Starting phenix.real_space_refine
on Wed Jan 15 14:54:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bbc_44417/01_2025/9bbc_44417.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bbc_44417/01_2025/9bbc_44417.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bbc_44417/01_2025/9bbc_44417.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bbc_44417/01_2025/9bbc_44417.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bbc_44417/01_2025/9bbc_44417.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bbc_44417/01_2025/9bbc_44417.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.034
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    5385      2.51       5
     N    1347      2.21       5
     O    1658      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8440
  Number of models: 1
  Model: ""
    Number of chains: 16
    Chain: "A"
      Number of atoms: 1932
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1932
          Classifications: {'peptide': 253}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 240}
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "B"
      Number of atoms: 2206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2206
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 268}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "D"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 810
          Classifications: {'peptide': 105}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 100}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "E"
      Number of atoms: 930
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 930
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 113}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 9
    Chain: "F"
      Number of atoms: 936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 936
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 113}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "G"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 888
          Classifications: {'peptide': 114}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 2, 'TRANS': 111}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
    Chain: "X"
      Number of atoms: 219
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 219
          Classifications: {'peptide': 30}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 1, 'TRANS': 28}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "Y"
      Number of atoms: 220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 220
          Classifications: {'peptide': 28}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 26}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "I"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "O"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "R"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "H"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 84
          Unusual residues: {'CLR': 1, 'NAG': 4}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "G"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "Y"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.53, per 1000 atoms: 0.66
  Number of scatterers: 8440
  At special positions: 0
  Unit cell: (88.56, 101.52, 138.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1658      8.00
     N    1347      7.00
     C    5385      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  42 " - pdb=" SG  CYS A 109 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 156 " - pdb=" SG  CYS A 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 228 " - pdb=" SG  CYS B 263 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  42 " - pdb=" SG  CYS B 110 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 163 " - pdb=" SG  CYS B 228 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  37 " - pdb=" SG  CYS D  73 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  93 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  49 " - pdb=" SG  CYS E  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 119 " - pdb=" SG  CYS E 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  49 " - pdb=" SG  CYS F  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 119 " - pdb=" SG  CYS F 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  46 " - pdb=" SG  CYS G  87 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G 104 " - pdb=" SG  CYS G 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS X  32 " - pdb=" SG  CYS Y  32 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG H   1 " - " NAG H   2 "
      " NAG H   2 " - " BMA H   3 "
      " NAG I   1 " - " NAG I   2 "
      " NAG O   1 " - " NAG O   2 "
      " NAG O   2 " - " BMA O   3 "
      " NAG R   1 " - " NAG R   2 "
    NAG-ASN
      " NAG A 301 " - " ASN A  82 "
      " NAG A 302 " - " ASN A 166 "
      " NAG A 303 " - " ASN A 200 "
      " NAG A 304 " - " ASN A 211 "
      " NAG C   1 " - " ASN D  38 "
      " NAG G 201 " - " ASN G  92 "
      " NAG H   1 " - " ASN D  74 "
      " NAG I   1 " - " ASN A  41 "
      " NAG O   1 " - " ASN B  84 "
      " NAG R   1 " - " ASN G  52 "
  Time building additional restraints: 2.51
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1962

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 17 sheets defined
      28.1% alpha, 31.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 100 through 104
    Processing helix  chain 'A' and resid 205 through 210
      removed outlier: 3.685A  pdb=" N   ALA A 209 " --> pdb=" O   ALA A 205 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   PHE A 210 " --> pdb=" O   CYS A 206 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 205 through 210'
    Processing helix  chain 'A' and resid 229 through 235
      removed outlier: 3.661A  pdb=" N   VAL A 233 " --> pdb=" O   ASP A 229 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS A 235 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 273
    Processing helix  chain 'B' and resid 101 through 105
      removed outlier: 3.503A  pdb=" N   THR B 105 " --> pdb=" O   PRO B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 138
      removed outlier: 3.980A  pdb=" N   ASN B 137 " --> pdb=" O   ASP B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 156
      removed outlier: 3.517A  pdb=" N   ILE B 153 " --> pdb=" O   SER B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 220
    Processing helix  chain 'B' and resid 266 through 305
    Processing helix  chain 'D' and resid 64 through 66
      No H-bonds generated for 'chain 'D' and resid 64 through 66'
    Processing helix  chain 'D' and resid 100 through 126
    Processing helix  chain 'E' and resid 88 through 93
      removed outlier: 3.653A  pdb=" N   SER E  93 " --> pdb=" O   GLU E  89 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 126 through 149
      removed outlier: 3.957A  pdb=" N   ILE E 133 " --> pdb=" O   SER E 129 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   VAL E 134 " --> pdb=" O   VAL E 130 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ILE E 135 " --> pdb=" O   ALA E 131 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   LEU E 147 " --> pdb=" O   GLY E 143 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 88 through 93
      removed outlier: 3.587A  pdb=" N   SER F  93 " --> pdb=" O   GLU F  89 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 104 through 108
    Processing helix  chain 'F' and resid 126 through 151
      removed outlier: 3.636A  pdb=" N   ALA F 131 " --> pdb=" O   VAL F 127 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   THR F 132 " --> pdb=" O   MET F 128 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ILE F 133 " --> pdb=" O   SER F 129 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   VAL F 134 " --> pdb=" O   VAL F 130 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE F 135 " --> pdb=" O   ALA F 131 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ILE F 138 " --> pdb=" O   VAL F 134 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLY F 143 " --> pdb=" O   CYS F 139 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LEU F 144 " --> pdb=" O   ILE F 140 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   LEU F 146 " --> pdb=" O   GLY F 142 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   LEU F 147 " --> pdb=" O   GLY F 143 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL F 148 " --> pdb=" O   LEU F 144 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 24 through 28
    Processing helix  chain 'G' and resid 78 through 80
      No H-bonds generated for 'chain 'G' and resid 78 through 80'
    Processing helix  chain 'G' and resid 111 through 137
    Processing helix  chain 'X' and resid 28 through 33
      removed outlier: 3.947A  pdb=" N   CYS X  32 " --> pdb=" O   ASP X  28 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 36 through 47
      removed outlier: 4.388A  pdb=" N   TYR X  42 " --> pdb=" O   ILE X  38 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ILE X  45 " --> pdb=" O   ILE X  41 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 48 through 51
    Processing helix  chain 'Y' and resid 29 through 55
    Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 26
      removed outlier: 3.601A  pdb=" N   ASN A  41 " --> pdb=" O   ILE A  26 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33
      removed outlier: 6.441A  pdb=" N   LEU A  30 " --> pdb=" O   ILE A 130 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   HIS A 132 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   VAL A  32 " --> pdb=" O   HIS A 132 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 145
      removed outlier: 4.407A  pdb=" N   VAL A 155 " --> pdb=" O   LEU A 145 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 145
      removed outlier: 4.407A  pdb=" N   VAL A 155 " --> pdb=" O   LEU A 145 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 26
    Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 33
      removed outlier: 3.531A  pdb=" N   VAL B 107 " --> pdb=" O   GLN B  56 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   TRP B  53 " --> pdb=" O   HIS B  66 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   HIS B  66 " --> pdb=" O   TRP B  53 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ARG B  55 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   LEU B  64 " --> pdb=" O   ARG B  55 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   ASP B  57 " --> pdb=" O   LEU B  62 " (cutoff:3.500A)
      removed outlier: 5.761A  pdb=" N   LEU B  62 " --> pdb=" O   ASP B  57 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 33
    Processing sheet with id=AA8, first strand: chain 'B' and resid 142 through 146
      removed outlier: 5.723A  pdb=" N   TYR B 206 " --> pdb=" O   GLY B 167 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 142 through 146
      removed outlier: 5.723A  pdb=" N   TYR B 206 " --> pdb=" O   GLY B 167 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 182 through 183
    Processing sheet with id=AB2, first strand: chain 'D' and resid 26 through 27
      removed outlier: 5.670A  pdb=" N   VAL D  33 " --> pdb=" O   LEU D  60 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 42 through 46
      removed outlier: 4.121A  pdb=" N   ILE D  70 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
      removed outlier: 4.779A  pdb=" N   GLY D  46 " --> pdb=" O   ARG D  68 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   ARG D  68 " --> pdb=" O   GLY D  46 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   THR D  85 " --> pdb=" O   TYR E 111 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   TYR E 113 " --> pdb=" O   THR D  85 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   GLN D  87 " --> pdb=" O   TYR E 113 " (cutoff:3.500A)
      removed outlier: 8.149A  pdb=" N   ARG E 115 " --> pdb=" O   GLN D  87 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   HIS D  89 " --> pdb=" O   ARG E 115 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   PHE E 110 " --> pdb=" O   CYS E  98 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   CYS E  98 " --> pdb=" O   PHE E 110 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 96 through 98
      removed outlier: 3.961A  pdb=" N   VAL D  97 " --> pdb=" O   MET E 123 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   MET E 123 " --> pdb=" O   VAL D  97 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'E' and resid 37 through 41
    Processing sheet with id=AB6, first strand: chain 'F' and resid 37 through 41
    Processing sheet with id=AB7, first strand: chain 'F' and resid 64 through 66
      removed outlier: 3.952A  pdb=" N   TRP F  59 " --> pdb=" O   ILE F  66 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   TYR F 111 " --> pdb=" O   GLN G  98 " (cutoff:3.500A)
      removed outlier: 8.041A  pdb=" N   TYR G 100 " --> pdb=" O   TYR F 111 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   TYR F 113 " --> pdb=" O   TYR G 100 " (cutoff:3.500A)
      removed outlier: 7.749A  pdb=" N   ARG G 102 " --> pdb=" O   TYR F 113 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ARG F 115 " --> pdb=" O   ARG G 102 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   THR G  54 " --> pdb=" O   LYS G  88 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ILE G  53 " --> pdb=" O   LEU G  65 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLY G  63 " --> pdb=" O   TRP G  55 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   LYS G  57 " --> pdb=" O   MET G  61 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   MET G  61 " --> pdb=" O   LYS G  57 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'G' and resid 31 through 34
      removed outlier: 5.784A  pdb=" N   VAL G  42 " --> pdb=" O   LEU G  74 " (cutoff:3.500A)

    402 hydrogen bonds defined for protein.
    1065 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.50

  Time building geometry restraints manager: 2.83 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2645
        1.34 -     1.46: 2087
        1.46 -     1.58: 3821
        1.58 -     1.71: 0
        1.71 -     1.83: 68
  Bond restraints: 8621
  Sorted by residual:
  bond pdb=" CA  ASP D  31 "
       pdb=" CB  ASP D  31 "
    ideal  model  delta    sigma   weight residual
    1.530  1.558 -0.027 1.69e-02 3.50e+03 2.63e+00
  bond pdb=" CG1 ILE B 283 "
       pdb=" CD1 ILE B 283 "
    ideal  model  delta    sigma   weight residual
    1.513  1.452  0.061 3.90e-02 6.57e+02 2.43e+00
  bond pdb=" CG1 ILE D 108 "
       pdb=" CD1 ILE D 108 "
    ideal  model  delta    sigma   weight residual
    1.513  1.454  0.059 3.90e-02 6.57e+02 2.28e+00
  bond pdb=" C   TYR F  52 "
       pdb=" O   TYR F  52 "
    ideal  model  delta    sigma   weight residual
    1.235  1.228  0.007 4.70e-03 4.53e+04 2.26e+00
  bond pdb=" CB  CYS G 104 "
       pdb=" SG  CYS G 104 "
    ideal  model  delta    sigma   weight residual
    1.808  1.761  0.047 3.30e-02 9.18e+02 2.02e+00
  ... (remaining 8616 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 11398
        2.41 -     4.82: 251
        4.82 -     7.23: 60
        7.23 -     9.64: 17
        9.64 -    12.05: 8
  Bond angle restraints: 11734
  Sorted by residual:
  angle pdb=" C   GLU D  30 "
        pdb=" N   ASP D  31 "
        pdb=" CA  ASP D  31 "
      ideal   model   delta    sigma   weight residual
     121.54  133.59  -12.05 1.91e+00 2.74e-01 3.98e+01
  angle pdb=" CB  LYS A 149 "
        pdb=" CG  LYS A 149 "
        pdb=" CD  LYS A 149 "
      ideal   model   delta    sigma   weight residual
     111.30  120.54   -9.24 2.30e+00 1.89e-01 1.61e+01
  angle pdb=" N   PHE Y  50 "
        pdb=" CA  PHE Y  50 "
        pdb=" CB  PHE Y  50 "
      ideal   model   delta    sigma   weight residual
     110.40  116.78   -6.38 1.63e+00 3.76e-01 1.53e+01
  angle pdb=" C   LEU Y  49 "
        pdb=" N   PHE Y  50 "
        pdb=" CA  PHE Y  50 "
      ideal   model   delta    sigma   weight residual
     121.14  114.35    6.79 1.75e+00 3.27e-01 1.51e+01
  angle pdb=" N   ILE D 107 "
        pdb=" CA  ILE D 107 "
        pdb=" CB  ILE D 107 "
      ideal   model   delta    sigma   weight residual
     110.57  115.53   -4.96 1.28e+00 6.10e-01 1.50e+01
  ... (remaining 11729 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 4807
       17.68 -    35.35: 506
       35.35 -    53.03: 127
       53.03 -    70.71: 23
       70.71 -    88.38: 7
  Dihedral angle restraints: 5470
    sinusoidal: 2415
      harmonic: 3055
  Sorted by residual:
  dihedral pdb=" CA  CYS G 104 "
           pdb=" C   CYS G 104 "
           pdb=" N   GLN G 105 "
           pdb=" CA  GLN G 105 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.55   35.45     0      5.00e+00 4.00e-02 5.03e+01
  dihedral pdb=" CA  GLN G  91 "
           pdb=" C   GLN G  91 "
           pdb=" N   ASN G  92 "
           pdb=" CA  ASN G  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.53   26.47     0      5.00e+00 4.00e-02 2.80e+01
  dihedral pdb=" CA  LYS A 201 "
           pdb=" C   LYS A 201 "
           pdb=" N   SER A 202 "
           pdb=" CA  SER A 202 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.59   26.41     0      5.00e+00 4.00e-02 2.79e+01
  ... (remaining 5467 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 1248
       0.084 -    0.169: 135
       0.169 -    0.253: 6
       0.253 -    0.337: 3
       0.337 -    0.421: 1
  Chirality restraints: 1393
  Sorted by residual:
  chirality pdb=" C2  NAG G 201 "
            pdb=" C1  NAG G 201 "
            pdb=" C3  NAG G 201 "
            pdb=" N2  NAG G 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.07   -0.42 2.00e-01 2.50e+01 4.44e+00
  chirality pdb=" C1  NAG O   1 "
            pdb=" ND2 ASN B  84 "
            pdb=" C2  NAG O   1 "
            pdb=" O5  NAG O   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.07   -0.33 2.00e-01 2.50e+01 2.75e+00
  chirality pdb=" CG  LEU G 129 "
            pdb=" CB  LEU G 129 "
            pdb=" CD1 LEU G 129 "
            pdb=" CD2 LEU G 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.32   -0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 1390 not shown)

  Planarity restraints: 1474
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU D  30 "   -0.015 2.00e-02 2.50e+03   3.06e-02 9.38e+00
        pdb=" C   GLU D  30 "    0.053 2.00e-02 2.50e+03
        pdb=" O   GLU D  30 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ASP D  31 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE X  40 "    0.009 2.00e-02 2.50e+03   1.51e-02 4.01e+00
        pdb=" CG  PHE X  40 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE X  40 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE X  40 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE X  40 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE X  40 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE X  40 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D  74 "   -0.019 2.00e-02 2.50e+03   1.75e-02 3.85e+00
        pdb=" CG  ASN D  74 "    0.022 2.00e-02 2.50e+03
        pdb=" OD1 ASN D  74 "   -0.002 2.00e-02 2.50e+03
        pdb=" ND2 ASN D  74 "    0.018 2.00e-02 2.50e+03
        pdb=" C1  NAG H   1 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1471 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 847
        2.74 -     3.28: 8677
        3.28 -     3.82: 13853
        3.82 -     4.36: 15506
        4.36 -     4.90: 26845
  Nonbonded interactions: 65728
  Sorted by model distance:
  nonbonded pdb=" N   GLU E  91 "
            pdb=" OE1 GLU E  91 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" O   THR D  47 "
            pdb=" OH  TYR D  71 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   ASP D 100 "
            pdb=" OG1 THR D 103 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   ASP F 137 "
            pdb=" OG1 THR F 141 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OE1 GLU E 120 "
            pdb=" ND2 ASN E 121 "
     model   vdw
     2.230 3.120
  ... (remaining 65723 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 'C'
  selection = chain 'H'
  selection = chain 'O'
}
ncs_group {
  reference = (chain 'E' and ((resid 33 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 34 through 151))
  selection = (chain 'F' and (resid 33 through 54 or (resid 55 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 56 through 62 or (resid 63 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 64 through 68 or (resid 69 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 70 or (resid 71 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 72 through 151))
}
ncs_group {
  reference = chain 'I'
  selection = chain 'R'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.920
  Find NCS groups from input model:        0.170
  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:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
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      :  0.003   0.061   8621  Z= 0.215
  Angle     :  0.923  12.048  11734  Z= 0.438
  Chirality :  0.051   0.421   1393
  Planarity :  0.004   0.067   1464
  Dihedral  : 15.190  88.382   3466
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.67 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 25.65 %
    Favored  : 73.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.63 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.26), residues: 1036
  helix:  0.63 (0.34), residues: 214
  sheet:  1.85 (0.32), residues: 286
  loop : -0.64 (0.26), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E  59 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.034   0.002   PHE X  40 
 TYR   0.022   0.001   TYR A 119 
 ARG   0.012   0.001   ARG E 115 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 187
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 MET cc_start: 0.8676 (mmp) cc_final: 0.8091 (mmp)
REVERT: B  169 TYR cc_start: 0.8760 (t80) cc_final: 0.8537 (t80)
REVERT: D   30 GLU cc_start: 0.8565 (pt0) cc_final: 0.8169 (pp20)
REVERT: E   91 GLU cc_start: 0.8624 (pm20) cc_final: 0.8311 (pm20)
REVERT: X   30 LYS cc_start: 0.9520 (mtmt) cc_final: 0.8992 (mmmt)
REVERT: X   46 LEU cc_start: 0.7927 (pp) cc_final: 0.7703 (pt)
  outliers start: 5
  outliers final: 4
  residues processed: 190
  average time/residue: 0.2063
  time to fit residues: 53.6419
Evaluate side-chains
  172 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 168
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   73 CYS
Chi-restraints excluded: chain D residue   93 CYS
Chi-restraints excluded: chain G residue   47 ASP
Chi-restraints excluded: chain Y residue   30 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.6980
   chunk 76 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 51 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 58 optimal weight:    7.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
B  48 HIS
F  74 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.061086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.048661 restraints weight = 39968.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 5.23
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8621  Z= 0.296
  Angle     :  0.804   9.174  11734  Z= 0.389
  Chirality :  0.049   0.368   1393
  Planarity :  0.004   0.033   1464
  Dihedral  :  9.015  59.365   1638
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.67 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 18.34 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.63 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.25), residues: 1036
  helix:  0.91 (0.33), residues: 228
  sheet:  1.68 (0.32), residues: 269
  loop : -0.72 (0.26), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 198 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.045   0.002   PHE Y  50 
 TYR   0.028   0.002   TYR Y  33 
 ARG   0.003   0.000   ARG E 115 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 175
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 TYR cc_start: 0.8802 (t80) cc_final: 0.8553 (t80)
REVERT: A  267 MET cc_start: 0.8739 (mmp) cc_final: 0.8526 (mmm)
REVERT: B   46 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8673 (ptm)
REVERT: G   38 GLU cc_start: 0.9012 (pm20) cc_final: 0.8665 (pm20)
REVERT: X   30 LYS cc_start: 0.9577 (mtmt) cc_final: 0.9046 (mmmt)
  outliers start: 37
  outliers final: 22
  residues processed: 198
  average time/residue: 0.2103
  time to fit residues: 57.1000
Evaluate side-chains
  184 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 161
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue   46 MET
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain D residue   73 CYS
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   93 CYS
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  119 CYS
Chi-restraints excluded: chain E residue  122 CYS
Chi-restraints excluded: chain E residue  134 VAL
Chi-restraints excluded: chain E residue  146 LEU
Chi-restraints excluded: chain F residue  126 ASP
Chi-restraints excluded: chain F residue  133 ILE
Chi-restraints excluded: chain F residue  134 VAL
Chi-restraints excluded: chain F residue  140 ILE
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue  129 LEU
Chi-restraints excluded: chain X residue   23 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 85 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9980
   chunk 94 optimal weight:    0.8980
   chunk 81 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 54 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   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  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.061477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.048999 restraints weight = 40040.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 5.28
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.1645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8621  Z= 0.198
  Angle     :  0.766  12.101  11734  Z= 0.365
  Chirality :  0.047   0.337   1393
  Planarity :  0.003   0.034   1464
  Dihedral  :  8.536  59.568   1632
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.86 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 19.69 %
    Favored  : 76.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.63 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.26), residues: 1036
  helix:  0.89 (0.33), residues: 228
  sheet:  1.62 (0.32), residues: 269
  loop : -0.74 (0.25), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 198 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.013   0.001   PHE A 263 
 TYR   0.013   0.001   TYR D  79 
 ARG   0.003   0.000   ARG A 186 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 175
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 TYR cc_start: 0.8786 (t80) cc_final: 0.8543 (t80)
REVERT: A  267 MET cc_start: 0.8747 (mmp) cc_final: 0.8534 (mmm)
REVERT: B   46 MET cc_start: 0.9154 (mtp) cc_final: 0.8728 (ptm)
REVERT: B  301 MET cc_start: 0.9065 (ppp) cc_final: 0.8860 (ppp)
REVERT: E  120 GLU cc_start: 0.9145 (pp20) cc_final: 0.8896 (tm-30)
REVERT: G   37 GLN cc_start: 0.7013 (tm-30) cc_final: 0.6716 (tm-30)
REVERT: X   30 LYS cc_start: 0.9558 (mtmt) cc_final: 0.9088 (mmmt)
  outliers start: 30
  outliers final: 20
  residues processed: 193
  average time/residue: 0.2068
  time to fit residues: 54.7540
Evaluate side-chains
  183 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 163
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   93 CYS
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  122 CYS
Chi-restraints excluded: chain E residue  134 VAL
Chi-restraints excluded: chain E residue  146 LEU
Chi-restraints excluded: chain F residue  126 ASP
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue  129 LEU
Chi-restraints excluded: chain X residue   23 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 88 optimal weight:    5.9990
   chunk 75 optimal weight:    7.9990
   chunk 56 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.060271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.047882 restraints weight = 39759.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 5.23
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   8621  Z= 0.284
  Angle     :  0.766  10.970  11734  Z= 0.369
  Chirality :  0.049   0.404   1393
  Planarity :  0.004   0.032   1464
  Dihedral  :  8.381  59.823   1631
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.34 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 21.48 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.63 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.26), residues: 1036
  helix:  0.76 (0.33), residues: 230
  sheet:  1.59 (0.32), residues: 269
  loop : -0.77 (0.26), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 198 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.037   0.002   PHE Y  50 
 TYR   0.015   0.001   TYR D  79 
 ARG   0.003   0.000   ARG E 115 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 166
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8239 (m)
REVERT: A  267 MET cc_start: 0.8757 (mmp) cc_final: 0.8323 (mmp)
REVERT: E  120 GLU cc_start: 0.9020 (pp20) cc_final: 0.8672 (tm-30)
REVERT: G   37 GLN cc_start: 0.6909 (tm-30) cc_final: 0.6655 (tm-30)
REVERT: X   30 LYS cc_start: 0.9572 (mtmt) cc_final: 0.9119 (mmmt)
  outliers start: 32
  outliers final: 26
  residues processed: 187
  average time/residue: 0.1949
  time to fit residues: 50.8729
Evaluate side-chains
  185 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 158
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue   46 MET
Chi-restraints excluded: chain B residue   84 ASN
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   93 CYS
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   98 CYS
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  119 CYS
Chi-restraints excluded: chain E residue  145 LEU
Chi-restraints excluded: chain E residue  146 LEU
Chi-restraints excluded: chain F residue  126 ASP
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   33 VAL
Chi-restraints excluded: chain G residue  129 LEU
Chi-restraints excluded: chain X residue   23 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 67 optimal weight:    9.9990
   chunk 44 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 97 optimal weight:    7.9990
   chunk 31 optimal weight:    0.7980
   chunk 57 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.060206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.047911 restraints weight = 39651.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 5.19
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8621  Z= 0.254
  Angle     :  0.762  12.292  11734  Z= 0.367
  Chirality :  0.048   0.388   1393
  Planarity :  0.003   0.033   1464
  Dihedral  :  8.237  58.975   1631
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.34 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 22.27 %
    Favored  : 73.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.63 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.26), residues: 1036
  helix:  0.64 (0.33), residues: 233
  sheet:  1.58 (0.32), residues: 269
  loop : -0.78 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 198 
 HIS   0.002   0.001   HIS F  61 
 PHE   0.020   0.001   PHE Y  50 
 TYR   0.014   0.001   TYR D  79 
 ARG   0.003   0.000   ARG A 186 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 163
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8253 (m)
REVERT: A  267 MET cc_start: 0.8715 (mmp) cc_final: 0.8318 (mmp)
REVERT: E   91 GLU cc_start: 0.8642 (pm20) cc_final: 0.8309 (pm20)
REVERT: X   30 LYS cc_start: 0.9560 (mtmt) cc_final: 0.9123 (mmmt)
  outliers start: 34
  outliers final: 28
  residues processed: 186
  average time/residue: 0.1957
  time to fit residues: 50.4965
Evaluate side-chains
  182 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 153
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue   46 MET
Chi-restraints excluded: chain B residue   84 ASN
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   93 CYS
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   98 CYS
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  119 CYS
Chi-restraints excluded: chain E residue  122 CYS
Chi-restraints excluded: chain E residue  134 VAL
Chi-restraints excluded: chain E residue  146 LEU
Chi-restraints excluded: chain F residue  126 ASP
Chi-restraints excluded: chain G residue   33 VAL
Chi-restraints excluded: chain G residue  129 LEU
Chi-restraints excluded: chain X residue   23 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 89 optimal weight:    0.7980
   chunk 86 optimal weight:    7.9990
   chunk 90 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 85 optimal weight:    9.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.059548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.047201 restraints weight = 40298.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 5.19
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   8621  Z= 0.307
  Angle     :  0.785  13.456  11734  Z= 0.381
  Chirality :  0.048   0.388   1393
  Planarity :  0.004   0.037   1464
  Dihedral  :  8.282  58.626   1631
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.34 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 23.28 %
    Favored  : 72.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.63 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.26), residues: 1036
  helix:  0.64 (0.33), residues: 233
  sheet:  1.50 (0.32), residues: 267
  loop : -0.79 (0.26), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 198 
 HIS   0.003   0.001   HIS B  66 
 PHE   0.037   0.002   PHE Y  50 
 TYR   0.016   0.001   TYR D  79 
 ARG   0.008   0.000   ARG E 115 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 159
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 SER cc_start: 0.8675 (OUTLIER) cc_final: 0.8259 (m)
REVERT: D   92 MET cc_start: 0.9300 (mmp) cc_final: 0.8816 (mmp)
REVERT: E   86 GLU cc_start: 0.8596 (mp0) cc_final: 0.8308 (pm20)
REVERT: F  147 LEU cc_start: 0.8546 (tp) cc_final: 0.8158 (mm)
REVERT: X   30 LYS cc_start: 0.9562 (mtmt) cc_final: 0.9134 (mmmt)
  outliers start: 37
  outliers final: 31
  residues processed: 183
  average time/residue: 0.1843
  time to fit residues: 47.0666
Evaluate side-chains
  184 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 152
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue   46 MET
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue   84 ASN
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   93 CYS
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   98 CYS
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  119 CYS
Chi-restraints excluded: chain E residue  145 LEU
Chi-restraints excluded: chain E residue  146 LEU
Chi-restraints excluded: chain F residue  126 ASP
Chi-restraints excluded: chain F residue  133 ILE
Chi-restraints excluded: chain G residue   33 VAL
Chi-restraints excluded: chain G residue  129 LEU
Chi-restraints excluded: chain X residue   23 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0980
   chunk 50 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0670
   chunk 69 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 67 optimal weight:    7.9990
   chunk 73 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 95 optimal weight:    0.8980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A  25 GLN
** A  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 106 ASN ** 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 = 0.3409 r_free = 0.3409 target = 0.060835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.048485 restraints weight = 39566.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 5.19
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8621  Z= 0.191
  Angle     :  0.800  15.847  11734  Z= 0.382
  Chirality :  0.048   0.380   1393
  Planarity :  0.003   0.047   1464
  Dihedral  :  8.132  57.520   1631
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.44 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 23.28 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.63 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.26), residues: 1036
  helix:  0.67 (0.33), residues: 233
  sheet:  1.55 (0.32), residues: 269
  loop : -0.74 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  43 
 HIS   0.002   0.000   HIS B  66 
 PHE   0.020   0.001   PHE Y  50 
 TYR   0.015   0.001   TYR D  79 
 ARG   0.009   0.000   ARG E 115 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 165
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 TYR cc_start: 0.8792 (t80) cc_final: 0.8383 (t80)
REVERT: A  213 SER cc_start: 0.8628 (OUTLIER) cc_final: 0.8226 (m)
REVERT: A  238 GLU cc_start: 0.7582 (pp20) cc_final: 0.7184 (pp20)
REVERT: A  254 ARG cc_start: 0.9078 (mtp180) cc_final: 0.8800 (mtp180)
REVERT: A  263 PHE cc_start: 0.8736 (t80) cc_final: 0.8364 (t80)
REVERT: A  266 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.7998 (tt)
REVERT: A  267 MET cc_start: 0.8337 (mmp) cc_final: 0.7586 (mmp)
REVERT: D   28 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7870 (mt-10)
REVERT: F  147 LEU cc_start: 0.8555 (tp) cc_final: 0.8177 (mm)
REVERT: X   30 LYS cc_start: 0.9553 (mtmt) cc_final: 0.9115 (mmmt)
  outliers start: 36
  outliers final: 26
  residues processed: 187
  average time/residue: 0.1839
  time to fit residues: 48.1953
Evaluate side-chains
  187 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 159
  time to evaluate  : 1.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue   46 MET
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue   84 ASN
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   93 CYS
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain E residue   98 CYS
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  119 CYS
Chi-restraints excluded: chain E residue  122 CYS
Chi-restraints excluded: chain E residue  134 VAL
Chi-restraints excluded: chain E residue  145 LEU
Chi-restraints excluded: chain E residue  146 LEU
Chi-restraints excluded: chain G residue  129 LEU
Chi-restraints excluded: chain X residue   23 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 72 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 84 optimal weight:    0.0980
   chunk 4 optimal weight:    0.0980
   chunk 33 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0980
   chunk 35 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.4182

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.061199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.048810 restraints weight = 39672.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 5.23
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.2529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   8621  Z= 0.198
  Angle     :  0.840  15.415  11734  Z= 0.397
  Chirality :  0.050   0.384   1393
  Planarity :  0.003   0.031   1464
  Dihedral  :  8.123  57.392   1631
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.15 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 23.96 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.63 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.26), residues: 1036
  helix:  0.60 (0.33), residues: 235
  sheet:  1.58 (0.32), residues: 269
  loop : -0.77 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  43 
 HIS   0.002   0.000   HIS F  61 
 PHE   0.041   0.001   PHE Y  50 
 TYR   0.015   0.001   TYR D  79 
 ARG   0.006   0.000   ARG E 115 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 164
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 TYR cc_start: 0.8769 (t80) cc_final: 0.8332 (t80)
REVERT: A  213 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8217 (m)
REVERT: A  254 ARG cc_start: 0.9024 (mtp180) cc_final: 0.8749 (mtp180)
REVERT: A  266 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8052 (tt)
REVERT: A  267 MET cc_start: 0.8269 (mmp) cc_final: 0.7927 (mmm)
REVERT: B   46 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8614 (ptm)
REVERT: E   86 GLU cc_start: 0.8633 (mp0) cc_final: 0.8260 (pm20)
REVERT: F  147 LEU cc_start: 0.8526 (tp) cc_final: 0.8193 (mm)
REVERT: X   30 LYS cc_start: 0.9556 (mtmt) cc_final: 0.9104 (mmmt)
  outliers start: 33
  outliers final: 23
  residues processed: 185
  average time/residue: 0.1941
  time to fit residues: 50.0325
Evaluate side-chains
  184 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 158
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue   46 MET
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   93 CYS
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain E residue   98 CYS
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  119 CYS
Chi-restraints excluded: chain E residue  122 CYS
Chi-restraints excluded: chain E residue  134 VAL
Chi-restraints excluded: chain E residue  146 LEU
Chi-restraints excluded: chain G residue   33 VAL
Chi-restraints excluded: chain G residue  129 LEU
Chi-restraints excluded: chain X residue   23 SER
Chi-restraints excluded: chain X residue   31 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 92 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 66 optimal weight:   10.0000
   chunk 79 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 212 ASN
** G 106 ASN ** 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 = 0.3391 r_free = 0.3391 target = 0.060129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.047939 restraints weight = 40832.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 5.21
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.2587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080   8621  Z= 0.250
  Angle     :  0.842  14.167  11734  Z= 0.403
  Chirality :  0.051   0.451   1393
  Planarity :  0.003   0.032   1464
  Dihedral  :  8.201  57.270   1631
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.34 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 23.51 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.63 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.26), residues: 1036
  helix:  0.55 (0.33), residues: 235
  sheet:  1.58 (0.32), residues: 269
  loop : -0.76 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 198 
 HIS   0.002   0.001   HIS F  61 
 PHE   0.021   0.001   PHE Y  50 
 TYR   0.015   0.001   TYR D  79 
 ARG   0.006   0.000   ARG E 115 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 158
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 SER cc_start: 0.8619 (OUTLIER) cc_final: 0.8218 (m)
REVERT: A  254 ARG cc_start: 0.9102 (mtp180) cc_final: 0.8798 (mtp180)
REVERT: A  263 PHE cc_start: 0.8771 (t80) cc_final: 0.8448 (t80)
REVERT: A  267 MET cc_start: 0.8298 (mmp) cc_final: 0.8007 (mmp)
REVERT: B   46 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8616 (ptm)
REVERT: D   28 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7911 (mt-10)
REVERT: E   86 GLU cc_start: 0.8641 (mp0) cc_final: 0.8256 (pm20)
REVERT: F  147 LEU cc_start: 0.8523 (tp) cc_final: 0.8181 (mm)
REVERT: X   30 LYS cc_start: 0.9555 (mtmt) cc_final: 0.9107 (mmmt)
  outliers start: 34
  outliers final: 28
  residues processed: 180
  average time/residue: 0.1949
  time to fit residues: 49.0365
Evaluate side-chains
  187 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 157
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue   46 MET
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   93 CYS
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain E residue   48 THR
Chi-restraints excluded: chain E residue   98 CYS
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  119 CYS
Chi-restraints excluded: chain E residue  122 CYS
Chi-restraints excluded: chain E residue  145 LEU
Chi-restraints excluded: chain E residue  146 LEU
Chi-restraints excluded: chain G residue   33 VAL
Chi-restraints excluded: chain G residue  129 LEU
Chi-restraints excluded: chain X residue   23 SER
Chi-restraints excluded: chain X residue   31 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 34 optimal weight:    6.9990
   chunk 57 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 88 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0030
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  53 GLN
** G 106 ASN ** 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 = 0.3411 r_free = 0.3411 target = 0.060954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.048781 restraints weight = 39877.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 5.16
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.2705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   8621  Z= 0.211
  Angle     :  0.865  15.645  11734  Z= 0.410
  Chirality :  0.050   0.417   1393
  Planarity :  0.003   0.030   1464
  Dihedral  :  8.246  56.951   1631
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 24.41 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.63 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.26), residues: 1036
  helix:  0.52 (0.33), residues: 235
  sheet:  1.59 (0.32), residues: 269
  loop : -0.78 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  43 
 HIS   0.002   0.000   HIS B  66 
 PHE   0.043   0.002   PHE Y  50 
 TYR   0.012   0.001   TYR D  79 
 ARG   0.005   0.000   ARG E 115 

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 167
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 TYR cc_start: 0.8808 (t80) cc_final: 0.8355 (t80)
REVERT: A  213 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.8191 (m)
REVERT: A  254 ARG cc_start: 0.9032 (mtp180) cc_final: 0.8757 (mtp180)
REVERT: A  263 PHE cc_start: 0.8767 (t80) cc_final: 0.8399 (t80)
REVERT: A  267 MET cc_start: 0.8325 (mmp) cc_final: 0.7911 (mmp)
REVERT: B  301 MET cc_start: 0.8981 (ppp) cc_final: 0.8757 (ppp)
REVERT: D   28 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7947 (mt-10)
REVERT: E   86 GLU cc_start: 0.8694 (mp0) cc_final: 0.8284 (pm20)
REVERT: F  147 LEU cc_start: 0.8534 (tp) cc_final: 0.8164 (mm)
REVERT: X   30 LYS cc_start: 0.9547 (mtmt) cc_final: 0.9086 (mmmt)
  outliers start: 26
  outliers final: 24
  residues processed: 183
  average time/residue: 0.2053
  time to fit residues: 51.3110
Evaluate side-chains
  188 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 163
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   53 GLN
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  173 SER
Chi-restraints excluded: chain A residue  185 MET
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue   46 MET
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  252 ILE
Chi-restraints excluded: chain B residue  293 VAL
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   93 CYS
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain E residue   98 CYS
Chi-restraints excluded: chain E residue  112 LEU
Chi-restraints excluded: chain E residue  119 CYS
Chi-restraints excluded: chain E residue  122 CYS
Chi-restraints excluded: chain E residue  146 LEU
Chi-restraints excluded: chain G residue   33 VAL
Chi-restraints excluded: chain G residue  129 LEU
Chi-restraints excluded: chain X residue   23 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 100 optimal weight:    8.9990
   chunk 55 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 68 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   chunk 34 optimal weight:    9.9990
   chunk 70 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.060046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.047783 restraints weight = 41203.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 5.21
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   8621  Z= 0.276
  Angle     :  0.845  13.195  11734  Z= 0.404
  Chirality :  0.050   0.435   1393
  Planarity :  0.003   0.032   1464
  Dihedral  :  8.389  59.025   1631
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.63 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 24.18 %
    Favored  : 72.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.63 %
    Cis-general     : 0.20 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.26), residues: 1036
  helix:  0.62 (0.32), residues: 235
  sheet:  1.54 (0.32), residues: 269
  loop : -0.78 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 198 
 HIS   0.002   0.001   HIS B 225 
 PHE   0.019   0.001   PHE Y  50 
 TYR   0.013   0.001   TYR D  79 
 ARG   0.005   0.000   ARG E 115 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3286.70 seconds
wall clock time: 59 minutes 47.18 seconds (3587.18 seconds total)