Starting phenix.real_space_refine
on Mon Jul 28 04:20:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jr9_22444/07_2025/7jr9_22444.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jr9_22444/07_2025/7jr9_22444.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jr9_22444/07_2025/7jr9_22444.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jr9_22444/07_2025/7jr9_22444.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jr9_22444/07_2025/7jr9_22444.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jr9_22444/07_2025/7jr9_22444.cif"
  }
  resolution = 2.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    6391      2.51       5
     N    1706      2.21       5
     O    1887      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10021
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1970
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 12, 'TRANS': 241}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 1946
          Classifications: {'peptide': 251}
          Link IDs: {'PTRANS': 11, 'TRANS': 239}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2110
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 22, 'TRANS': 257}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 2574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2574
          Classifications: {'peptide': 339}
          Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 301}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 40
          Classifications: {'peptide': 8}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'TRANS': 7}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'UNK:plan-1': 8}
          Unresolved non-hydrogen planarities: 8
    Chain: "G"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 30
          Classifications: {'peptide': 6}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'TRANS': 5}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'UNK:plan-1': 6}
          Unresolved non-hydrogen planarities: 6
    Chain: "E"
      Number of atoms: 1351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 1351
          Classifications: {'peptide': 176}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 169}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 8.49, per 1000 atoms: 0.85
  Number of scatterers: 10021
  At special positions: 0
  Unit cell: (88.92, 97.47, 164.16, 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      37     16.00
     O    1887      8.00
     N    1706      7.00
     C    6391      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 105 " - pdb=" SG  CYS A 155 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.77
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2370

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 18 sheets defined
      23.4% alpha, 30.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 16
    Processing helix  chain 'A' and resid 17 through 19
      No H-bonds generated for 'chain 'A' and resid 17 through 19'
    Processing helix  chain 'A' and resid 23 through 41
      removed outlier: 3.755A  pdb=" N   HIS A  32 " --> pdb=" O   ALA A  28 " (cutoff:3.500A)
      Proline residue:  A  35  - end of helix
    Processing helix  chain 'A' and resid 98 through 106
    Processing helix  chain 'A' and resid 149 through 164
    Processing helix  chain 'A' and resid 194 through 196
      No H-bonds generated for 'chain 'A' and resid 194 through 196'
    Processing helix  chain 'A' and resid 210 through 214
      removed outlier: 3.531A  pdb=" N   GLN A 213 " --> pdb=" O   THR A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 269
    Processing helix  chain 'B' and resid 7 through 15
    Processing helix  chain 'B' and resid 23 through 42
      removed outlier: 3.567A  pdb=" N   ALA B  28 " --> pdb=" O   ALA B  24 " (cutoff:3.500A)
      Proline residue:  B  35  - end of helix
    Processing helix  chain 'B' and resid 98 through 107
      removed outlier: 3.995A  pdb=" N   THR B 103 " --> pdb=" O   SER B  99 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ARG B 104 " --> pdb=" O   GLU B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 164
    Processing helix  chain 'B' and resid 194 through 196
      No H-bonds generated for 'chain 'B' and resid 194 through 196'
    Processing helix  chain 'B' and resid 210 through 214
    Processing helix  chain 'B' and resid 264 through 269
    Processing helix  chain 'C' and resid 76 through 85
    Processing helix  chain 'C' and resid 113 through 125
    Processing helix  chain 'C' and resid 130 through 145
    Processing helix  chain 'C' and resid 211 through 215
      removed outlier: 3.913A  pdb=" N   ASN C 214 " --> pdb=" O   LYS C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 235 through 245
      removed outlier: 3.647A  pdb=" N   ARG C 244 " --> pdb=" O   LYS C 240 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ILE C 245 " --> pdb=" O   ALA C 241 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 266 through 283
      removed outlier: 3.542A  pdb=" N   VAL C 283 " --> pdb=" O   SER C 279 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 310 through 315
      removed outlier: 4.006A  pdb=" N   ALA C 315 " --> pdb=" O   GLU C 312 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 81
    Processing helix  chain 'D' and resid 109 through 121
    Processing helix  chain 'D' and resid 125 through 142
    Processing helix  chain 'D' and resid 191 through 195
    Processing helix  chain 'D' and resid 215 through 224
    Processing helix  chain 'D' and resid 246 through 263
      removed outlier: 3.711A  pdb=" N   VAL D 263 " --> pdb=" O   SER D 259 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 289 through 295
      removed outlier: 3.631A  pdb=" N   GLU D 292 " --> pdb=" O   LYS D 289 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   LEU D 295 " --> pdb=" O   GLU D 292 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 345 through 349
      removed outlier: 3.686A  pdb=" N   ASP D 349 " --> pdb=" O   LEU D 346 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 85
      removed outlier: 3.536A  pdb=" N   GLU A  79 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 5.496A  pdb=" N   VAL A  68 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   LYS A  81 " --> pdb=" O   TYR A  66 " (cutoff:3.500A)
      removed outlier: 5.372A  pdb=" N   TYR A  66 " --> pdb=" O   LYS A  81 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   PHE A  83 " --> pdb=" O   GLU A  64 " (cutoff:3.500A)
      removed outlier: 5.458A  pdb=" N   GLU A  64 " --> pdb=" O   PHE A  83 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   SER A  85 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
      removed outlier: 5.368A  pdb=" N   VAL A  62 " --> pdb=" O   SER A  85 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   GLU A  64 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 5.478A  pdb=" N   LEU A  48 " --> pdb=" O   GLU A  64 " (cutoff:3.500A)
      removed outlier: 7.861A  pdb=" N   TYR A  66 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   LEU A  46 " --> pdb=" O   TYR A  66 " (cutoff:3.500A)
      removed outlier: 16.418A  pdb=" N   TRP A 251 " --> pdb=" O   SER A  45 " (cutoff:3.500A)
      removed outlier: 11.212A  pdb=" N   THR A  47 " --> pdb=" O   TRP A 251 " (cutoff:3.500A)
      removed outlier: 9.796A  pdb=" N   SER A 253 " --> pdb=" O   THR A  47 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   TRP A  49 " --> pdb=" O   SER A 253 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   TYR A 240 " --> pdb=" O   SER A 234 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 123
    Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168
    Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 174
    Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 93
      removed outlier: 5.798A  pdb=" N   ALA B  75 " --> pdb=" O   SER B  71 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   SER B  71 " --> pdb=" O   ALA B  75 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   VAL B  77 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   ALA B  69 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   GLU B  79 " --> pdb=" O   ASN B  67 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   ASN B  67 " --> pdb=" O   GLU B  79 " (cutoff:3.500A)
      removed outlier: 5.827A  pdb=" N   GLU B  64 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
      removed outlier: 5.387A  pdb=" N   LEU B  48 " --> pdb=" O   GLU B  64 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   TYR B  66 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      removed outlier: 5.860A  pdb=" N   LEU B  46 " --> pdb=" O   TYR B  66 " (cutoff:3.500A)
      removed outlier: 16.010A  pdb=" N   TRP B 251 " --> pdb=" O   SER B  45 " (cutoff:3.500A)
      removed outlier: 11.177A  pdb=" N   THR B  47 " --> pdb=" O   TRP B 251 " (cutoff:3.500A)
      removed outlier: 9.774A  pdb=" N   SER B 253 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   TRP B  49 " --> pdb=" O   SER B 253 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   TYR B 240 " --> pdb=" O   SER B 234 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL B 229 " --> pdb=" O   ASP B 224 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 119 through 123
    Processing sheet with id=AA7, first strand: chain 'B' and resid 166 through 168
    Processing sheet with id=AA8, first strand: chain 'B' and resid 172 through 174
    Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 230
      removed outlier: 6.458A  pdb=" N   TYR C 167 " --> pdb=" O   LYS C 159 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   LYS C 159 " --> pdb=" O   TYR C 167 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   VAL C 169 " --> pdb=" O   PHE C 157 " (cutoff:3.500A)
      removed outlier: 9.448A  pdb=" N   ARG C 155 " --> pdb=" O   CYS C 414 " (cutoff:3.500A)
      removed outlier: 9.895A  pdb=" N   TYR C 416 " --> pdb=" O   ARG C 155 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   PHE C 157 " --> pdb=" O   TYR C 416 " (cutoff:3.500A)
      removed outlier: 8.144A  pdb=" N   GLY C 418 " --> pdb=" O   PHE C 157 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   LYS C 159 " --> pdb=" O   GLY C 418 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   ALA C 403 " --> pdb=" O   SER C 397 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 284 through 286
    Processing sheet with id=AB2, first strand: chain 'C' and resid 290 through 292
    Processing sheet with id=AB3, first strand: chain 'D' and resid 209 through 210
      removed outlier: 6.515A  pdb=" N   TYR D 163 " --> pdb=" O   LYS D 155 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   LYS D 155 " --> pdb=" O   TYR D 163 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   VAL D 165 " --> pdb=" O   PHE D 153 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   THR D 149 " --> pdb=" O   THR D 169 " (cutoff:3.500A)
      removed outlier: 21.775A  pdb=" N   PHE D 400 " --> pdb=" O   VAL D 147 " (cutoff:3.500A)
      removed outlier: 16.070A  pdb=" N   THR D 149 " --> pdb=" O   PHE D 400 " (cutoff:3.500A)
      removed outlier: 14.927A  pdb=" N   SER D 402 " --> pdb=" O   THR D 149 " (cutoff:3.500A)
      removed outlier: 9.346A  pdb=" N   ARG D 151 " --> pdb=" O   SER D 402 " (cutoff:3.500A)
      removed outlier: 9.723A  pdb=" N   TYR D 404 " --> pdb=" O   ARG D 151 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   PHE D 153 " --> pdb=" O   TYR D 404 " (cutoff:3.500A)
      removed outlier: 8.239A  pdb=" N   GLY D 406 " --> pdb=" O   PHE D 153 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   LYS D 155 " --> pdb=" O   GLY D 406 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 264 through 266
    Processing sheet with id=AB5, first strand: chain 'D' and resid 270 through 272
    Processing sheet with id=AB6, first strand: chain 'D' and resid 365 through 369
    Processing sheet with id=AB7, first strand: chain 'G' and resid -3 through -1
      removed outlier: 3.560A  pdb=" N   UNK G  -3 " --> pdb=" O   GLU E  29 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLU E  29 " --> pdb=" O   UNK G  -3 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 50 through 53
      removed outlier: 5.893A  pdb=" N   THR E  51 " --> pdb=" O   THR E  58 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   THR E  58 " --> pdb=" O   THR E  51 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL E  56 " --> pdb=" O   GLU E  53 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   LYS E  84 " --> pdb=" O   ASP E  75 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   VAL E  77 " --> pdb=" O   HIS E  82 " (cutoff:3.500A)
      removed outlier: 5.507A  pdb=" N   HIS E  82 " --> pdb=" O   VAL E  77 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLY E  97 " --> pdb=" O   GLY E  85 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   GLN E 107 " --> pdb=" O   ASP E  98 " (cutoff:3.500A)
      removed outlier: 5.347A  pdb=" N   LYS E 130 " --> pdb=" O   ALA E 121 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   TRP E 123 " --> pdb=" O   HIS E 128 " (cutoff:3.500A)
      removed outlier: 5.164A  pdb=" N   HIS E 128 " --> pdb=" O   TRP E 123 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   GLN E 141 " --> pdb=" O   TRP E 156 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   TRP E 156 " --> pdb=" O   GLN E 141 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   VAL E 143 " --> pdb=" O   GLY E 154 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   GLY E 154 " --> pdb=" O   VAL E 143 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   ASP E 145 " --> pdb=" O   THR E 152 " (cutoff:3.500A)
      removed outlier: 5.533A  pdb=" N   THR E 152 " --> pdb=" O   PHE E 168 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   THR E 178 " --> pdb=" O   PHE E 195 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 50 through 53
      removed outlier: 5.893A  pdb=" N   THR E  51 " --> pdb=" O   THR E  58 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   THR E  58 " --> pdb=" O   THR E  51 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL E  56 " --> pdb=" O   GLU E  53 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   LYS E  84 " --> pdb=" O   ASP E  75 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   VAL E  77 " --> pdb=" O   HIS E  82 " (cutoff:3.500A)
      removed outlier: 5.507A  pdb=" N   HIS E  82 " --> pdb=" O   VAL E  77 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLY E  97 " --> pdb=" O   GLY E  85 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   GLN E 107 " --> pdb=" O   ASP E  98 " (cutoff:3.500A)
      removed outlier: 5.347A  pdb=" N   LYS E 130 " --> pdb=" O   ALA E 121 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   TRP E 123 " --> pdb=" O   HIS E 128 " (cutoff:3.500A)
      removed outlier: 5.164A  pdb=" N   HIS E 128 " --> pdb=" O   TRP E 123 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   GLN E 141 " --> pdb=" O   TRP E 156 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   TRP E 156 " --> pdb=" O   GLN E 141 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   VAL E 143 " --> pdb=" O   GLY E 154 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   GLY E 154 " --> pdb=" O   VAL E 143 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   ASP E 145 " --> pdb=" O   THR E 152 " (cutoff:3.500A)
      removed outlier: 5.533A  pdb=" N   THR E 152 " --> pdb=" O   PHE E 168 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   THR E 178 " --> pdb=" O   PHE E 195 " (cutoff:3.500A)

    428 hydrogen bonds defined for protein.
    1173 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.38

  Time building geometry restraints manager: 3.26 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: 3191
        1.34 -     1.45: 1777
        1.45 -     1.57: 5256
        1.57 -     1.69: 0
        1.69 -     1.80: 56
  Bond restraints: 10280
  Sorted by residual:
  bond pdb=" C   ALA D 294 "
       pdb=" N   LEU D 295 "
    ideal  model  delta    sigma   weight residual
    1.332  1.289  0.042 1.92e-02 2.71e+03 4.89e+00
  bond pdb=" CA  GLY D 121 "
       pdb=" C   GLY D 121 "
    ideal  model  delta    sigma   weight residual
    1.514  1.489  0.025 1.41e-02 5.03e+03 3.25e+00
  bond pdb=" CG  LEU D 134 "
       pdb=" CD1 LEU D 134 "
    ideal  model  delta    sigma   weight residual
    1.521  1.466  0.055 3.30e-02 9.18e+02 2.74e+00
  bond pdb=" CB  ARG C 396 "
       pdb=" CG  ARG C 396 "
    ideal  model  delta    sigma   weight residual
    1.520  1.472  0.048 3.00e-02 1.11e+03 2.52e+00
  bond pdb=" C   THR E 111 "
       pdb=" N   TYR E 112 "
    ideal  model  delta    sigma   weight residual
    1.329  1.300  0.029 1.86e-02 2.89e+03 2.36e+00
  ... (remaining 10275 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 13125
        1.54 -     3.07: 719
        3.07 -     4.61: 115
        4.61 -     6.14: 18
        6.14 -     7.68: 8
  Bond angle restraints: 13985
  Sorted by residual:
  angle pdb=" C   THR E 111 "
        pdb=" N   TYR E 112 "
        pdb=" CA  TYR E 112 "
      ideal   model   delta    sigma   weight residual
     121.48  128.38   -6.90 2.04e+00 2.40e-01 1.14e+01
  angle pdb=" C   VAL B 157 "
        pdb=" N   ASP B 158 "
        pdb=" CA  ASP B 158 "
      ideal   model   delta    sigma   weight residual
     121.58  115.41    6.17 1.95e+00 2.63e-01 1.00e+01
  angle pdb=" CA  TYR A  78 "
        pdb=" CB  TYR A  78 "
        pdb=" CG  TYR A  78 "
      ideal   model   delta    sigma   weight residual
     113.90  119.52   -5.62 1.80e+00 3.09e-01 9.74e+00
  angle pdb=" C   GLY C 372 "
        pdb=" N   GLU C 373 "
        pdb=" CA  GLU C 373 "
      ideal   model   delta    sigma   weight residual
     122.40  126.92   -4.52 1.45e+00 4.76e-01 9.73e+00
  angle pdb=" C   THR B 164 "
        pdb=" N   SER B 165 "
        pdb=" CA  SER B 165 "
      ideal   model   delta    sigma   weight residual
     122.82  127.22   -4.40 1.42e+00 4.96e-01 9.60e+00
  ... (remaining 13980 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.84: 5821
       14.84 -    29.68: 186
       29.68 -    44.52: 24
       44.52 -    59.35: 1
       59.35 -    74.19: 5
  Dihedral angle restraints: 6037
    sinusoidal: 2309
      harmonic: 3728
  Sorted by residual:
  dihedral pdb=" CA  TYR C 260 "
           pdb=" C   TYR C 260 "
           pdb=" N   PRO C 261 "
           pdb=" CA  PRO C 261 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.62   25.38     0      5.00e+00 4.00e-02 2.58e+01
  dihedral pdb=" CA  THR D 168 "
           pdb=" C   THR D 168 "
           pdb=" N   THR D 169 "
           pdb=" CA  THR D 169 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.45   24.55     0      5.00e+00 4.00e-02 2.41e+01
  dihedral pdb=" CA  SER A  92 "
           pdb=" C   SER A  92 "
           pdb=" N   ASP A  93 "
           pdb=" CA  ASP A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.70  -23.30     0      5.00e+00 4.00e-02 2.17e+01
  ... (remaining 6034 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1073
       0.052 -    0.105: 355
       0.105 -    0.157: 63
       0.157 -    0.210: 9
       0.210 -    0.262: 3
  Chirality restraints: 1503
  Sorted by residual:
  chirality pdb=" CB  VAL E  71 "
            pdb=" CA  VAL E  71 "
            pdb=" CG1 VAL E  71 "
            pdb=" CG2 VAL E  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" CB  VAL E  88 "
            pdb=" CA  VAL E  88 "
            pdb=" CG1 VAL E  88 "
            pdb=" CG2 VAL E  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CB  ILE B   8 "
            pdb=" CA  ILE B   8 "
            pdb=" CG1 ILE B   8 "
            pdb=" CG2 ILE B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.14e+00
  ... (remaining 1500 not shown)

  Planarity restraints: 1828
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 184 "   -0.022 2.00e-02 2.50e+03   1.97e-02 7.76e+00
        pdb=" CG  TYR E 184 "    0.048 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 184 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 184 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 184 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 184 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 184 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR E 184 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 168 "   -0.010 2.00e-02 2.50e+03   1.93e-02 6.52e+00
        pdb=" CG  PHE E 168 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 168 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 168 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 168 "    0.012 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 168 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 168 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  78 "   -0.018 2.00e-02 2.50e+03   1.79e-02 6.42e+00
        pdb=" CG  TYR B  78 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  78 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  78 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  78 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  78 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  78 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B  78 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1825 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1999
        2.77 -     3.30: 8334
        3.30 -     3.83: 16447
        3.83 -     4.37: 19983
        4.37 -     4.90: 34353
  Nonbonded interactions: 81116
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 383 "
            pdb=" OE1 GLN C 391 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OG  SER A 234 "
            pdb=" O   PHE A 237 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OH  TYR A 255 "
            pdb=" O   ASP A 258 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OG1 THR D 230 "
            pdb=" OE1 GLU D 247 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OG1 THR C 250 "
            pdb=" OE1 GLU C 267 "
     model   vdw
     2.313 3.040
  ... (remaining 81111 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 2 through 124 or resid 142 through 269))
  selection = chain 'B'
}

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:             2.820
  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:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.130
  Process input model:                     30.540
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
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      :  0.008   0.057  10281  Z= 0.339
  Angle     :  0.818   7.675  13987  Z= 0.460
  Chirality :  0.054   0.262   1503
  Planarity :  0.008   0.055   1828
  Dihedral  :  8.260  74.192   3664
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.53 (0.20), residues: 1274
  helix: -2.33 (0.23), residues: 266
  sheet: -1.43 (0.26), residues: 310
  loop : -1.46 (0.20), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP E 156 
 HIS   0.006   0.002   HIS C 321 
 PHE   0.040   0.004   PHE E 168 
 TYR   0.048   0.004   TYR E 184 
 ARG   0.015   0.002   ARG D 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15977 (  368)
  hydrogen bonds       : angle       7.10334 ( 1173)
  SS BOND              : bond        0.01287 (    1)
  SS BOND              : angle       5.66267 (    2)
  covalent geometry    : bond        0.00795 (10280)
  covalent geometry    : angle       0.81525 (13985)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 1.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  325 HIS cc_start: 0.7901 (p-80) cc_final: 0.7218 (t-170)
REVERT: E   87 MET cc_start: 0.7786 (tpt) cc_final: 0.6798 (tpt)
REVERT: E  119 GLN cc_start: 0.7860 (mt0) cc_final: 0.7575 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 1.6317
  time to fit residues: 303.5298
Evaluate side-chains
  73 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 1.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 116 optimal weight:    4.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  95 GLN
C  80 GLN
C 238 GLN
C 374 GLN
C 391 GLN
** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.091282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.068520 restraints weight = 17130.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.2840 rms_B_bonded: 2.23
r_work: 0.2725 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2603 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8816
moved from start:          0.1889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10281  Z= 0.127
  Angle     :  0.530   7.906  13987  Z= 0.278
  Chirality :  0.040   0.148   1503
  Planarity :  0.005   0.041   1828
  Dihedral  :  4.430  17.443   1422
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  8.71 %
    Favored  : 89.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.22), residues: 1274
  helix: -0.59 (0.29), residues: 276
  sheet: -0.95 (0.28), residues: 294
  loop : -0.78 (0.22), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 415 
 HIS   0.002   0.001   HIS B 200 
 PHE   0.010   0.001   PHE A 267 
 TYR   0.017   0.002   TYR B 255 
 ARG   0.003   0.000   ARG B 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04046 (  368)
  hydrogen bonds       : angle       5.01185 ( 1173)
  SS BOND              : bond        0.00079 (    1)
  SS BOND              : angle       1.49530 (    2)
  covalent geometry    : bond        0.00286 (10280)
  covalent geometry    : angle       0.52957 (13985)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLN cc_start: 0.8284 (mm-40) cc_final: 0.8053 (mm-40)
REVERT: C  303 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7353 (pm20)
REVERT: C  325 HIS cc_start: 0.8251 (p-80) cc_final: 0.6942 (t-170)
REVERT: C  366 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8041 (mp0)
REVERT: D  191 GLU cc_start: 0.8036 (tt0) cc_final: 0.7795 (tt0)
REVERT: E   87 MET cc_start: 0.8298 (tpt) cc_final: 0.7581 (tpt)
REVERT: E  197 LYS cc_start: 0.9032 (mttt) cc_final: 0.8572 (mppt)
  outliers start: 17
  outliers final: 4
  residues processed: 91
  average time/residue: 1.5901
  time to fit residues: 153.7950
Evaluate side-chains
  75 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 1.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LYS
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain C residue  366 GLU
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue  200 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 113 optimal weight:   10.0000
   chunk 70 optimal weight:    0.0870
   chunk 74 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 86 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 117 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.9964

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

Flipped N/Q/H residues before XYZ refinement:
** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 119 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.089169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.066245 restraints weight = 17523.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.2793 rms_B_bonded: 2.24
r_work: 0.2678 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2558 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8856
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10281  Z= 0.142
  Angle     :  0.510   7.069  13987  Z= 0.265
  Chirality :  0.040   0.147   1503
  Planarity :  0.004   0.033   1828
  Dihedral  :  4.189  17.532   1422
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  9.49 %
    Favored  : 88.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.22), residues: 1274
  helix:  0.19 (0.31), residues: 276
  sheet: -0.64 (0.29), residues: 287
  loop : -0.43 (0.22), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E  99 
 HIS   0.002   0.001   HIS B 200 
 PHE   0.010   0.001   PHE A 186 
 TYR   0.021   0.002   TYR D 198 
 ARG   0.002   0.000   ARG D 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04025 (  368)
  hydrogen bonds       : angle       4.67995 ( 1173)
  SS BOND              : bond        0.01061 (    1)
  SS BOND              : angle       1.72087 (    2)
  covalent geometry    : bond        0.00327 (10280)
  covalent geometry    : angle       0.50976 (13985)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 1.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  325 HIS cc_start: 0.8282 (p-80) cc_final: 0.6895 (t-170)
REVERT: C  366 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7899 (mp0)
REVERT: D  191 GLU cc_start: 0.8113 (tt0) cc_final: 0.7852 (tt0)
REVERT: E   57 ARG cc_start: 0.7410 (mtm180) cc_final: 0.6902 (mtm-85)
REVERT: E  197 LYS cc_start: 0.9016 (mttt) cc_final: 0.8588 (mppt)
  outliers start: 17
  outliers final: 5
  residues processed: 83
  average time/residue: 1.6517
  time to fit residues: 146.0967
Evaluate side-chains
  75 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LYS
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain C residue  366 GLU
Chi-restraints excluded: chain D residue  184 ILE
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue  181 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 122 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 127 optimal weight:    6.9990
   chunk 80 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0020
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
A   7 ASN
** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.090120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.067363 restraints weight = 17107.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.2819 rms_B_bonded: 2.22
r_work: 0.2706 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2585 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8834
moved from start:          0.2603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  10281  Z= 0.107
  Angle     :  0.472   6.971  13987  Z= 0.244
  Chirality :  0.039   0.139   1503
  Planarity :  0.004   0.033   1828
  Dihedral  :  3.935  17.016   1422
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 10.27 %
    Favored  : 88.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.23), residues: 1274
  helix:  0.56 (0.32), residues: 277
  sheet: -0.34 (0.29), residues: 287
  loop : -0.27 (0.23), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E  99 
 HIS   0.002   0.001   HIS E 134 
 PHE   0.008   0.001   PHE A 267 
 TYR   0.015   0.001   TYR D 198 
 ARG   0.002   0.000   ARG D 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03477 (  368)
  hydrogen bonds       : angle       4.42336 ( 1173)
  SS BOND              : bond        0.00545 (    1)
  SS BOND              : angle       1.28989 (    2)
  covalent geometry    : bond        0.00244 (10280)
  covalent geometry    : angle       0.47157 (13985)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 1.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  213 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8671 (mp10)
REVERT: C  325 HIS cc_start: 0.8261 (p-80) cc_final: 0.6823 (t-170)
REVERT: C  366 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7893 (mp0)
REVERT: D  191 GLU cc_start: 0.8080 (tt0) cc_final: 0.7826 (tt0)
REVERT: E   47 LYS cc_start: 0.8631 (mttt) cc_final: 0.8351 (mmtm)
REVERT: E   57 ARG cc_start: 0.7345 (mtm180) cc_final: 0.6871 (mtm-85)
REVERT: E  197 LYS cc_start: 0.9004 (mttt) cc_final: 0.8556 (mppt)
  outliers start: 15
  outliers final: 5
  residues processed: 88
  average time/residue: 1.5739
  time to fit residues: 147.6356
Evaluate side-chains
  74 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 1.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LYS
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain C residue  366 GLU
Chi-restraints excluded: chain D residue  184 ILE
Chi-restraints excluded: chain E residue  200 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 35 optimal weight:    0.2980
   chunk 113 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 379 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 = 0.3205 r_free = 0.3205 target = 0.088626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.065646 restraints weight = 17106.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.2784 rms_B_bonded: 2.22
r_work: 0.2670 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2549 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10281  Z= 0.140
  Angle     :  0.496   6.572  13987  Z= 0.255
  Chirality :  0.040   0.149   1503
  Planarity :  0.004   0.032   1828
  Dihedral  :  3.958  17.145   1422
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 10.86 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.23), residues: 1274
  helix:  0.67 (0.32), residues: 277
  sheet: -0.11 (0.29), residues: 287
  loop : -0.14 (0.23), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E  99 
 HIS   0.002   0.001   HIS E 134 
 PHE   0.008   0.001   PHE B 242 
 TYR   0.019   0.001   TYR D 198 
 ARG   0.002   0.000   ARG C 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03838 (  368)
  hydrogen bonds       : angle       4.45222 ( 1173)
  SS BOND              : bond        0.00641 (    1)
  SS BOND              : angle       1.44217 (    2)
  covalent geometry    : bond        0.00326 (10280)
  covalent geometry    : angle       0.49613 (13985)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 PHE cc_start: 0.8140 (m-80) cc_final: 0.7816 (m-80)
REVERT: A  213 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.7528 (mt0)
REVERT: B  213 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8661 (mp10)
REVERT: C  325 HIS cc_start: 0.8372 (p-80) cc_final: 0.6970 (t-170)
REVERT: C  366 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7874 (mp0)
REVERT: D  193 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8871 (t)
REVERT: E   57 ARG cc_start: 0.7368 (mtm180) cc_final: 0.7083 (mtm-85)
REVERT: E  197 LYS cc_start: 0.8994 (mttt) cc_final: 0.8575 (mppt)
  outliers start: 17
  outliers final: 6
  residues processed: 80
  average time/residue: 1.5440
  time to fit residues: 131.6793
Evaluate side-chains
  79 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LYS
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  366 GLU
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue  181 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 105 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 116 optimal weight:    4.9990
   chunk 114 optimal weight:    5.9990
   chunk 107 optimal weight:    2.9990
   chunk 83 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 124 optimal weight:    0.7980
   chunk 126 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   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  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 119 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.087140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.064045 restraints weight = 17228.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.2749 rms_B_bonded: 2.22
r_work: 0.2630 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2507 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8896
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10281  Z= 0.187
  Angle     :  0.523   6.811  13987  Z= 0.271
  Chirality :  0.041   0.157   1503
  Planarity :  0.004   0.032   1828
  Dihedral  :  4.112  17.992   1422
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 10.96 %
    Favored  : 87.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.23), residues: 1274
  helix:  0.63 (0.32), residues: 277
  sheet: -0.02 (0.30), residues: 273
  loop : -0.10 (0.23), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E  99 
 HIS   0.002   0.001   HIS D 301 
 PHE   0.010   0.001   PHE B 242 
 TYR   0.019   0.002   TYR E 184 
 ARG   0.004   0.000   ARG C 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04253 (  368)
  hydrogen bonds       : angle       4.57981 ( 1173)
  SS BOND              : bond        0.00758 (    1)
  SS BOND              : angle       1.51072 (    2)
  covalent geometry    : bond        0.00443 (10280)
  covalent geometry    : angle       0.52302 (13985)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8347 (ptm-80)
REVERT: A   95 GLN cc_start: 0.8287 (mm-40) cc_final: 0.8016 (mm-40)
REVERT: A  145 PHE cc_start: 0.8193 (m-80) cc_final: 0.7718 (m-80)
REVERT: B  213 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8729 (mp10)
REVERT: C  325 HIS cc_start: 0.8339 (p-80) cc_final: 0.6858 (t-170)
REVERT: C  366 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7789 (mp0)
REVERT: D  193 VAL cc_start: 0.9140 (OUTLIER) cc_final: 0.8904 (t)
REVERT: E   57 ARG cc_start: 0.7351 (mtm180) cc_final: 0.7032 (mtm-85)
REVERT: E   78 ASN cc_start: 0.8863 (t0) cc_final: 0.8612 (t0)
  outliers start: 18
  outliers final: 8
  residues processed: 82
  average time/residue: 2.1564
  time to fit residues: 187.4935
Evaluate side-chains
  77 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LYS
Chi-restraints excluded: chain A residue   90 ARG
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  366 GLU
Chi-restraints excluded: chain D residue  184 ILE
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue  181 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 102 optimal weight:    6.9990
   chunk 122 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 118 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 126 optimal weight:    3.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 379 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 = 0.3188 r_free = 0.3188 target = 0.087712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.064585 restraints weight = 17410.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.2760 rms_B_bonded: 2.25
r_work: 0.2641 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2517 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8888
moved from start:          0.2869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10281  Z= 0.156
  Angle     :  0.510   7.442  13987  Z= 0.263
  Chirality :  0.040   0.150   1503
  Planarity :  0.004   0.032   1828
  Dihedral  :  4.029  17.566   1422
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.25 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.23), residues: 1274
  helix:  0.88 (0.32), residues: 270
  sheet:  0.06 (0.30), residues: 276
  loop : -0.00 (0.23), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E  99 
 HIS   0.002   0.001   HIS D 315 
 PHE   0.009   0.001   PHE B 242 
 TYR   0.015   0.001   TYR E 184 
 ARG   0.003   0.000   ARG C 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03996 (  368)
  hydrogen bonds       : angle       4.52139 ( 1173)
  SS BOND              : bond        0.00667 (    1)
  SS BOND              : angle       1.46824 (    2)
  covalent geometry    : bond        0.00367 (10280)
  covalent geometry    : angle       0.50933 (13985)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 1.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8320 (ptm-80)
REVERT: A  145 PHE cc_start: 0.8237 (m-80) cc_final: 0.7849 (m-80)
REVERT: B  213 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8727 (mp10)
REVERT: C  325 HIS cc_start: 0.8352 (p-80) cc_final: 0.6857 (t-170)
REVERT: C  366 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7819 (mp0)
REVERT: D  193 VAL cc_start: 0.9150 (OUTLIER) cc_final: 0.8906 (t)
REVERT: E   57 ARG cc_start: 0.7328 (mtm180) cc_final: 0.7003 (mtm-85)
REVERT: E   78 ASN cc_start: 0.8887 (t0) cc_final: 0.8646 (t0)
REVERT: E  197 LYS cc_start: 0.9007 (mttt) cc_final: 0.8598 (mppt)
  outliers start: 17
  outliers final: 7
  residues processed: 75
  average time/residue: 1.5744
  time to fit residues: 126.0687
Evaluate side-chains
  73 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LYS
Chi-restraints excluded: chain A residue   90 ARG
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  366 GLU
Chi-restraints excluded: chain D residue  184 ILE
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue  181 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 80 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 102 optimal weight:    7.9990
   chunk 57 optimal weight:    1.9990
   chunk 120 optimal weight:    6.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 379 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 = 0.3194 r_free = 0.3194 target = 0.088046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.065001 restraints weight = 17168.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.2770 rms_B_bonded: 2.22
r_work: 0.2656 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2535 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8874
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10281  Z= 0.143
  Angle     :  0.502   7.771  13987  Z= 0.258
  Chirality :  0.040   0.148   1503
  Planarity :  0.004   0.032   1828
  Dihedral  :  3.961  17.437   1422
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.25 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.23), residues: 1274
  helix:  0.98 (0.32), residues: 270
  sheet:  0.12 (0.30), residues: 276
  loop :  0.05 (0.23), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E  99 
 HIS   0.002   0.001   HIS D 315 
 PHE   0.009   0.001   PHE B 242 
 TYR   0.014   0.001   TYR E 184 
 ARG   0.003   0.000   ARG C 323 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03848 (  368)
  hydrogen bonds       : angle       4.47541 ( 1173)
  SS BOND              : bond        0.00590 (    1)
  SS BOND              : angle       1.48935 (    2)
  covalent geometry    : bond        0.00335 (10280)
  covalent geometry    : angle       0.50213 (13985)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8234 (ptm-80)
REVERT: A   95 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7968 (mm-40)
REVERT: A  145 PHE cc_start: 0.8204 (m-80) cc_final: 0.7860 (m-80)
REVERT: A  268 MET cc_start: 0.9127 (mmm) cc_final: 0.8915 (mtt)
REVERT: B  213 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8746 (mp10)
REVERT: C  325 HIS cc_start: 0.8372 (p-80) cc_final: 0.6892 (t-170)
REVERT: C  366 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7783 (mp0)
REVERT: D  193 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8888 (t)
REVERT: E   47 LYS cc_start: 0.8684 (mttt) cc_final: 0.8404 (mmtm)
REVERT: E   57 ARG cc_start: 0.7291 (mtm180) cc_final: 0.6841 (mtm-85)
REVERT: E   78 ASN cc_start: 0.8884 (t0) cc_final: 0.8674 (t0)
REVERT: E  197 LYS cc_start: 0.9009 (mttt) cc_final: 0.8576 (mppt)
  outliers start: 18
  outliers final: 6
  residues processed: 80
  average time/residue: 1.4726
  time to fit residues: 125.8481
Evaluate side-chains
  75 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LYS
Chi-restraints excluded: chain A residue   90 ARG
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  366 GLU
Chi-restraints excluded: chain D residue  184 ILE
Chi-restraints excluded: chain D residue  193 VAL
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue  181 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 84 optimal weight:    2.9990
   chunk 115 optimal weight:    8.9990
   chunk 65 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 113 optimal weight:   10.0000
   chunk 105 optimal weight:    0.4980
   chunk 125 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 379 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 = 0.3175 r_free = 0.3175 target = 0.087015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.063906 restraints weight = 17160.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.2746 rms_B_bonded: 2.22
r_work: 0.2626 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2503 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8899
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10281  Z= 0.184
  Angle     :  0.529   8.037  13987  Z= 0.272
  Chirality :  0.041   0.156   1503
  Planarity :  0.004   0.032   1828
  Dihedral  :  4.088  18.234   1422
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 11.84 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.23), residues: 1274
  helix:  0.88 (0.32), residues: 271
  sheet:  0.10 (0.30), residues: 274
  loop :  0.05 (0.23), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E  99 
 HIS   0.003   0.001   HIS D 315 
 PHE   0.010   0.001   PHE B 242 
 TYR   0.017   0.002   TYR E 184 
 ARG   0.005   0.000   ARG C 323 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04221 (  368)
  hydrogen bonds       : angle       4.57138 ( 1173)
  SS BOND              : bond        0.00706 (    1)
  SS BOND              : angle       1.53809 (    2)
  covalent geometry    : bond        0.00436 (10280)
  covalent geometry    : angle       0.52874 (13985)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 1.128 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8304 (ptm-80)
REVERT: A  145 PHE cc_start: 0.8190 (m-80) cc_final: 0.7798 (m-80)
REVERT: A  268 MET cc_start: 0.9145 (mmm) cc_final: 0.8908 (mtt)
REVERT: B  213 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8742 (mp10)
REVERT: C  303 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7824 (pm20)
REVERT: C  325 HIS cc_start: 0.8411 (p-80) cc_final: 0.6848 (t-170)
REVERT: C  366 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7832 (mp0)
REVERT: E   57 ARG cc_start: 0.7398 (mtm180) cc_final: 0.6877 (mtm-85)
REVERT: E   78 ASN cc_start: 0.8871 (t0) cc_final: 0.8669 (t0)
REVERT: E  197 LYS cc_start: 0.9027 (mttt) cc_final: 0.8592 (mppt)
  outliers start: 12
  outliers final: 6
  residues processed: 75
  average time/residue: 1.5650
  time to fit residues: 125.5548
Evaluate side-chains
  73 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LYS
Chi-restraints excluded: chain A residue   90 ARG
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain C residue  366 GLU
Chi-restraints excluded: chain D residue  184 ILE
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue  181 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 119 optimal weight:    0.8980
   chunk 116 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0070
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0050
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.5814

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

Flipped N/Q/H residues before XYZ refinement:
** A  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 379 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 = 0.3216 r_free = 0.3216 target = 0.089390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.066526 restraints weight = 17172.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.2799 rms_B_bonded: 2.23
r_work: 0.2682 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2560 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8854
moved from start:          0.3067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10281  Z= 0.102
  Angle     :  0.477   8.033  13987  Z= 0.245
  Chirality :  0.039   0.140   1503
  Planarity :  0.004   0.034   1828
  Dihedral  :  3.831  16.710   1422
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 11.84 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.24), residues: 1274
  helix:  1.08 (0.33), residues: 271
  sheet:  0.18 (0.31), residues: 277
  loop :  0.18 (0.23), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  99 
 HIS   0.002   0.001   HIS D 315 
 PHE   0.008   0.001   PHE A 267 
 TYR   0.011   0.001   TYR B 255 
 ARG   0.003   0.000   ARG C 323 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03416 (  368)
  hydrogen bonds       : angle       4.32035 ( 1173)
  SS BOND              : bond        0.00459 (    1)
  SS BOND              : angle       1.49407 (    2)
  covalent geometry    : bond        0.00232 (10280)
  covalent geometry    : angle       0.47707 (13985)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 PHE cc_start: 0.8179 (m-80) cc_final: 0.7780 (m-80)
REVERT: A  268 MET cc_start: 0.9122 (mmm) cc_final: 0.8902 (mtt)
REVERT: B   81 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8819 (mmmt)
REVERT: B  213 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8727 (mp10)
REVERT: C  303 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7758 (pm20)
REVERT: C  325 HIS cc_start: 0.8376 (p-80) cc_final: 0.6866 (t-170)
REVERT: C  366 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7838 (mp0)
REVERT: E   53 GLU cc_start: 0.8607 (tt0) cc_final: 0.8219 (mm-30)
REVERT: E   57 ARG cc_start: 0.7484 (mtm180) cc_final: 0.6963 (mtm-85)
REVERT: E  197 LYS cc_start: 0.9021 (mttt) cc_final: 0.8581 (mppt)
  outliers start: 10
  outliers final: 6
  residues processed: 72
  average time/residue: 1.4858
  time to fit residues: 114.6022
Evaluate side-chains
  74 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LYS
Chi-restraints excluded: chain A residue   81 LYS
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  213 GLN
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  303 GLU
Chi-restraints excluded: chain C residue  366 GLU
Chi-restraints excluded: chain D residue  184 ILE
Chi-restraints excluded: chain E residue   51 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 121 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 125 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 33 optimal weight:    0.1980
   chunk 62 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 119 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.089560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.066722 restraints weight = 17104.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.2801 rms_B_bonded: 2.23
r_work: 0.2684 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2563 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8852
moved from start:          0.3118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10281  Z= 0.109
  Angle     :  0.483   7.858  13987  Z= 0.249
  Chirality :  0.039   0.141   1503
  Planarity :  0.004   0.033   1828
  Dihedral  :  3.778  16.930   1422
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 11.84 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.19 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.23), residues: 1274
  helix:  1.13 (0.33), residues: 271
  sheet:  0.20 (0.31), residues: 275
  loop :  0.15 (0.23), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  99 
 HIS   0.002   0.001   HIS D 315 
 PHE   0.008   0.001   PHE B 242 
 TYR   0.011   0.001   TYR B 255 
 ARG   0.003   0.000   ARG C 323 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03437 (  368)
  hydrogen bonds       : angle       4.28104 ( 1173)
  SS BOND              : bond        0.00479 (    1)
  SS BOND              : angle       1.46568 (    2)
  covalent geometry    : bond        0.00251 (10280)
  covalent geometry    : angle       0.48289 (13985)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7185.47 seconds
wall clock time: 125 minutes 22.89 seconds (7522.89 seconds total)