %
    Favored  : 87.76 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  6.65 %
    Favored  : 92.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.21 (0.18), residues: 1536
  helix: -2.40 (0.31), residues: 180
  sheet: -2.38 (0.24), residues: 372
  loop : -3.22 (0.17), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  54 
 TYR   0.012   0.002   TYR H  47 
 PHE   0.033   0.002   PHE D  76 
 TRP   0.019   0.002   TRP L  78 
 HIS   0.008   0.002   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (12432)
  covalent geometry    : angle       0.82271 (16824)
  hydrogen bonds       : bond        0.04102 (  285)
  hydrogen bonds       : angle       6.40743 (  801)

*********************** 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
  481 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 473
  time to evaluate  : 0.466 
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: A   35 ASN cc_start: 0.8996 (m-40) cc_final: 0.8587 (p0)
REVERT: A   81 GLN cc_start: 0.8975 (tp40) cc_final: 0.8227 (tp40)
REVERT: A   85 ASP cc_start: 0.8962 (m-30) cc_final: 0.8520 (m-30)
REVERT: B   85 ASP cc_start: 0.8931 (m-30) cc_final: 0.8427 (m-30)
REVERT: B  111 ASP cc_start: 0.8318 (p0) cc_final: 0.7994 (p0)
REVERT: C   53 LEU cc_start: 0.7489 (mt) cc_final: 0.6398 (mt)
REVERT: C   60 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7520 (pt0)
REVERT: C  193 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8325 (mp10)
REVERT: E   35 ASN cc_start: 0.8965 (m-40) cc_final: 0.8646 (p0)
REVERT: E   81 GLN cc_start: 0.8955 (tp40) cc_final: 0.8291 (tp40)
REVERT: E   85 ASP cc_start: 0.8833 (m-30) cc_final: 0.8302 (m-30)
REVERT: E   92 GLN cc_start: 0.8167 (tt0) cc_final: 0.7089 (tt0)
REVERT: E  102 GLN cc_start: 0.8417 (tp40) cc_final: 0.7198 (tp40)
REVERT: E  134 PHE cc_start: 0.7312 (m-80) cc_final: 0.6929 (m-10)
REVERT: G   57 ASP cc_start: 0.8357 (t70) cc_final: 0.8068 (t0)
REVERT: G   69 ARG cc_start: 0.7213 (ptp90) cc_final: 0.6846 (ptp90)
REVERT: G  167 GLN cc_start: 0.6900 (tp-100) cc_final: 0.6512 (mm-40)
REVERT: G  193 GLN cc_start: 0.8751 (mm110) cc_final: 0.8331 (pt0)
REVERT: H   34 GLU cc_start: 0.7076 (pt0) cc_final: 0.6728 (pt0)
REVERT: H   67 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7378 (tm-30)
REVERT: I   78 ARG cc_start: 0.8628 (tpt-90) cc_final: 0.8276 (tpt-90)
REVERT: I  102 GLN cc_start: 0.8533 (tp-100) cc_final: 0.8019 (mm110)
REVERT: J    5 ASN cc_start: 0.8142 (t0) cc_final: 0.7893 (t0)
REVERT: J   35 ASN cc_start: 0.9087 (m-40) cc_final: 0.8480 (m-40)
REVERT: J   85 ASP cc_start: 0.8777 (m-30) cc_final: 0.8411 (t0)
REVERT: J  124 LEU cc_start: 0.9121 (tt) cc_final: 0.8825 (tp)
REVERT: L   53 LEU cc_start: 0.7325 (mt) cc_final: 0.6043 (mt)
REVERT: L   57 ASP cc_start: 0.8781 (t0) cc_final: 0.8466 (t0)
  outliers start: 8
  outliers final: 1
  residues processed: 480
  average time/residue: 0.1063
  time to fit residues: 73.5162
Evaluate side-chains
  362 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 361
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   chunk 88 optimal weight:    0.5980
   chunk 91 optimal weight:    3.9990
   chunk 113 optimal weight:    8.9990
   chunk 60 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 19 optimal weight:   10.0000
   chunk 1 optimal weight:    6.9990
   overall best weight:    2.3188

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  20 GLN
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  20 GLN
H 193 GLN
I  20 GLN
** I  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 102 GLN
J  20 GLN
** J  92 GLN ** 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 = 0.3572 r_free = 0.3572 target = 0.098063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.083863 restraints weight = 43070.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.085854 restraints weight = 25426.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.087178 restraints weight = 17057.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.088116 restraints weight = 12593.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.088693 restraints weight = 10018.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.7055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  12432  Z= 0.252
  Angle     :  0.890   9.447  16824  Z= 0.467
  Chirality :  0.054   0.198   1800
  Planarity :  0.008   0.095   2262
  Dihedral  :  7.509  32.067   1698
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 24.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.39 %
    Favored  : 85.61 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  6.25 %
    Favored  : 93.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.39 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.27 (0.18), residues: 1536
  helix: -2.40 (0.31), residues: 186
  sheet: -2.53 (0.23), residues: 402
  loop : -3.22 (0.17), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG H  69 
 TYR   0.015   0.002   TYR H  47 
 PHE   0.044   0.003   PHE C  76 
 TRP   0.023   0.003   TRP D  78 
 HIS   0.009   0.002   HIS L  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00564 (12432)
  covalent geometry    : angle       0.88958 (16824)
  hydrogen bonds       : bond        0.04482 (  285)
  hydrogen bonds       : angle       6.44189 (  801)

*********************** 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
  437 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 431
  time to evaluate  : 0.419 
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: 0.9038 (m-40) cc_final: 0.8657 (p0)
REVERT: A   82 ILE cc_start: 0.9552 (tp) cc_final: 0.9103 (tp)
REVERT: A  111 ASP cc_start: 0.8348 (p0) cc_final: 0.8072 (p0)
REVERT: A  124 LEU cc_start: 0.9118 (tt) cc_final: 0.8892 (tt)
REVERT: B   35 ASN cc_start: 0.8541 (m110) cc_final: 0.8333 (m-40)
REVERT: B   85 ASP cc_start: 0.9074 (m-30) cc_final: 0.8785 (m-30)
REVERT: C   56 LEU cc_start: 0.9385 (mm) cc_final: 0.9174 (mm)
REVERT: C   60 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7578 (pt0)
REVERT: C  193 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8454 (mp10)
REVERT: E   35 ASN cc_start: 0.8979 (m-40) cc_final: 0.8678 (p0)
REVERT: E   82 ILE cc_start: 0.9455 (tp) cc_final: 0.9107 (tp)
REVERT: E   85 ASP cc_start: 0.9101 (m-30) cc_final: 0.8176 (p0)
REVERT: E   92 GLN cc_start: 0.8131 (tt0) cc_final: 0.6688 (tt0)
REVERT: E  102 GLN cc_start: 0.8572 (tp40) cc_final: 0.7454 (tp40)
REVERT: F   80 ARG cc_start: 0.9286 (tmm160) cc_final: 0.8615 (tmm160)
REVERT: G   57 ASP cc_start: 0.8412 (t70) cc_final: 0.8125 (t0)
REVERT: G  167 GLN cc_start: 0.6908 (tp-100) cc_final: 0.6624 (mm-40)
REVERT: H   67 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7358 (tm-30)
REVERT: I   85 ASP cc_start: 0.9204 (m-30) cc_final: 0.8887 (m-30)
REVERT: I   92 GLN cc_start: 0.8335 (tt0) cc_final: 0.7752 (tt0)
REVERT: I  102 GLN cc_start: 0.8503 (tp40) cc_final: 0.7141 (tp40)
REVERT: J    5 ASN cc_start: 0.8161 (t0) cc_final: 0.7960 (t0)
REVERT: J   35 ASN cc_start: 0.9131 (m-40) cc_final: 0.8692 (m110)
REVERT: J   85 ASP cc_start: 0.8983 (m-30) cc_final: 0.8592 (m-30)
REVERT: J   92 GLN cc_start: 0.8286 (tt0) cc_final: 0.7595 (tt0)
REVERT: J  102 GLN cc_start: 0.8700 (tp40) cc_final: 0.7082 (tp40)
REVERT: L   57 ASP cc_start: 0.8802 (t0) cc_final: 0.8505 (t0)
  outliers start: 6
  outliers final: 0
  residues processed: 437
  average time/residue: 0.0998
  time to fit residues: 63.3808
Evaluate side-chains
  335 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 335
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 144 optimal weight:    6.9990
   chunk 132 optimal weight:    0.2980
   chunk 137 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 152 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 116 optimal weight:   10.0000
   chunk 82 optimal weight:    6.9990
   chunk 37 optimal weight:    0.6980
   chunk 17 optimal weight:    5.9990
   overall best weight:    1.5984

-------------------------------------------------------------------------------
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 ** 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
G 193 GLN
H 193 GLN
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: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.100074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.085877 restraints weight = 42718.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.087840 restraints weight = 25253.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.089224 restraints weight = 17080.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.090175 restraints weight = 12554.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.090746 restraints weight = 10013.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.7293

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= 0.204
  Angle     :  0.880   9.828  16824  Z= 0.455
  Chirality :  0.053   0.210   1800
  Planarity :  0.007   0.082   2262
  Dihedral  :  7.238  33.068   1698
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 22.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.35 %
    Favored  : 86.65 %
  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 : 2.78 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.22 (0.18), residues: 1536
  helix: -2.39 (0.31), residues: 186
  sheet: -2.28 (0.24), residues: 360
  loop : -3.28 (0.17), residues: 990

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG H  69 
 TYR   0.016   0.002   TYR H  47 
 PHE   0.037   0.002   PHE C  76 
 TRP   0.026   0.002   TRP H  78 
 HIS   0.008   0.002   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 (12432)
  covalent geometry    : angle       0.87954 (16824)
  hydrogen bonds       : bond        0.04184 (  285)
  hydrogen bonds       : angle       6.17460 (  801)

*********************** 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
  434 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 428
  time to evaluate  : 0.441 
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: 0.8968 (m-40) cc_final: 0.8598 (p0)
REVERT: A   85 ASP cc_start: 0.9079 (m-30) cc_final: 0.8155 (p0)
REVERT: A  111 ASP cc_start: 0.8515 (p0) cc_final: 0.8114 (p0)
REVERT: A  124 LEU cc_start: 0.9165 (tt) cc_final: 0.8941 (tt)
REVERT: B   35 ASN cc_start: 0.8501 (m110) cc_final: 0.8066 (m-40)
REVERT: D   56 LEU cc_start: 0.9296 (mm) cc_final: 0.9027 (mm)
REVERT: C   60 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7654 (mt-10)
REVERT: E   31 ARG cc_start: 0.8113 (ttt90) cc_final: 0.7895 (tpt-90)
REVERT: E   92 GLN cc_start: 0.8258 (tt0) cc_final: 0.7128 (tt0)
REVERT: E  100 ILE cc_start: 0.8347 (pt) cc_final: 0.8104 (pt)
REVERT: E  102 GLN cc_start: 0.8618 (tp40) cc_final: 0.7523 (tp40)
REVERT: G   57 ASP cc_start: 0.8323 (t70) cc_final: 0.7997 (t0)
REVERT: G   69 ARG cc_start: 0.7276 (ptp90) cc_final: 0.6403 (ptp90)
REVERT: G  167 GLN cc_start: 0.6804 (tp-100) cc_final: 0.6365 (mm-40)
REVERT: H   67 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7148 (tm-30)
REVERT: I   85 ASP cc_start: 0.9129 (m-30) cc_final: 0.8835 (m-30)
REVERT: I   92 GLN cc_start: 0.8131 (tt0) cc_final: 0.7451 (tt0)
REVERT: I  102 GLN cc_start: 0.8666 (tp40) cc_final: 0.7199 (tp40)
REVERT: I  132 LEU cc_start: 0.8568 (mm) cc_final: 0.7884 (mp)
REVERT: J   35 ASN cc_start: 0.8878 (m-40) cc_final: 0.8602 (m-40)
REVERT: J  111 ASP cc_start: 0.8659 (p0) cc_final: 0.8269 (p0)
REVERT: K  194 SER cc_start: 0.9102 (m) cc_final: 0.8846 (m)
REVERT: L   11 ASN cc_start: 0.8890 (t0) cc_final: 0.8662 (t0)
REVERT: L   69 ARG cc_start: 0.7144 (ptp90) cc_final: 0.6732 (ptp90)
REVERT: L  193 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8511 (mp10)
  outliers start: 6
  outliers final: 0
  residues processed: 434
  average time/residue: 0.0922
  time to fit residues: 59.3014
Evaluate side-chains
  337 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 337
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 155 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 97 optimal weight:    0.5980
   chunk 120 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 141 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 117 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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
E  20 GLN
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  20 GLN
** G  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  11 ASN
I  20 GLN
J  20 GLN
** J  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  11 ASN
L  11 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.102650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.088561 restraints weight = 41883.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.090582 restraints weight = 24523.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.091881 restraints weight = 16467.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.092868 restraints weight = 12293.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.093460 restraints weight = 9804.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.7559

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= 0.165
  Angle     :  0.870   9.499  16824  Z= 0.444
  Chirality :  0.053   0.203   1800
  Planarity :  0.007   0.076   2262
  Dihedral  :  6.938  33.160   1698
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 22.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.09 %
    Favored  : 86.91 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  2.96 %
    Favored  : 96.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.13 (0.18), residues: 1536
  helix: -2.24 (0.32), residues: 180
  sheet: -2.16 (0.24), residues: 360
  loop : -3.27 (0.17), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  69 
 TYR   0.010   0.002   TYR E 122 
 PHE   0.035   0.002   PHE G  76 
 TRP   0.033   0.002   TRP C  78 
 HIS   0.007   0.001   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (12432)
  covalent geometry    : angle       0.86961 (16824)
  hydrogen bonds       : bond        0.04051 (  285)
  hydrogen bonds       : angle       5.92195 (  801)

*********************** 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
  445 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 438
  time to evaluate  : 0.423 
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   82 ILE cc_start: 0.9372 (tp) cc_final: 0.8878 (tp)
REVERT: A   85 ASP cc_start: 0.8968 (m-30) cc_final: 0.8766 (m-30)
REVERT: B   35 ASN cc_start: 0.8516 (m110) cc_final: 0.8262 (m-40)
REVERT: B   63 SER cc_start: 0.9363 (m) cc_final: 0.8966 (p)
REVERT: B   82 ILE cc_start: 0.9527 (tp) cc_final: 0.9174 (tp)
REVERT: B   85 ASP cc_start: 0.8516 (m-30) cc_final: 0.7954 (p0)
REVERT: C   60 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7342 (mt-10)
REVERT: C  193 GLN cc_start: 0.8451 (mp10) cc_final: 0.8046 (pm20)
REVERT: E   34 PHE cc_start: 0.9336 (m-10) cc_final: 0.9066 (m-10)
REVERT: E   82 ILE cc_start: 0.9337 (tp) cc_final: 0.9064 (tp)
REVERT: E   85 ASP cc_start: 0.8794 (m-30) cc_final: 0.8068 (p0)
REVERT: E   92 GLN cc_start: 0.8174 (tt0) cc_final: 0.7147 (tt0)
REVERT: E  100 ILE cc_start: 0.8185 (pt) cc_final: 0.7952 (pt)
REVERT: E  102 GLN cc_start: 0.8656 (tp40) cc_final: 0.7502 (tp40)
REVERT: E  111 ASP cc_start: 0.8144 (p0) cc_final: 0.7760 (p0)
REVERT: G   57 ASP cc_start: 0.8263 (t70) cc_final: 0.7874 (t0)
REVERT: G  167 GLN cc_start: 0.6560 (tp-100) cc_final: 0.6066 (mm-40)
REVERT: H   67 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7140 (tm-30)
REVERT: I   53 LEU cc_start: 0.9287 (mm) cc_final: 0.9051 (mp)
REVERT: I   85 ASP cc_start: 0.8947 (m-30) cc_final: 0.8694 (m-30)
REVERT: I   92 GLN cc_start: 0.7857 (tt0) cc_final: 0.6946 (tt0)
REVERT: I  102 GLN cc_start: 0.8635 (tp40) cc_final: 0.7878 (tp40)
REVERT: I  132 LEU cc_start: 0.8541 (mm) cc_final: 0.7928 (mp)
REVERT: J    5 ASN cc_start: 0.8119 (t0) cc_final: 0.7906 (t0)
REVERT: K   69 ARG cc_start: 0.7158 (ptp90) cc_final: 0.6361 (ptp90)
REVERT: L   69 ARG cc_start: 0.7015 (ptp90) cc_final: 0.6513 (ptp90)
  outliers start: 7
  outliers final: 0
  residues processed: 444
  average time/residue: 0.0962
  time to fit residues: 62.7207
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  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0980
   chunk 22 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 63 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 118 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 119 optimal weight:    4.9990
   chunk 99 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   overall best weight:    1.5384

-------------------------------------------------------------------------------
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
E  20 GLN
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  20 GLN
G  11 ASN
H 193 GLN
I  20 GLN
J  20 GLN
** J  92 GLN ** 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 = 0.3623 r_free = 0.3623 target = 0.100531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.086341 restraints weight = 41877.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.088311 restraints weight = 24704.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.089710 restraints weight = 16663.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.090580 restraints weight = 12308.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.091227 restraints weight = 9852.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.7712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12432  Z= 0.201
  Angle     :  0.899  11.423  16824  Z= 0.462
  Chirality :  0.054   0.262   1800
  Planarity :  0.007   0.072   2262
  Dihedral  :  7.016  34.752   1698
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 23.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.67 %
    Favored  : 86.33 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  2.16 %
    Favored  : 97.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.08 (0.18), residues: 1536
  helix: -2.24 (0.33), residues: 180
  sheet: -2.13 (0.23), residues: 360
  loop : -3.22 (0.17), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  69 
 TYR   0.014   0.002   TYR H  47 
 PHE   0.047   0.003   PHE G  76 
 TRP   0.027   0.003   TRP K  78 
 HIS   0.007   0.002   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 (12432)
  covalent geometry    : angle       0.89896 (16824)
  hydrogen bonds       : bond        0.04079 (  285)
  hydrogen bonds       : angle       5.99387 (  801)

*********************** 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
  421 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 415
  time to evaluate  : 0.487 
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: B   35 ASN cc_start: 0.8492 (m110) cc_final: 0.8073 (m-40)
REVERT: B   82 ILE cc_start: 0.9588 (tp) cc_final: 0.9200 (tp)
REVERT: B   85 ASP cc_start: 0.8636 (m-30) cc_final: 0.8148 (p0)
REVERT: B   92 GLN cc_start: 0.7884 (tt0) cc_final: 0.7634 (tt0)
REVERT: B  100 ILE cc_start: 0.8009 (pt) cc_final: 0.7539 (pt)
REVERT: B  102 GLN cc_start: 0.8650 (tp40) cc_final: 0.6681 (tp40)
REVERT: D   23 ARG cc_start: 0.7317 (tpp-160) cc_final: 0.7061 (tpm170)
REVERT: C   60 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7295 (mt-10)
REVERT: C  193 GLN cc_start: 0.8502 (mp10) cc_final: 0.8239 (pt0)
REVERT: E   82 ILE cc_start: 0.9377 (tp) cc_final: 0.9097 (tp)
REVERT: E   85 ASP cc_start: 0.8826 (m-30) cc_final: 0.8084 (p0)
REVERT: E   92 GLN cc_start: 0.8156 (tt0) cc_final: 0.7173 (tt0)
REVERT: E  102 GLN cc_start: 0.8618 (tp40) cc_final: 0.7523 (tp40)
REVERT: E  107 ILE cc_start: 0.9366 (tt) cc_final: 0.9024 (tt)
REVERT: F   85 ASP cc_start: 0.8623 (t0) cc_final: 0.8320 (t0)
REVERT: G   57 ASP cc_start: 0.8266 (t70) cc_final: 0.7940 (t0)
REVERT: G  167 GLN cc_start: 0.6663 (tp-100) cc_final: 0.6217 (mm-40)
REVERT: H   63 ILE cc_start: 0.9696 (pt) cc_final: 0.9436 (mt)
REVERT: H   67 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7166 (tm-30)
REVERT: I   85 ASP cc_start: 0.9018 (m-30) cc_final: 0.8778 (m-30)
REVERT: I   92 GLN cc_start: 0.7887 (tt0) cc_final: 0.6539 (tt0)
REVERT: I  100 ILE cc_start: 0.7804 (pt) cc_final: 0.7280 (pt)
REVERT: I  102 GLN cc_start: 0.8647 (tp40) cc_final: 0.8120 (tp40)
REVERT: I  132 LEU cc_start: 0.8636 (mm) cc_final: 0.7926 (mp)
REVERT: J    5 ASN cc_start: 0.8128 (t0) cc_final: 0.7912 (t0)
REVERT: L   67 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7190 (tm-30)
REVERT: L  193 GLN cc_start: 0.8458 (mp10) cc_final: 0.8033 (pm20)
  outliers start: 6
  outliers final: 0
  residues processed: 421
  average time/residue: 0.0983
  time to fit residues: 60.5646
Evaluate side-chains
  340 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 340
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 115 optimal weight:    9.9990
   chunk 113 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0020
   chunk 22 optimal weight:    0.7980
   chunk 52 optimal weight:   10.0000
   chunk 134 optimal weight:    6.9990
   chunk 132 optimal weight:    0.2980
   chunk 97 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0770
   chunk 39 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.4346

-------------------------------------------------------------------------------
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
C  11 ASN
E  20 GLN
** E  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 102 GLN
F  20 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**
L  11 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.105080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.091006 restraints weight = 41823.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.093106 restraints weight = 24674.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.094417 restraints weight = 16532.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.095414 restraints weight = 12445.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.096024 restraints weight = 9851.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.7851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12432  Z= 0.155
  Angle     :  0.899  13.834  16824  Z= 0.456
  Chirality :  0.054   0.249   1800
  Planarity :  0.007   0.080   2262
  Dihedral  :  6.651  33.180   1698
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 19.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.33 %
    Favored  : 88.67 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  1.28 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.39 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.96 (0.18), residues: 1536
  helix: -2.05 (0.34), residues: 180
  sheet: -2.10 (0.25), residues: 336
  loop : -3.12 (0.16), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  69 
 TYR   0.010   0.001   TYR J 122 
 PHE   0.039   0.002   PHE C  76 
 TRP   0.028   0.002   TRP C  78 
 HIS   0.006   0.001   HIS K  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (12432)
  covalent geometry    : angle       0.89884 (16824)
  hydrogen bonds       : bond        0.03884 (  285)
  hydrogen bonds       : angle       5.79311 (  801)

*********************** 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
  440 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 434
  time to evaluate  : 0.490 
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: B   50 TRP cc_start: 0.8508 (m100) cc_final: 0.8169 (m100)
REVERT: B   63 SER cc_start: 0.9325 (m) cc_final: 0.8859 (p)
REVERT: B   82 ILE cc_start: 0.9471 (tp) cc_final: 0.9127 (tp)
REVERT: B   85 ASP cc_start: 0.8392 (m-30) cc_final: 0.8102 (p0)
REVERT: B  102 GLN cc_start: 0.8743 (tp40) cc_final: 0.8292 (tp40)
REVERT: D   63 ILE cc_start: 0.9619 (pt) cc_final: 0.9299 (mt)
REVERT: C   53 LEU cc_start: 0.6637 (mt) cc_final: 0.6332 (mt)
REVERT: C   60 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7233 (mt-10)
REVERT: C  193 GLN cc_start: 0.8514 (mp10) cc_final: 0.8154 (pm20)
REVERT: E   82 ILE cc_start: 0.9294 (tp) cc_final: 0.9059 (tp)
REVERT: E   85 ASP cc_start: 0.8672 (m-30) cc_final: 0.8294 (p0)
REVERT: E   92 GLN cc_start: 0.7860 (tt0) cc_final: 0.7051 (tt0)
REVERT: E  100 ILE cc_start: 0.8282 (pt) cc_final: 0.8031 (pt)
REVERT: E  102 GLN cc_start: 0.8577 (tp-100) cc_final: 0.7577 (tp40)
REVERT: E  107 ILE cc_start: 0.9044 (tt) cc_final: 0.8751 (tt)
REVERT: G   57 ASP cc_start: 0.8365 (t70) cc_final: 0.8016 (t0)
REVERT: G   69 ARG cc_start: 0.7085 (ptp90) cc_final: 0.6314 (ptp90)
REVERT: H   25 GLU cc_start: 0.8453 (pm20) cc_final: 0.8166 (pm20)
REVERT: H   67 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7155 (tm-30)
REVERT: I   92 GLN cc_start: 0.7703 (tt0) cc_final: 0.6568 (tt0)
REVERT: I  100 ILE cc_start: 0.7320 (pt) cc_final: 0.7050 (pt)
REVERT: I  102 GLN cc_start: 0.8661 (tp40) cc_final: 0.7907 (tp40)
REVERT: I  132 LEU cc_start: 0.8505 (mm) cc_final: 0.7795 (mp)
REVERT: J    5 ASN cc_start: 0.8128 (t0) cc_final: 0.7899 (t0)
REVERT: J   35 ASN cc_start: 0.8376 (m110) cc_final: 0.8070 (m-40)
REVERT: J   63 SER cc_start: 0.9287 (m) cc_final: 0.8874 (p)
REVERT: J  102 GLN cc_start: 0.8701 (tp40) cc_final: 0.7027 (tp40)
REVERT: L   69 ARG cc_start: 0.7089 (ptp90) cc_final: 0.6370 (ptp90)
REVERT: L  193 GLN cc_start: 0.8465 (mp10) cc_final: 0.7971 (pm20)
  outliers start: 6
  outliers final: 0
  residues processed: 440
  average time/residue: 0.0964
  time to fit residues: 62.6958
Evaluate side-chains
  342 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 342
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 104 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 111 optimal weight:    3.9990
   chunk 101 optimal weight:    0.5980
   chunk 110 optimal weight:    9.9990
   chunk 59 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 133 optimal weight:    6.9990
   chunk 138 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    1.6584

-------------------------------------------------------------------------------
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
D   4 HIS
** D  11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  11 ASN
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**
H 196 GLN
I  20 GLN
J  20 GLN
** J  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  11 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.101055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.086833 restraints weight = 42930.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.088799 restraints weight = 25123.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.090138 restraints weight = 16927.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.091012 restraints weight = 12525.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.091663 restraints weight = 10073.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.8023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12432  Z= 0.213
  Angle     :  0.952  15.310  16824  Z= 0.487
  Chirality :  0.055   0.256   1800
  Planarity :  0.008   0.071   2262
  Dihedral  :  6.933  34.626   1698
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 24.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.09 %
    Favored  : 86.91 %
  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 : 4.17 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.85 (0.18), residues: 1536
  helix: -1.89 (0.37), residues: 150
  sheet: -2.04 (0.23), residues: 372
  loop : -3.06 (0.17), residues: 1014

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG F  78 
 TYR   0.014   0.002   TYR H  47 
 PHE   0.052   0.003   PHE K  76 
 TRP   0.023   0.003   TRP C  78 
 HIS   0.008   0.002   HIS D   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 (12432)
  covalent geometry    : angle       0.95193 (16824)
  hydrogen bonds       : bond        0.04146 (  285)
  hydrogen bonds       : angle       5.86311 (  801)

********************** 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
  418 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 412
  time to evaluate  : 0.480 
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   85 ASP cc_start: 0.9110 (m-30) cc_final: 0.8856 (m-30)
REVERT: A  124 LEU cc_start: 0.9107 (tt) cc_final: 0.8773 (tt)
REVERT: B   63 SER cc_start: 0.9329 (m) cc_final: 0.8884 (p)
REVERT: B   82 ILE cc_start: 0.9494 (tp) cc_final: 0.9180 (tp)
REVERT: B   85 ASP cc_start: 0.8682 (m-30) cc_final: 0.7938 (p0)
REVERT: B   87 GLU cc_start: 0.7442 (pm20) cc_final: 0.7188 (pm20)
REVERT: B   92 GLN cc_start: 0.7621 (tt0) cc_final: 0.6545 (tt0)
REVERT: B  100 ILE cc_start: 0.8096 (pt) cc_final: 0.7335 (pt)
REVERT: B  102 GLN cc_start: 0.8694 (tp40) cc_final: 0.7352 (tp40)
REVERT: D  202 GLN cc_start: 0.8423 (pm20) cc_final: 0.8149 (pm20)
REVERT: C   60 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7216 (mt-10)
REVERT: C  193 GLN cc_start: 0.8534 (mp10) cc_final: 0.8249 (pm20)
REVERT: E   63 SER cc_start: 0.9348 (m) cc_final: 0.8949 (p)
REVERT: E   82 ILE cc_start: 0.9343 (tp) cc_final: 0.9044 (tp)
REVERT: E   85 ASP cc_start: 0.8711 (m-30) cc_final: 0.8014 (p0)
REVERT: E   92 GLN cc_start: 0.8017 (tt0) cc_final: 0.7239 (tt0)
REVERT: E  102 GLN cc_start: 0.8582 (tp-100) cc_final: 0.7509 (tp40)
REVERT: E  107 ILE cc_start: 0.9286 (tt) cc_final: 0.9057 (tt)
REVERT: E  111 ASP cc_start: 0.8078 (p0) cc_final: 0.7719 (p0)
REVERT: E  124 LEU cc_start: 0.9128 (tt) cc_final: 0.8883 (tt)
REVERT: F   82 ILE cc_start: 0.9522 (pt) cc_final: 0.9314 (tp)
REVERT: G   57 ASP cc_start: 0.8373 (t70) cc_final: 0.7985 (t0)
REVERT: G  167 GLN cc_start: 0.6583 (tp-100) cc_final: 0.6110 (mm-40)
REVERT: H   67 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7342 (tm-30)
REVERT: I   35 ASN cc_start: 0.8824 (m110) cc_final: 0.8617 (m-40)
REVERT: I   85 ASP cc_start: 0.9001 (m-30) cc_final: 0.8722 (m-30)
REVERT: I   92 GLN cc_start: 0.7903 (tt0) cc_final: 0.7334 (tt0)
REVERT: I  102 GLN cc_start: 0.8558 (tp40) cc_final: 0.7532 (tp40)
REVERT: I  132 LEU cc_start: 0.8589 (mm) cc_final: 0.8338 (mt)
REVERT: J   63 SER cc_start: 0.9311 (m) cc_final: 0.8874 (p)
REVERT: J   92 GLN cc_start: 0.8152 (tt0) cc_final: 0.7585 (tt0)
REVERT: J  102 GLN cc_start: 0.8676 (tp40) cc_final: 0.7150 (tp40)
REVERT: L   67 GLU cc_start: 0.7373 (tm-30) cc_final: 0.7079 (tm-30)
REVERT: L  193 GLN cc_start: 0.8598 (mp10) cc_final: 0.8023 (pm20)
  outliers start: 6
  outliers final: 0
  residues processed: 418
  average time/residue: 0.1027
  time to fit residues: 62.6226
Evaluate side-chains
  334 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 334
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 58 optimal weight:   10.0000
   chunk 119 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 128 optimal weight:    0.1980
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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
** 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
H  11 ASN
H 196 GLN
I  20 GLN
I 102 GLN
J  20 GLN
** J  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  11 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.104088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.089930 restraints weight = 41686.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.091996 restraints weight = 24497.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.093377 restraints weight = 16392.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.094337 restraints weight = 12055.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.094891 restraints weight = 9592.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.8137

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= 0.162
  Angle     :  0.915  15.606  16824  Z= 0.465
  Chirality :  0.054   0.254   1800
  Planarity :  0.007   0.074   2262
  Dihedral  :  6.679  33.149   1698
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 20.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.78 %
    Favored  : 88.22 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  1.12 %
    Favored  : 98.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.75 (0.18), residues: 1536
  helix: -1.70 (0.39), residues: 144
  sheet: -1.85 (0.24), residues: 372
  loop : -3.06 (0.16), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG K  54 
 TYR   0.010   0.002   TYR H  47 
 PHE   0.050   0.002   PHE K  76 
 TRP   0.025   0.002   TRP C  78 
 HIS   0.006   0.002   HIS K  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (12432)
  covalent geometry    : angle       0.91483 (16824)
  hydrogen bonds       : bond        0.03996 (  285)
  hydrogen bonds       : angle       5.76603 (  801)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2040.54 seconds
wall clock time: 35 minutes 54.51 seconds (2154.51 seconds total)