Starting phenix.real_space_refine
on Fri Mar  6 11:24:19 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6o1m_0592/03_2026/6o1m_0592.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6o1m_0592/03_2026/6o1m_0592.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6o1m_0592/03_2026/6o1m_0592.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6o1m_0592/03_2026/6o1m_0592.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6o1m_0592/03_2026/6o1m_0592.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6o1m_0592/03_2026/6o1m_0592.map"
  }
  resolution = 3.15
  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=   0.004 sd=   0.050
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      34      5.49       5
     S      48      5.16       5
     C    9894      2.51       5
     N    2777      2.21       5
     O    2923      1.98       5
     H   15371      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 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: 31047
  Number of models: 1
  Model: ""
    Number of chains: 18
    Chain: "A"
      Number of atoms: 4170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 4170
          Classifications: {'peptide': 262}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 249}
    Chain: "B"
      Number of atoms: 4170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 4170
          Classifications: {'peptide': 262}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 249}
    Chain: "C"
      Number of atoms: 1081
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 1081
          Classifications: {'peptide': 65}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 60}
    Chain: "D"
      Number of atoms: 1114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 1114
          Classifications: {'peptide': 67}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 61}
    Chain: "E"
      Number of atoms: 1114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 1114
          Classifications: {'peptide': 67}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 61}
    Chain: "F"
      Number of atoms: 1081
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 1081
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 4, 'TRANS': 60}
    Chain: "G"
      Number of atoms: 1100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 1100
          Classifications: {'peptide': 66}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 61}
    Chain: "H"
      Number of atoms: 1114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 1114
          Classifications: {'peptide': 67}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 61}
    Chain: "I"
      Number of atoms: 1114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 1114
          Classifications: {'peptide': 67}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 61}
    Chain: "J"
      Number of atoms: 1081
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 1081
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 4, 'TRANS': 60}
    Chain: "K"
      Number of atoms: 1081
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 1081
          Classifications: {'peptide': 65}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 60}
    Chain: "L"
      Number of atoms: 1095
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 1095
          Classifications: {'peptide': 66}
          Link IDs: {'PTRANS': 5, 'TRANS': 60}
    Chain: "M"
      Number of atoms: 1114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 1114
          Classifications: {'peptide': 67}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 61}
    Chain: "N"
      Number of atoms: 1100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 1100
          Classifications: {'peptide': 66}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 61}
    Chain: "O"
      Number of atoms: 589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 589
          Classifications: {'RNA': 18}
          Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 15, 'rna2p_pyr': 3}
          Link IDs: {'rna2p': 17}
    Chain: "P"
      Number of atoms: 589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 589
          Classifications: {'RNA': 18}
          Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 15, 'rna2p_pyr': 3}
          Link IDs: {'rna2p': 17}
    Chain: "R"
      Number of atoms: 4170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 4170
          Classifications: {'peptide': 262}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 249}
    Chain: "S"
      Number of atoms: 4170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 4170
          Classifications: {'peptide': 262}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 249}
  Time building chain proxies: 5.08, per 1000 atoms: 0.16
  Number of scatterers: 31047
  At special positions: 0
  Unit cell: (101.37, 122.08, 107.91, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      48     16.00
     P      34     15.00
     O    2923      8.00
     N    2777      7.00
     C    9894      6.00
     H   15371      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.65
  Conformation dependent library (CDL) restraints added in 802.7 milliseconds
  

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3490

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 11 sheets defined
      25.3% alpha, 26.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 4.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 16
      removed outlier: 3.616A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 18 through 24
      removed outlier: 3.522A  pdb=" N   TRP A  22 " --> pdb=" O   GLY A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 90
      removed outlier: 3.553A  pdb=" N   ARG A  90 " --> pdb=" O   GLU A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 137
    Processing helix  chain 'A' and resid 154 through 158
      removed outlier: 3.553A  pdb=" N   VAL A 158 " --> pdb=" O   LYS A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 164
      removed outlier: 3.500A  pdb=" N   GLU A 163 " --> pdb=" O   ASN A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 184
    Processing helix  chain 'A' and resid 190 through 195
      removed outlier: 3.993A  pdb=" N   VAL A 194 " --> pdb=" O   ALA A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 213
      removed outlier: 3.765A  pdb=" N   LEU A 213 " --> pdb=" O   GLN A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 229
      removed outlier: 3.598A  pdb=" N   ARG A 229 " --> pdb=" O   PRO A 226 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 226 through 229'
    Processing helix  chain 'B' and resid 10 through 17
    Processing helix  chain 'B' and resid 19 through 24
    Processing helix  chain 'B' and resid 39 through 44
      removed outlier: 3.829A  pdb=" N   ASP B  44 " --> pdb=" O   ALA B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 90
    Processing helix  chain 'B' and resid 115 through 136
      removed outlier: 3.791A  pdb=" N   LYS B 135 " --> pdb=" O   HIS B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 139
      No H-bonds generated for 'chain 'B' and resid 137 through 139'
    Processing helix  chain 'B' and resid 160 through 164
    Processing helix  chain 'B' and resid 171 through 182
    Processing helix  chain 'B' and resid 207 through 213
    Processing helix  chain 'B' and resid 226 through 229
      removed outlier: 3.756A  pdb=" N   ARG B 229 " --> pdb=" O   PRO B 226 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 226 through 229'
    Processing helix  chain 'C' and resid 7 through 18
    Processing helix  chain 'D' and resid 7 through 18
      removed outlier: 3.768A  pdb=" N   TYR D  11 " --> pdb=" O   LEU D   7 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 7 through 18
      removed outlier: 3.635A  pdb=" N   TYR E  11 " --> pdb=" O   LEU E   7 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLU E  18 " --> pdb=" O   THR E  14 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 7 through 18
    Processing helix  chain 'G' and resid 7 through 18
      removed outlier: 4.232A  pdb=" N   TYR G  11 " --> pdb=" O   LEU G   7 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU G  12 " --> pdb=" O   GLN G   8 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 10 through 18
    Processing helix  chain 'I' and resid 7 through 18
      removed outlier: 3.596A  pdb=" N   GLU I  18 " --> pdb=" O   THR I  14 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 7 through 18
      removed outlier: 3.632A  pdb=" N   TYR J  11 " --> pdb=" O   LEU J   7 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   GLU J  18 " --> pdb=" O   THR J  14 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 7 through 19
      removed outlier: 3.771A  pdb=" N   TYR K  11 " --> pdb=" O   LEU K   7 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 7 through 18
      removed outlier: 3.569A  pdb=" N   TYR L  11 " --> pdb=" O   LEU L   7 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 7 through 18
      removed outlier: 3.829A  pdb=" N   TYR M  11 " --> pdb=" O   LEU M   7 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 7 through 18
      removed outlier: 3.980A  pdb=" N   TYR N  11 " --> pdb=" O   LEU N   7 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ARG N  16 " --> pdb=" O   LEU N  12 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   GLU N  18 " --> pdb=" O   THR N  14 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 10 through 16
      removed outlier: 3.755A  pdb=" N   GLU R  16 " --> pdb=" O   GLN R  12 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 18 through 24
    Processing helix  chain 'R' and resid 25 through 27
      No H-bonds generated for 'chain 'R' and resid 25 through 27'
    Processing helix  chain 'R' and resid 85 through 90
      removed outlier: 3.682A  pdb=" N   ASP R  89 " --> pdb=" O   PHE R  85 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ARG R  90 " --> pdb=" O   GLU R  86 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 85 through 90'
    Processing helix  chain 'R' and resid 115 through 137
      removed outlier: 3.590A  pdb=" N   LEU R 119 " --> pdb=" O   GLY R 115 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 160 through 164
      removed outlier: 3.842A  pdb=" N   GLU R 163 " --> pdb=" O   ASN R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 182
      removed outlier: 3.540A  pdb=" N   LEU R 178 " --> pdb=" O   GLU R 174 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 190 through 195
      removed outlier: 4.210A  pdb=" N   VAL R 194 " --> pdb=" O   ALA R 190 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 207 through 213
    Processing helix  chain 'R' and resid 228 through 230
      No H-bonds generated for 'chain 'R' and resid 228 through 230'
    Processing helix  chain 'S' and resid 10 through 16
    Processing helix  chain 'S' and resid 18 through 25
      removed outlier: 3.954A  pdb=" N   ALA S  25 " --> pdb=" O   SER S  21 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 41 through 45
      removed outlier: 3.593A  pdb=" N   ASP S  45 " --> pdb=" O   ASP S  42 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 62 through 66
      removed outlier: 3.625A  pdb=" N   GLY S  66 " --> pdb=" O   PRO S  63 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 85 through 90
      removed outlier: 3.674A  pdb=" N   ASP S  89 " --> pdb=" O   PHE S  85 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ARG S  90 " --> pdb=" O   GLU S  86 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 85 through 90'
    Processing helix  chain 'S' and resid 115 through 137
    Processing helix  chain 'S' and resid 154 through 158
      removed outlier: 4.029A  pdb=" N   VAL S 158 " --> pdb=" O   LYS S 155 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 160 through 164
      removed outlier: 3.906A  pdb=" N   GLU S 163 " --> pdb=" O   ASN S 160 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   CYS S 164 " --> pdb=" O   TRP S 161 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 160 through 164'
    Processing helix  chain 'S' and resid 171 through 182
      removed outlier: 3.697A  pdb=" N   LEU S 178 " --> pdb=" O   GLU S 174 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 207 through 213
    Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 58
      removed outlier: 6.719A  pdb=" N   ARG A   2 " --> pdb=" O   VAL A  30 " (cutoff:3.500A)
      removed outlier: 7.947A  pdb=" N   CYS A  32 " --> pdb=" O   ARG A   2 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ILE A   4 " --> pdb=" O   CYS A  32 " (cutoff:3.500A)
      removed outlier: 7.678A  pdb=" N   GLN A  34 " --> pdb=" O   ILE A   4 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81
      removed outlier: 7.040A  pdb=" N   SER A 103 " --> pdb=" O   ILE A 144 " (cutoff:3.500A)
      removed outlier: 7.623A  pdb=" N   CYS A 146 " --> pdb=" O   SER A 103 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   ALA A 105 " --> pdb=" O   CYS A 146 " (cutoff:3.500A)
      removed outlier: 8.154A  pdb=" N   SER A 148 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   LEU A 107 " --> pdb=" O   SER A 148 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 58
      removed outlier: 6.688A  pdb=" N   ARG B   2 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   CYS B  32 " --> pdb=" O   ARG B   2 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ILE B   4 " --> pdb=" O   CYS B  32 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   GLN B  34 " --> pdb=" O   ILE B   4 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 81
      removed outlier: 6.843A  pdb=" N   SER B 103 " --> pdb=" O   ILE B 144 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   CYS B 146 " --> pdb=" O   SER B 103 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ALA B 105 " --> pdb=" O   CYS B 146 " (cutoff:3.500A)
      removed outlier: 7.812A  pdb=" N   SER B 148 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
      removed outlier: 7.267A  pdb=" N   LEU B 107 " --> pdb=" O   SER B 148 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 54 through 55
      removed outlier: 3.932A  pdb=" N   SER D  38 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   LYS D  47 " --> pdb=" O   ILE D  36 " (cutoff:3.500A)
      removed outlier: 5.777A  pdb=" N   ILE D  36 " --> pdb=" O   LYS D  47 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLY D  34 " --> pdb=" O   VAL D  22 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   THR D  61 " --> pdb=" O   TYR D  25 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   VAL C  43 " --> pdb=" O   PHE C  39 " (cutoff:3.500A)
      removed outlier: 5.114A  pdb=" N   PHE C  39 " --> pdb=" O   VAL C  43 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   LEU C  45 " --> pdb=" O   GLU C  37 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   SER C  23 " --> pdb=" O   VAL C  62 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   VAL C  62 " --> pdb=" O   SER C  23 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   TYR C  25 " --> pdb=" O   SER C  60 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   SER C  60 " --> pdb=" O   TYR G  55 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   VAL G  43 " --> pdb=" O   PHE G  39 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   PHE G  39 " --> pdb=" O   VAL G  43 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   LEU G  45 " --> pdb=" O   GLU G  37 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   SER G  60 " --> pdb=" O   TYR H  55 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   MET H  53 " --> pdb=" O   VAL G  62 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   SER H  51 " --> pdb=" O   PRO G  64 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   SER H  38 " --> pdb=" O   LEU H  45 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   LYS H  47 " --> pdb=" O   ILE H  36 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ILE H  36 " --> pdb=" O   LYS H  47 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   SER H  60 " --> pdb=" O   TYR F  55 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   VAL F  43 " --> pdb=" O   PHE F  39 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   PHE F  39 " --> pdb=" O   VAL F  43 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   LEU F  45 " --> pdb=" O   GLU F  37 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   SER F  60 " --> pdb=" O   TYR E  55 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 31 through 34
      removed outlier: 6.545A  pdb=" N   SER E  23 " --> pdb=" O   VAL E  62 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   VAL E  62 " --> pdb=" O   SER E  23 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   TYR E  25 " --> pdb=" O   SER E  60 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'I' and resid 22 through 26
      removed outlier: 6.777A  pdb=" N   LEU I  45 " --> pdb=" O   GLU I  37 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   PHE I  39 " --> pdb=" O   VAL I  43 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   VAL I  43 " --> pdb=" O   PHE I  39 " (cutoff:3.500A)
      removed outlier: 5.767A  pdb=" N   SER I  51 " --> pdb=" O   PRO J  64 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   SER J  60 " --> pdb=" O   TYR I  55 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   LEU J  45 " --> pdb=" O   GLU J  37 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   PHE J  39 " --> pdb=" O   VAL J  43 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   VAL J  43 " --> pdb=" O   PHE J  39 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   SER J  51 " --> pdb=" O   PRO K  64 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   SER K  60 " --> pdb=" O   TYR J  55 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   LEU K  45 " --> pdb=" O   GLU K  37 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   PHE K  39 " --> pdb=" O   VAL K  43 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   VAL K  43 " --> pdb=" O   PHE K  39 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   SER K  51 " --> pdb=" O   PRO L  64 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   MET K  53 " --> pdb=" O   VAL L  62 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   SER L  60 " --> pdb=" O   TYR K  55 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   ILE L  36 " --> pdb=" O   LYS L  47 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   LYS L  47 " --> pdb=" O   ILE L  36 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   MET L  53 " --> pdb=" O   VAL M  62 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   SER M  60 " --> pdb=" O   TYR L  55 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   LEU M  45 " --> pdb=" O   GLU M  37 " (cutoff:3.500A)
      removed outlier: 4.765A  pdb=" N   PHE M  39 " --> pdb=" O   VAL M  43 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   VAL M  43 " --> pdb=" O   PHE M  39 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   SER N  60 " --> pdb=" O   TYR M  55 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   LEU N  45 " --> pdb=" O   GLU N  37 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   PHE N  39 " --> pdb=" O   VAL N  43 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   VAL N  43 " --> pdb=" O   PHE N  39 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   SER I  60 " --> pdb=" O   TYR N  55 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   TYR I  25 " --> pdb=" O   SER I  60 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   VAL I  62 " --> pdb=" O   SER I  23 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   SER I  23 " --> pdb=" O   VAL I  62 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'R' and resid 54 through 58
      removed outlier: 6.555A  pdb=" N   ARG R   2 " --> pdb=" O   VAL R  30 " (cutoff:3.500A)
      removed outlier: 7.875A  pdb=" N   CYS R  32 " --> pdb=" O   ARG R   2 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   ILE R   4 " --> pdb=" O   CYS R  32 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   GLN R  34 " --> pdb=" O   ILE R   4 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   VAL R   6 " --> pdb=" O   GLN R  34 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 78 through 81
    Processing sheet with id=AB1, first strand: chain 'S' and resid 54 through 58
      removed outlier: 6.542A  pdb=" N   ARG S   2 " --> pdb=" O   VAL S  30 " (cutoff:3.500A)
      removed outlier: 7.865A  pdb=" N   CYS S  32 " --> pdb=" O   ARG S   2 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ILE S   4 " --> pdb=" O   CYS S  32 " (cutoff:3.500A)
      removed outlier: 7.485A  pdb=" N   GLN S  34 " --> pdb=" O   ILE S   4 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   VAL S   6 " --> pdb=" O   GLN S  34 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 78 through 81
      removed outlier: 3.560A  pdb=" N   SER S 148 " --> pdb=" O   LEU S 107 " (cutoff:3.500A)

    561 hydrogen bonds defined for protein.
    1545 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: 6.22

  Time building geometry restraints manager: 3.52 seconds

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

  Histogram of bond lengths:
        0.85 -     1.04: 3622
        1.04 -     1.23: 12089
        1.23 -     1.42: 6605
        1.42 -     1.62: 9090
        1.62 -     1.81: 80
  Bond restraints: 31486
  Sorted by residual:
  bond pdb=" ND2 ASN H  28 "
       pdb="HD22 ASN H  28 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" CE2 TYR I  55 "
       pdb=" HE2 TYR I  55 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" CD1 PHE S 219 "
       pdb=" HD1 PHE S 219 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" N   VAL H  43 "
       pdb=" H   VAL H  43 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" N   ASP A 220 "
       pdb=" H   ASP A 220 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
  ... (remaining 31481 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.80: 56365
        5.80 -    11.59: 482
       11.59 -    17.39: 7
       17.39 -    23.18: 0
       23.18 -    28.98: 2
  Bond angle restraints: 56856
  Sorted by residual:
  angle pdb=" C6    A O   2 "
        pdb=" N6    A O   2 "
        pdb=" H62   A O   2 "
      ideal   model   delta    sigma   weight residual
     120.00   91.02   28.98 3.00e+00 1.11e-01 9.33e+01
  angle pdb=" C6    A O   2 "
        pdb=" N6    A O   2 "
        pdb=" H61   A O   2 "
      ideal   model   delta    sigma   weight residual
     120.00  145.38  -25.38 3.00e+00 1.11e-01 7.16e+01
  angle pdb=" OE1 GLN G  52 "
        pdb=" CD  GLN G  52 "
        pdb=" NE2 GLN G  52 "
      ideal   model   delta    sigma   weight residual
     122.60  116.60    6.00 1.00e+00 1.00e+00 3.60e+01
  angle pdb=" C   GLN C  41 "
        pdb=" N   PHE C  42 "
        pdb=" CA  PHE C  42 "
      ideal   model   delta    sigma   weight residual
     122.08  130.27   -8.19 1.47e+00 4.63e-01 3.10e+01
  angle pdb=" C6    A P   4 "
        pdb=" N6    A P   4 "
        pdb=" H61   A P   4 "
      ideal   model   delta    sigma   weight residual
     120.00  103.42   16.58 3.00e+00 1.11e-01 3.05e+01
  ... (remaining 56851 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 13397
       17.97 -    35.93: 679
       35.93 -    53.90: 298
       53.90 -    71.87: 318
       71.87 -    89.83: 52
  Dihedral angle restraints: 14744
    sinusoidal: 8342
      harmonic: 6402
  Sorted by residual:
  dihedral pdb=" CA  ASP H   9 "
           pdb=" C   ASP H   9 "
           pdb=" N   PRO H  10 "
           pdb=" CA  PRO H  10 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  139.08   40.92     0      5.00e+00 4.00e-02 6.70e+01
  dihedral pdb=" CA  LYS M  47 "
           pdb=" C   LYS M  47 "
           pdb=" N   ASN M  48 "
           pdb=" CA  ASN M  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.19   28.81     0      5.00e+00 4.00e-02 3.32e+01
  dihedral pdb=" CA  LEU A  62 "
           pdb=" C   LEU A  62 "
           pdb=" N   PRO A  63 "
           pdb=" CA  PRO A  63 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.07  -24.93     0      5.00e+00 4.00e-02 2.49e+01
  ... (remaining 14741 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1924
       0.070 -    0.140: 436
       0.140 -    0.211: 67
       0.211 -    0.281: 15
       0.281 -    0.351: 3
  Chirality restraints: 2445
  Sorted by residual:
  chirality pdb=" CB  VAL C  43 "
            pdb=" CA  VAL C  43 "
            pdb=" CG1 VAL C  43 "
            pdb=" CG2 VAL C  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.35 2.00e-01 2.50e+01 3.08e+00
  chirality pdb=" CB  ILE N  24 "
            pdb=" CA  ILE N  24 "
            pdb=" CG1 ILE N  24 "
            pdb=" CG2 ILE N  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.34 2.00e-01 2.50e+01 2.96e+00
  chirality pdb=" CB  ILE D  24 "
            pdb=" CA  ILE D  24 "
            pdb=" CG1 ILE D  24 "
            pdb=" CG2 ILE D  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.47e+00
  ... (remaining 2442 not shown)

  Planarity restraints: 4465
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN S 240 "   -0.215 2.00e-02 2.50e+03   4.06e-01 2.48e+03
        pdb=" CD  GLN S 240 "    0.029 2.00e-02 2.50e+03
        pdb=" OE1 GLN S 240 "    0.205 2.00e-02 2.50e+03
        pdb=" NE2 GLN S 240 "   -0.000 2.00e-02 2.50e+03
        pdb="HE21 GLN S 240 "    0.662 2.00e-02 2.50e+03
        pdb="HE22 GLN S 240 "   -0.681 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN R 240 "   -0.224 2.00e-02 2.50e+03   2.56e-01 9.80e+02
        pdb=" CD  GLN R 240 "    0.026 2.00e-02 2.50e+03
        pdb=" OE1 GLN R 240 "    0.209 2.00e-02 2.50e+03
        pdb=" NE2 GLN R 240 "    0.001 2.00e-02 2.50e+03
        pdb="HE21 GLN R 240 "    0.379 2.00e-02 2.50e+03
        pdb="HE22 GLN R 240 "   -0.392 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C6    A P  10 "   -0.066 2.00e-02 2.50e+03   1.51e-01 2.29e+02
        pdb=" N6    A P  10 "    0.261 2.00e-02 2.50e+03
        pdb=" H61   A P  10 "   -0.095 2.00e-02 2.50e+03
        pdb=" H62   A P  10 "   -0.100 2.00e-02 2.50e+03
  ... (remaining 4462 not shown)

  Histogram of nonbonded interaction distances:
        1.11 -     1.81: 360
        1.81 -     2.51: 21717
        2.51 -     3.20: 93512
        3.20 -     3.90: 128795
        3.90 -     4.60: 196130
  Nonbonded interactions: 440514
  Sorted by model distance:
  nonbonded pdb=" HG  SER K  38 "
            pdb=" H   PHE K  39 "
     model   vdw
     1.108 2.100
  nonbonded pdb=" HG  SER I  38 "
            pdb=" H   PHE I  39 "
     model   vdw
     1.179 2.100
  nonbonded pdb=" HG  SER N  60 "
            pdb=" H   THR N  61 "
     model   vdw
     1.261 2.100
  nonbonded pdb=" HG  SER F  60 "
            pdb=" H   THR F  61 "
     model   vdw
     1.294 2.100
  nonbonded pdb=" H1  HIS N   5 "
            pdb=" H   SER N   6 "
     model   vdw
     1.302 2.100
  ... (remaining 440509 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'R'
  selection = chain 'S'
}
ncs_group {
  reference = (chain 'C' and resid 6 through 69)
  selection = (chain 'D' and resid 6 through 69)
  selection = (chain 'E' and resid 6 through 69)
  selection = (chain 'F' and resid 6 through 69)
  selection = (chain 'G' and resid 6 through 69)
  selection = (chain 'H' and resid 6 through 69)
  selection = (chain 'I' and resid 6 through 69)
  selection = (chain 'J' and resid 6 through 69)
  selection = (chain 'K' and resid 6 through 69)
  selection = (chain 'L' and resid 6 through 69)
  selection = (chain 'M' and resid 6 through 69)
  selection = (chain 'N' and resid 6 through 69)
}
ncs_group {
  reference = chain 'O'
  selection = chain 'P'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.430
  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:             0.170
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.090
  Set scattering table:                    0.080
  Process input model:                     29.410
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
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      :  0.006   0.069  16115  Z= 0.280
  Angle     :  0.993  13.362  22023  Z= 0.556
  Chirality :  0.062   0.351   2445
  Planarity :  0.008   0.111   2708
  Dihedral  : 12.658  89.831   6205
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  5.55 %
    Favored  : 93.91 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.98 %
    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: -3.39 (0.17), residues: 1809
  helix: -2.95 (0.19), residues: 345
  sheet: -2.23 (0.19), residues: 582
  loop : -1.83 (0.18), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  93 
 TYR   0.042   0.003   TYR C  11 
 PHE   0.032   0.003   PHE G  42 
 TRP   0.035   0.003   TRP A 217 
 HIS   0.010   0.003   HIS F  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00578 (16115)
  covalent geometry    : angle       0.99286 (22023)
  hydrogen bonds       : bond        0.16417 (  561)
  hydrogen bonds       : angle       7.58727 ( 1545)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  430 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 421
  time to evaluate  : 0.853 
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: 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   41 PHE cc_start: 0.7389 (t80) cc_final: 0.7156 (t80)
REVERT: B  234 ASN cc_start: 0.7363 (m-40) cc_final: 0.7051 (m110)
REVERT: E   60 SER cc_start: 0.8791 (t) cc_final: 0.8566 (p)
REVERT: I   66 ARG cc_start: 0.8060 (ttp-110) cc_final: 0.7747 (mtm110)
REVERT: M   18 GLU cc_start: 0.7131 (mp0) cc_final: 0.6867 (mp0)
  outliers start: 9
  outliers final: 6
  residues processed: 427
  average time/residue: 0.4296
  time to fit residues: 241.4918
Evaluate side-chains
  286 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 280
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain F residue    9 ASP
Chi-restraints excluded: chain J residue    9 ASP
Chi-restraints excluded: chain S residue  180 GLU
Chi-restraints excluded: chain S residue  243 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A   7 ASN
A 214 ASN
B   7 ASN
B 214 ASN
E   8 GLN
E  52 GLN
F   8 GLN
G  28 ASN
H  48 ASN
I  41 GLN
J   8 GLN
J  28 ASN
K   8 GLN
K  48 ASN
L  28 ASN
L  41 GLN
L  48 ASN
L  52 GLN
N  52 GLN
R  34 GLN
R 214 ASN
S 214 ASN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.133062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.104029 restraints weight = 71529.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.96
r_work: 0.3311 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  16115  Z= 0.134
  Angle     :  0.610   7.289  22023  Z= 0.319
  Chirality :  0.046   0.170   2445
  Planarity :  0.006   0.096   2708
  Dihedral  : 10.811  73.639   2532
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  9.45 %
    Favored  : 88.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.98 %
    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: -2.45 (0.19), residues: 1809
  helix: -1.42 (0.25), residues: 395
  sheet: -1.93 (0.20), residues: 599
  loop : -1.28 (0.22), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  19 
 TYR   0.014   0.001   TYR B 221 
 PHE   0.018   0.001   PHE B  41 
 TRP   0.013   0.001   TRP A 217 
 HIS   0.004   0.001   HIS F  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (16115)
  covalent geometry    : angle       0.61048 (22023)
  hydrogen bonds       : bond        0.04485 (  561)
  hydrogen bonds       : angle       5.75611 ( 1545)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 316
  time to evaluate  : 0.682 
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   12 GLN cc_start: 0.8209 (tp-100) cc_final: 0.7760 (tp-100)
REVERT: A   35 ASP cc_start: 0.8169 (t0) cc_final: 0.7887 (t0)
REVERT: A   41 PHE cc_start: 0.7812 (t80) cc_final: 0.7465 (t80)
REVERT: B  127 ASP cc_start: 0.8126 (m-30) cc_final: 0.7915 (m-30)
REVERT: B  131 HIS cc_start: 0.7130 (m170) cc_final: 0.6869 (m170)
REVERT: B  199 ASP cc_start: 0.7150 (t0) cc_final: 0.6845 (t0)
REVERT: B  234 ASN cc_start: 0.8037 (m-40) cc_final: 0.7711 (m110)
REVERT: I   66 ARG cc_start: 0.8182 (ttp-110) cc_final: 0.7835 (mtm110)
REVERT: J   19 ARG cc_start: 0.8355 (mtt90) cc_final: 0.7564 (mmt90)
REVERT: N   69 ARG cc_start: 0.7739 (mtp-110) cc_final: 0.6638 (mtm-85)
REVERT: R  101 LYS cc_start: 0.8678 (tptp) cc_final: 0.8194 (tppt)
REVERT: S   86 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7844 (mm-30)
REVERT: S  142 GLU cc_start: 0.6750 (mm-30) cc_final: 0.5896 (mm-30)
REVERT: S  208 GLU cc_start: 0.8280 (tp30) cc_final: 0.7950 (tp30)
REVERT: S  212 MET cc_start: 0.6988 (mmp) cc_final: 0.6779 (mmm)
  outliers start: 28
  outliers final: 18
  residues processed: 338
  average time/residue: 0.4100
  time to fit residues: 186.2677
Evaluate side-chains
  281 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 263
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain E residue   38 SER
Chi-restraints excluded: chain F residue    9 ASP
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain G residue   38 SER
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain J residue   38 SER
Chi-restraints excluded: chain K residue    8 GLN
Chi-restraints excluded: chain K residue   45 LEU
Chi-restraints excluded: chain K residue   51 SER
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   33 GLN
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain S residue  130 THR
Chi-restraints excluded: chain S residue  131 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 138 optimal weight:    9.9990
   chunk 119 optimal weight:    4.9990
   chunk 165 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 150 optimal weight:    9.9990
   chunk 132 optimal weight:    0.0980
   chunk 64 optimal weight:    5.9990
   chunk 113 optimal weight:    5.9990
   chunk 126 optimal weight:   10.0000
   overall best weight:    4.4188

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

Flipped N/Q/H residues before XYZ refinement:
A   9 ASN
A 153 HIS
B 136 GLN
C  57 HIS
D   8 GLN
E   8 GLN
J  28 ASN
K  52 GLN
** M  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  57 HIS
R  12 GLN
S 209 GLN
** S 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.126056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.096609 restraints weight = 72549.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.06
r_work: 0.3164 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3031 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.3721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.097  16115  Z= 0.332
  Angle     :  0.719   8.310  22023  Z= 0.379
  Chirality :  0.051   0.182   2445
  Planarity :  0.006   0.096   2708
  Dihedral  : 11.062  73.629   2524
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 10.05 %
    Favored  : 87.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.98 %
    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: -2.14 (0.20), residues: 1809
  helix: -0.55 (0.27), residues: 393
  sheet: -1.70 (0.20), residues: 588
  loop : -1.49 (0.21), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C  16 
 TYR   0.022   0.002   TYR B 221 
 PHE   0.017   0.002   PHE A 125 
 TRP   0.024   0.002   TRP A 217 
 HIS   0.011   0.002   HIS K  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00812 (16115)
  covalent geometry    : angle       0.71948 (22023)
  hydrogen bonds       : bond        0.05342 (  561)
  hydrogen bonds       : angle       5.59869 ( 1545)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 258
  time to evaluate  : 0.828 
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: A   12 GLN cc_start: 0.8328 (tp-100) cc_final: 0.7959 (tp-100)
REVERT: A   41 PHE cc_start: 0.7859 (t80) cc_final: 0.7480 (t80)
REVERT: A   59 ASP cc_start: 0.8291 (p0) cc_final: 0.8053 (p0)
REVERT: A  140 ARG cc_start: 0.6976 (mtm180) cc_final: 0.6738 (mtm180)
REVERT: B   83 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8041 (tt)
REVERT: B  199 ASP cc_start: 0.7934 (t0) cc_final: 0.7722 (t0)
REVERT: B  234 ASN cc_start: 0.8211 (m-40) cc_final: 0.7887 (m110)
REVERT: C   13 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.8065 (m-40)
REVERT: I   31 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8083 (tttt)
REVERT: I   66 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.7916 (mtm110)
REVERT: J   19 ARG cc_start: 0.8285 (mtt90) cc_final: 0.7588 (mmt-90)
REVERT: N   24 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7342 (mt)
REVERT: R   41 PHE cc_start: 0.6574 (m-80) cc_final: 0.5963 (m-10)
REVERT: R  100 ASP cc_start: 0.7827 (p0) cc_final: 0.7273 (p0)
REVERT: R  101 LYS cc_start: 0.8705 (tptp) cc_final: 0.8207 (tppt)
REVERT: S  212 MET cc_start: 0.6900 (mmp) cc_final: 0.6461 (mmp)
  outliers start: 41
  outliers final: 31
  residues processed: 287
  average time/residue: 0.4180
  time to fit residues: 160.5209
Evaluate side-chains
  269 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 234
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  111 SER
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain C residue   13 ASN
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   65 SER
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   38 SER
Chi-restraints excluded: chain F residue    9 ASP
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain G residue   38 SER
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain I residue   31 LYS
Chi-restraints excluded: chain I residue   38 SER
Chi-restraints excluded: chain J residue   44 ILE
Chi-restraints excluded: chain K residue   45 LEU
Chi-restraints excluded: chain K residue   51 SER
Chi-restraints excluded: chain L residue   33 GLN
Chi-restraints excluded: chain L residue   43 VAL
Chi-restraints excluded: chain M residue   33 GLN
Chi-restraints excluded: chain M residue   50 VAL
Chi-restraints excluded: chain N residue   20 VAL
Chi-restraints excluded: chain N residue   24 ILE
Chi-restraints excluded: chain N residue   63 VAL
Chi-restraints excluded: chain R residue  131 HIS
Chi-restraints excluded: chain S residue    5 SER
Chi-restraints excluded: chain S residue  130 THR
Chi-restraints excluded: chain S residue  131 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 151 optimal weight:   20.0000
   chunk 133 optimal weight:    9.9990
   chunk 92 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 125 optimal weight:    3.9990
   chunk 84 optimal weight:    0.7980
   chunk 115 optimal weight:    2.9990
   chunk 158 optimal weight:    0.3980
   chunk 81 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A   9 ASN
J  28 ASN
** M  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.129317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.100006 restraints weight = 70903.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.05
r_work: 0.3237 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.3931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  16115  Z= 0.116
  Angle     :  0.565   7.151  22023  Z= 0.293
  Chirality :  0.045   0.167   2445
  Planarity :  0.005   0.088   2708
  Dihedral  : 10.492  73.621   2524
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 12.13 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.98 %
    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: -1.58 (0.20), residues: 1809
  helix: -0.20 (0.28), residues: 393
  sheet: -1.42 (0.21), residues: 572
  loop : -1.04 (0.23), residues: 844

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG J  66 
 TYR   0.020   0.001   TYR S 187 
 PHE   0.013   0.001   PHE B  41 
 TRP   0.011   0.001   TRP A 217 
 HIS   0.006   0.001   HIS S 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (16115)
  covalent geometry    : angle       0.56531 (22023)
  hydrogen bonds       : bond        0.03994 (  561)
  hydrogen bonds       : angle       5.25474 ( 1545)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 258
  time to evaluate  : 0.537 
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: A   12 GLN cc_start: 0.8242 (tp-100) cc_final: 0.7920 (tp-100)
REVERT: A   41 PHE cc_start: 0.7762 (t80) cc_final: 0.7359 (t80)
REVERT: B   83 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8046 (tt)
REVERT: B  199 ASP cc_start: 0.7826 (t0) cc_final: 0.7579 (t0)
REVERT: B  234 ASN cc_start: 0.8051 (m-40) cc_final: 0.7733 (m110)
REVERT: C   37 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7474 (mm-30)
REVERT: I   66 ARG cc_start: 0.8207 (ttp-110) cc_final: 0.7846 (mtm110)
REVERT: J   19 ARG cc_start: 0.8352 (mtt90) cc_final: 0.7663 (mmt-90)
REVERT: K   17 LYS cc_start: 0.7949 (mtmm) cc_final: 0.7673 (mtpt)
REVERT: N   24 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7222 (mt)
REVERT: N   38 SER cc_start: 0.9358 (t) cc_final: 0.9119 (p)
REVERT: N   69 ARG cc_start: 0.7816 (mtp-110) cc_final: 0.6679 (mtm-85)
REVERT: R   41 PHE cc_start: 0.6497 (m-80) cc_final: 0.5915 (m-10)
REVERT: R  101 LYS cc_start: 0.8654 (tptp) cc_final: 0.8213 (tppt)
REVERT: S  212 MET cc_start: 0.6872 (mmp) cc_final: 0.6569 (mmp)
REVERT: S  213 LEU cc_start: 0.8526 (tt) cc_final: 0.8268 (mp)
  outliers start: 28
  outliers final: 23
  residues processed: 273
  average time/residue: 0.4055
  time to fit residues: 146.9619
Evaluate side-chains
  267 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 242
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain D residue   38 SER
Chi-restraints excluded: chain E residue   38 SER
Chi-restraints excluded: chain F residue    9 ASP
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain F residue   47 LYS
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain J residue   28 ASN
Chi-restraints excluded: chain K residue    9 ASP
Chi-restraints excluded: chain K residue   45 LEU
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   33 GLN
Chi-restraints excluded: chain L residue   43 VAL
Chi-restraints excluded: chain M residue   50 VAL
Chi-restraints excluded: chain N residue   24 ILE
Chi-restraints excluded: chain N residue   63 VAL
Chi-restraints excluded: chain R residue  131 HIS
Chi-restraints excluded: chain S residue    5 SER
Chi-restraints excluded: chain S residue  130 THR
Chi-restraints excluded: chain S residue  131 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 142 optimal weight:    0.0980
   chunk 145 optimal weight:    9.9990
   chunk 169 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 121 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 168 optimal weight:   10.0000
   chunk 105 optimal weight:    3.9990
   overall best weight:    2.6188

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

Flipped N/Q/H residues before XYZ refinement:
** M  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 214 ASN
** S 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.127266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.098024 restraints weight = 72159.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.06
r_work: 0.3192 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.4176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  16115  Z= 0.208
  Angle     :  0.600   5.957  22023  Z= 0.313
  Chirality :  0.046   0.195   2445
  Planarity :  0.005   0.088   2708
  Dihedral  : 10.481  73.515   2523
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 11.82 %
    Favored  : 85.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.98 %
    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: -1.51 (0.20), residues: 1809
  helix: -0.01 (0.28), residues: 401
  sheet: -1.34 (0.21), residues: 572
  loop : -1.11 (0.23), residues: 836

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG J  66 
 TYR   0.015   0.002   TYR B 221 
 PHE   0.016   0.001   PHE N  39 
 TRP   0.014   0.001   TRP A 217 
 HIS   0.006   0.001   HIS K  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 (16115)
  covalent geometry    : angle       0.59956 (22023)
  hydrogen bonds       : bond        0.04353 (  561)
  hydrogen bonds       : angle       5.24869 ( 1545)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 243
  time to evaluate  : 0.882 
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   12 GLN cc_start: 0.8311 (tp-100) cc_final: 0.7999 (tp-100)
REVERT: A   41 PHE cc_start: 0.7764 (t80) cc_final: 0.7363 (t80)
REVERT: B   61 GLU cc_start: 0.8299 (tp30) cc_final: 0.8097 (tp30)
REVERT: B   83 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8139 (tt)
REVERT: B  199 ASP cc_start: 0.7970 (t0) cc_final: 0.7727 (t0)
REVERT: B  234 ASN cc_start: 0.8120 (m-40) cc_final: 0.7797 (m110)
REVERT: C   53 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.7695 (tmm)
REVERT: I   31 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8048 (tttt)
REVERT: I   66 ARG cc_start: 0.8186 (ttp-110) cc_final: 0.7846 (mtm110)
REVERT: J   19 ARG cc_start: 0.8317 (mtt90) cc_final: 0.7649 (mmt-90)
REVERT: N   24 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7255 (mt)
REVERT: R   41 PHE cc_start: 0.6435 (m-80) cc_final: 0.5952 (m-10)
REVERT: R  101 LYS cc_start: 0.8720 (tptp) cc_final: 0.8314 (tppt)
REVERT: S  213 LEU cc_start: 0.8562 (tt) cc_final: 0.8304 (mp)
REVERT: S  251 VAL cc_start: 0.5383 (OUTLIER) cc_final: 0.5076 (p)
  outliers start: 41
  outliers final: 32
  residues processed: 274
  average time/residue: 0.4281
  time to fit residues: 155.4783
Evaluate side-chains
  271 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 234
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  127 ASP
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  111 SER
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain D residue    5 HIS
Chi-restraints excluded: chain D residue   38 SER
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   38 SER
Chi-restraints excluded: chain F residue    9 ASP
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain I residue   31 LYS
Chi-restraints excluded: chain I residue   38 SER
Chi-restraints excluded: chain I residue   43 VAL
Chi-restraints excluded: chain J residue   38 SER
Chi-restraints excluded: chain K residue   45 LEU
Chi-restraints excluded: chain L residue   33 GLN
Chi-restraints excluded: chain L residue   43 VAL
Chi-restraints excluded: chain L residue   63 VAL
Chi-restraints excluded: chain M residue   50 VAL
Chi-restraints excluded: chain N residue   24 ILE
Chi-restraints excluded: chain N residue   63 VAL
Chi-restraints excluded: chain R residue  131 HIS
Chi-restraints excluded: chain S residue    5 SER
Chi-restraints excluded: chain S residue   72 SER
Chi-restraints excluded: chain S residue  130 THR
Chi-restraints excluded: chain S residue  251 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 109 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 166 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 158 optimal weight:    8.9990
   chunk 53 optimal weight:    0.8980
   chunk 97 optimal weight:    5.9990
   chunk 135 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 138 optimal weight:    9.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
F  57 HIS
** M  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  49 GLN
S 121 GLN
** S 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.126855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.097208 restraints weight = 71034.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 2.05
r_work: 0.3190 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.4486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.086  16115  Z= 0.270
  Angle     :  0.648   6.270  22023  Z= 0.339
  Chirality :  0.049   0.220   2445
  Planarity :  0.006   0.088   2708
  Dihedral  : 10.612  73.732   2523
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 11.40 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.98 %
    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: -1.70 (0.20), residues: 1809
  helix: -0.13 (0.28), residues: 401
  sheet: -1.42 (0.21), residues: 574
  loop : -1.28 (0.22), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG N  69 
 TYR   0.024   0.002   TYR L  55 
 PHE   0.016   0.002   PHE C  42 
 TRP   0.017   0.002   TRP A 217 
 HIS   0.008   0.002   HIS K  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00655 (16115)
  covalent geometry    : angle       0.64799 (22023)
  hydrogen bonds       : bond        0.04760 (  561)
  hydrogen bonds       : angle       5.37279 ( 1545)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 237
  time to evaluate  : 0.530 
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   12 GLN cc_start: 0.8416 (tp-100) cc_final: 0.8104 (tp-100)
REVERT: A   41 PHE cc_start: 0.7802 (t80) cc_final: 0.7404 (t80)
REVERT: A  109 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7795 (mp)
REVERT: B  199 ASP cc_start: 0.8091 (t0) cc_final: 0.7871 (t0)
REVERT: B  234 ASN cc_start: 0.8178 (m-40) cc_final: 0.7869 (m110)
REVERT: C   37 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7498 (mm-30)
REVERT: C   53 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8595 (ttp)
REVERT: E   35 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8074 (mt0)
REVERT: I   31 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8075 (tttt)
REVERT: I   66 ARG cc_start: 0.8091 (ttp-110) cc_final: 0.7750 (mtm110)
REVERT: J   19 ARG cc_start: 0.8227 (mtt90) cc_final: 0.7663 (mmt-90)
REVERT: N   24 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7276 (mt)
REVERT: N   69 ARG cc_start: 0.7788 (mtp-110) cc_final: 0.6504 (mtm-85)
REVERT: R   41 PHE cc_start: 0.6530 (m-80) cc_final: 0.6043 (m-10)
REVERT: R  101 LYS cc_start: 0.8606 (tptp) cc_final: 0.8240 (tppt)
REVERT: S  214 ASN cc_start: 0.8127 (t0) cc_final: 0.7836 (t0)
  outliers start: 56
  outliers final: 47
  residues processed: 281
  average time/residue: 0.3954
  time to fit residues: 148.8840
Evaluate side-chains
  279 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 227
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  127 ASP
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  111 SER
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain D residue    5 HIS
Chi-restraints excluded: chain D residue   27 VAL
Chi-restraints excluded: chain D residue   38 SER
Chi-restraints excluded: chain D residue   50 VAL
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   35 GLN
Chi-restraints excluded: chain E residue   38 SER
Chi-restraints excluded: chain F residue    9 ASP
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain F residue   44 ILE
Chi-restraints excluded: chain G residue   38 SER
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain I residue   31 LYS
Chi-restraints excluded: chain I residue   38 SER
Chi-restraints excluded: chain J residue   44 ILE
Chi-restraints excluded: chain K residue   43 VAL
Chi-restraints excluded: chain K residue   45 LEU
Chi-restraints excluded: chain K residue   51 SER
Chi-restraints excluded: chain L residue   20 VAL
Chi-restraints excluded: chain L residue   33 GLN
Chi-restraints excluded: chain L residue   43 VAL
Chi-restraints excluded: chain L residue   63 VAL
Chi-restraints excluded: chain M residue   33 GLN
Chi-restraints excluded: chain M residue   50 VAL
Chi-restraints excluded: chain N residue   24 ILE
Chi-restraints excluded: chain N residue   27 VAL
Chi-restraints excluded: chain N residue   63 VAL
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain R residue  251 VAL
Chi-restraints excluded: chain S residue    1 MET
Chi-restraints excluded: chain S residue    5 SER
Chi-restraints excluded: chain S residue   72 SER
Chi-restraints excluded: chain S residue  130 THR
Chi-restraints excluded: chain S residue  131 HIS
Chi-restraints excluded: chain S residue  251 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 165 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 149 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 169 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 176 optimal weight:    9.9990
   chunk 49 optimal weight:    0.6980
   chunk 102 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
J  28 ASN
** M  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.128441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.099106 restraints weight = 71842.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.04
r_work: 0.3215 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.4564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  16115  Z= 0.124
  Angle     :  0.559   7.490  22023  Z= 0.289
  Chirality :  0.045   0.200   2445
  Planarity :  0.005   0.081   2708
  Dihedral  : 10.218  73.612   2523
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 13.04 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.98 %
    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: -1.30 (0.21), residues: 1809
  helix:  0.12 (0.28), residues: 401
  sheet: -1.28 (0.21), residues: 566
  loop : -0.90 (0.23), residues: 842

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG J  66 
 TYR   0.017   0.001   TYR S 132 
 PHE   0.014   0.001   PHE N  39 
 TRP   0.009   0.001   TRP A 217 
 HIS   0.004   0.001   HIS B 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (16115)
  covalent geometry    : angle       0.55890 (22023)
  hydrogen bonds       : bond        0.03892 (  561)
  hydrogen bonds       : angle       5.17275 ( 1545)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 250
  time to evaluate  : 0.647 
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   12 GLN cc_start: 0.8342 (tp-100) cc_final: 0.8079 (tp-100)
REVERT: A   41 PHE cc_start: 0.7723 (t80) cc_final: 0.7360 (t80)
REVERT: A  109 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7724 (mp)
REVERT: B  199 ASP cc_start: 0.8056 (t0) cc_final: 0.7822 (t0)
REVERT: B  234 ASN cc_start: 0.8094 (m-40) cc_final: 0.7771 (m110)
REVERT: C   37 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7451 (mm-30)
REVERT: I   66 ARG cc_start: 0.8134 (ttp-110) cc_final: 0.7780 (mtm110)
REVERT: J   19 ARG cc_start: 0.8250 (mtt90) cc_final: 0.7697 (mmt-90)
REVERT: N   24 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7232 (mt)
REVERT: N   38 SER cc_start: 0.9382 (t) cc_final: 0.9122 (p)
REVERT: N   69 ARG cc_start: 0.7814 (mtp-110) cc_final: 0.6542 (mtm-85)
REVERT: R   41 PHE cc_start: 0.6466 (m-80) cc_final: 0.6003 (m-10)
REVERT: R  101 LYS cc_start: 0.8568 (tptp) cc_final: 0.8202 (tppt)
REVERT: R  135 LYS cc_start: 0.7900 (ttmm) cc_final: 0.7511 (tptt)
REVERT: S  213 LEU cc_start: 0.8614 (tt) cc_final: 0.8348 (mp)
REVERT: S  214 ASN cc_start: 0.8099 (t0) cc_final: 0.7745 (t0)
REVERT: S  251 VAL cc_start: 0.5752 (OUTLIER) cc_final: 0.5436 (p)
  outliers start: 35
  outliers final: 26
  residues processed: 274
  average time/residue: 0.3866
  time to fit residues: 142.2419
Evaluate side-chains
  271 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 242
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain D residue    5 HIS
Chi-restraints excluded: chain E residue   38 SER
Chi-restraints excluded: chain F residue    9 ASP
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain F residue   48 ASN
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain I residue   43 VAL
Chi-restraints excluded: chain I residue   54 VAL
Chi-restraints excluded: chain J residue   38 SER
Chi-restraints excluded: chain K residue   45 LEU
Chi-restraints excluded: chain K residue   51 SER
Chi-restraints excluded: chain L residue   33 GLN
Chi-restraints excluded: chain L residue   43 VAL
Chi-restraints excluded: chain M residue   50 VAL
Chi-restraints excluded: chain N residue   24 ILE
Chi-restraints excluded: chain N residue   63 VAL
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain S residue    5 SER
Chi-restraints excluded: chain S residue   72 SER
Chi-restraints excluded: chain S residue  130 THR
Chi-restraints excluded: chain S residue  131 HIS
Chi-restraints excluded: chain S residue  251 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 126 optimal weight:   10.0000
   chunk 93 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 158 optimal weight:    0.0030
   chunk 64 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 83 optimal weight:    0.5980
   chunk 142 optimal weight:    4.9990
   chunk 51 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.9992

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

Flipped N/Q/H residues before XYZ refinement:
C  52 GLN
R 131 HIS
** S 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.130357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.100717 restraints weight = 70439.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 2.06
r_work: 0.3248 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.4652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16115  Z= 0.114
  Angle     :  0.539   6.911  22023  Z= 0.278
  Chirality :  0.044   0.191   2445
  Planarity :  0.005   0.079   2708
  Dihedral  :  9.944  73.521   2523
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 12.92 %
    Favored  : 85.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.98 %
    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: -1.02 (0.21), residues: 1809
  helix:  0.43 (0.29), residues: 400
  sheet: -1.24 (0.21), residues: 566
  loop : -0.65 (0.24), residues: 843

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG J  66 
 TYR   0.018   0.001   TYR S 132 
 PHE   0.013   0.001   PHE B  41 
 TRP   0.009   0.001   TRP B 217 
 HIS   0.004   0.001   HIS B 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (16115)
  covalent geometry    : angle       0.53917 (22023)
  hydrogen bonds       : bond        0.03671 (  561)
  hydrogen bonds       : angle       5.06608 ( 1545)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 249
  time to evaluate  : 0.878 
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: A   12 GLN cc_start: 0.8334 (tp-100) cc_final: 0.8068 (tp-100)
REVERT: A   41 PHE cc_start: 0.7721 (t80) cc_final: 0.7347 (t80)
REVERT: B  199 ASP cc_start: 0.8017 (t0) cc_final: 0.7764 (t0)
REVERT: B  234 ASN cc_start: 0.8101 (m-40) cc_final: 0.7778 (m110)
REVERT: D   47 LYS cc_start: 0.8848 (tttm) cc_final: 0.8539 (tppt)
REVERT: I   31 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7986 (tttt)
REVERT: I   66 ARG cc_start: 0.8063 (ttp-110) cc_final: 0.7678 (mtm110)
REVERT: J   19 ARG cc_start: 0.8193 (mtt90) cc_final: 0.7563 (mmt90)
REVERT: N   24 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7268 (mt)
REVERT: N   38 SER cc_start: 0.9340 (t) cc_final: 0.9107 (p)
REVERT: N   69 ARG cc_start: 0.7800 (mtp-110) cc_final: 0.6548 (mtm-85)
REVERT: R   41 PHE cc_start: 0.6559 (m-80) cc_final: 0.6102 (m-10)
REVERT: R  100 ASP cc_start: 0.7607 (p0) cc_final: 0.7338 (p0)
REVERT: R  101 LYS cc_start: 0.8574 (tptp) cc_final: 0.8186 (tppt)
REVERT: R  135 LYS cc_start: 0.7933 (ttmm) cc_final: 0.7593 (tptt)
REVERT: S  213 LEU cc_start: 0.8577 (tt) cc_final: 0.8337 (mp)
REVERT: S  214 ASN cc_start: 0.8065 (t0) cc_final: 0.7696 (t0)
REVERT: S  251 VAL cc_start: 0.5634 (OUTLIER) cc_final: 0.5304 (p)
  outliers start: 34
  outliers final: 27
  residues processed: 272
  average time/residue: 0.3860
  time to fit residues: 141.8867
Evaluate side-chains
  273 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 243
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain D residue    5 HIS
Chi-restraints excluded: chain E residue   38 SER
Chi-restraints excluded: chain E residue   48 ASN
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain I residue   31 LYS
Chi-restraints excluded: chain I residue   43 VAL
Chi-restraints excluded: chain I residue   54 VAL
Chi-restraints excluded: chain J residue   28 ASN
Chi-restraints excluded: chain K residue   45 LEU
Chi-restraints excluded: chain K residue   51 SER
Chi-restraints excluded: chain L residue   33 GLN
Chi-restraints excluded: chain L residue   63 VAL
Chi-restraints excluded: chain N residue   24 ILE
Chi-restraints excluded: chain N residue   63 VAL
Chi-restraints excluded: chain R residue  131 HIS
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain S residue    5 SER
Chi-restraints excluded: chain S residue   72 SER
Chi-restraints excluded: chain S residue  130 THR
Chi-restraints excluded: chain S residue  131 HIS
Chi-restraints excluded: chain S residue  251 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 105 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 162 optimal weight:    3.9990
   chunk 67 optimal weight:    6.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
F  48 ASN
K  33 GLN
** M  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.127962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.098419 restraints weight = 70713.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.04
r_work: 0.3209 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.4753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073  16115  Z= 0.226
  Angle     :  0.604   7.955  22023  Z= 0.315
  Chirality :  0.047   0.227   2445
  Planarity :  0.005   0.084   2708
  Dihedral  : 10.137  73.683   2521
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.28 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.98 %
    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: -1.20 (0.21), residues: 1809
  helix:  0.37 (0.29), residues: 401
  sheet: -1.36 (0.21), residues: 578
  loop : -0.81 (0.24), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG J  66 
 TYR   0.021   0.002   TYR L  55 
 PHE   0.014   0.001   PHE A 243 
 TRP   0.014   0.001   TRP A 217 
 HIS   0.006   0.001   HIS R 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00546 (16115)
  covalent geometry    : angle       0.60386 (22023)
  hydrogen bonds       : bond        0.04294 (  561)
  hydrogen bonds       : angle       5.17288 ( 1545)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 234
  time to evaluate  : 0.748 
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: A   12 GLN cc_start: 0.8386 (tp-100) cc_final: 0.8109 (tp-100)
REVERT: A   41 PHE cc_start: 0.7731 (t80) cc_final: 0.7369 (t80)
REVERT: A  109 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7778 (mp)
REVERT: B  199 ASP cc_start: 0.8159 (t0) cc_final: 0.7921 (t0)
REVERT: B  234 ASN cc_start: 0.8224 (m-40) cc_final: 0.7891 (m110)
REVERT: C   53 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8568 (ttp)
REVERT: D   47 LYS cc_start: 0.8881 (tttm) cc_final: 0.8548 (tppt)
REVERT: E   35 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8073 (mt0)
REVERT: F   48 ASN cc_start: 0.7100 (OUTLIER) cc_final: 0.6840 (t0)
REVERT: G   47 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7751 (ttpt)
REVERT: I   31 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8082 (tttt)
REVERT: J   19 ARG cc_start: 0.8236 (mtt90) cc_final: 0.7658 (mmt-90)
REVERT: N   24 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7259 (mt)
REVERT: R   41 PHE cc_start: 0.6655 (m-80) cc_final: 0.6180 (m-10)
REVERT: R  100 ASP cc_start: 0.7558 (p0) cc_final: 0.7328 (p0)
REVERT: R  101 LYS cc_start: 0.8581 (tptp) cc_final: 0.8203 (tppt)
REVERT: R  135 LYS cc_start: 0.7896 (ttmm) cc_final: 0.7543 (tptt)
REVERT: S  213 LEU cc_start: 0.8664 (tt) cc_final: 0.8450 (mp)
REVERT: S  214 ASN cc_start: 0.8088 (t0) cc_final: 0.7662 (t0)
REVERT: S  259 ILE cc_start: 0.9007 (pp) cc_final: 0.8399 (tt)
  outliers start: 39
  outliers final: 31
  residues processed: 263
  average time/residue: 0.3919
  time to fit residues: 138.5263
Evaluate side-chains
  273 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 235
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain D residue    5 HIS
Chi-restraints excluded: chain E residue   35 GLN
Chi-restraints excluded: chain E residue   38 SER
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain F residue   44 ILE
Chi-restraints excluded: chain F residue   48 ASN
Chi-restraints excluded: chain G residue   47 LYS
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain I residue   31 LYS
Chi-restraints excluded: chain I residue   54 VAL
Chi-restraints excluded: chain J residue   28 ASN
Chi-restraints excluded: chain J residue   44 ILE
Chi-restraints excluded: chain K residue   45 LEU
Chi-restraints excluded: chain K residue   51 SER
Chi-restraints excluded: chain L residue   33 GLN
Chi-restraints excluded: chain L residue   43 VAL
Chi-restraints excluded: chain L residue   63 VAL
Chi-restraints excluded: chain M residue   33 GLN
Chi-restraints excluded: chain M residue   50 VAL
Chi-restraints excluded: chain N residue   24 ILE
Chi-restraints excluded: chain N residue   63 VAL
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain S residue    5 SER
Chi-restraints excluded: chain S residue   72 SER
Chi-restraints excluded: chain S residue  130 THR
Chi-restraints excluded: chain S residue  131 HIS
Chi-restraints excluded: chain S residue  251 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 131 optimal weight:   10.0000
   chunk 173 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 98 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
F  48 ASN
K  33 GLN
** M  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.128324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.098784 restraints weight = 70675.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 2.04
r_work: 0.3213 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3076 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.4765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.144  16115  Z= 0.198
  Angle     :  0.776  59.192  22023  Z= 0.439
  Chirality :  0.047   0.410   2445
  Planarity :  0.005   0.084   2708
  Dihedral  : 10.135  73.682   2521
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 13.22 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.98 %
    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: -1.20 (0.21), residues: 1809
  helix:  0.37 (0.29), residues: 401
  sheet: -1.36 (0.21), residues: 578
  loop : -0.81 (0.23), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG S 230 
 TYR   0.017   0.001   TYR B 221 
 PHE   0.014   0.001   PHE C  42 
 TRP   0.011   0.001   TRP A 217 
 HIS   0.005   0.001   HIS R 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 (16115)
  covalent geometry    : angle       0.77629 (22023)
  hydrogen bonds       : bond        0.04217 (  561)
  hydrogen bonds       : angle       5.17491 ( 1545)

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

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

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3618 Ramachandran restraints generated.
    1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 236
  time to evaluate  : 0.792 
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: A   12 GLN cc_start: 0.8384 (tp-100) cc_final: 0.8117 (tp-100)
REVERT: A   41 PHE cc_start: 0.7736 (t80) cc_final: 0.7375 (t80)
REVERT: A  109 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7764 (mp)
REVERT: B  199 ASP cc_start: 0.8158 (t0) cc_final: 0.7917 (t0)
REVERT: B  234 ASN cc_start: 0.8235 (m-40) cc_final: 0.7900 (m110)
REVERT: C   53 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8567 (ttp)
REVERT: D   47 LYS cc_start: 0.8878 (tttm) cc_final: 0.8544 (tppt)
REVERT: E   35 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8065 (mt0)
REVERT: G   47 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7742 (ttpt)
REVERT: I   31 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8076 (tttt)
REVERT: J   19 ARG cc_start: 0.8224 (mtt90) cc_final: 0.7584 (mmt90)
REVERT: N   24 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7262 (mt)
REVERT: R   41 PHE cc_start: 0.6663 (m-80) cc_final: 0.6195 (m-10)
REVERT: R  100 ASP cc_start: 0.7572 (p0) cc_final: 0.7342 (p0)
REVERT: R  101 LYS cc_start: 0.8583 (tptp) cc_final: 0.8202 (tppt)
REVERT: R  135 LYS cc_start: 0.7891 (ttmm) cc_final: 0.7545 (tptt)
REVERT: S  213 LEU cc_start: 0.8663 (tt) cc_final: 0.8448 (mp)
REVERT: S  214 ASN cc_start: 0.8089 (t0) cc_final: 0.7659 (t0)
REVERT: S  259 ILE cc_start: 0.9005 (pp) cc_final: 0.8399 (tt)
  outliers start: 40
  outliers final: 34
  residues processed: 267
  average time/residue: 0.3831
  time to fit residues: 138.7347
Evaluate side-chains
  276 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 236
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   74 LEU
Chi-restraints excluded: chain B residue  111 SER
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain D residue    5 HIS
Chi-restraints excluded: chain E residue   35 GLN
Chi-restraints excluded: chain E residue   38 SER
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain F residue   44 ILE
Chi-restraints excluded: chain G residue   47 LYS
Chi-restraints excluded: chain H residue   63 VAL
Chi-restraints excluded: chain I residue   31 LYS
Chi-restraints excluded: chain I residue   54 VAL
Chi-restraints excluded: chain J residue   28 ASN
Chi-restraints excluded: chain J residue   38 SER
Chi-restraints excluded: chain J residue   44 ILE
Chi-restraints excluded: chain K residue   45 LEU
Chi-restraints excluded: chain K residue   51 SER
Chi-restraints excluded: chain L residue   33 GLN
Chi-restraints excluded: chain L residue   43 VAL
Chi-restraints excluded: chain L residue   63 VAL
Chi-restraints excluded: chain M residue   33 GLN
Chi-restraints excluded: chain M residue   50 VAL
Chi-restraints excluded: chain N residue   24 ILE
Chi-restraints excluded: chain N residue   27 VAL
Chi-restraints excluded: chain N residue   63 VAL
Chi-restraints excluded: chain R residue  224 LEU
Chi-restraints excluded: chain S residue    5 SER
Chi-restraints excluded: chain S residue   72 SER
Chi-restraints excluded: chain S residue  130 THR
Chi-restraints excluded: chain S residue  131 HIS
Chi-restraints excluded: chain S residue  251 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 167 optimal weight:    3.9990
   chunk 113 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 109 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 132 optimal weight:    0.1980
   chunk 52 optimal weight:    2.9990
   chunk 133 optimal weight:   10.0000
   chunk 158 optimal weight:    0.8980
   chunk 74 optimal weight:   50.0000
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
F  48 ASN
K  33 GLN
** M  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.128228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.098664 restraints weight = 70919.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.05
r_work: 0.3212 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.4763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.144  16115  Z= 0.198
  Angle     :  0.776  59.192  22023  Z= 0.439
  Chirality :  0.047   0.410   2445
  Planarity :  0.005   0.084   2708
  Dihedral  : 10.135  73.682   2521
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 13.22 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.98 %
    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: -1.20 (0.21), residues: 1809
  helix:  0.37 (0.29), residues: 401
  sheet: -1.36 (0.21), residues: 578
  loop : -0.81 (0.23), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG S 230 
 TYR   0.017   0.001   TYR B 221 
 PHE   0.014   0.001   PHE C  42 
 TRP   0.011   0.001   TRP A 217 
 HIS   0.005   0.001   HIS R 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 (16115)
  covalent geometry    : angle       0.77629 (22023)
  hydrogen bonds       : bond        0.04217 (  561)
  hydrogen bonds       : angle       5.17491 ( 1545)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8456.71 seconds
wall clock time: 143 minutes 57.19 seconds (8637.19 seconds total)