Starting phenix.real_space_refine
on Sun Jun 15 12:28:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7whs_32510/06_2025/7whs_32510.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7whs_32510/06_2025/7whs_32510.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7whs_32510/06_2025/7whs_32510.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7whs_32510/06_2025/7whs_32510.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7whs_32510/06_2025/7whs_32510.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7whs_32510/06_2025/7whs_32510.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.067
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      18      5.49       5
     Mg      6      5.21       5
     S     102      5.16       5
     C   10968      2.51       5
     N    2946      2.21       5
     O    3192      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17232
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 2839
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 2839
          Classifications: {'peptide': 366}
          Link IDs: {'PTRANS': 21, 'TRANS': 344}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2839
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 2839
          Classifications: {'peptide': 366}
          Link IDs: {'PTRANS': 21, 'TRANS': 344}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2839
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 2839
          Classifications: {'peptide': 366}
          Link IDs: {'PTRANS': 21, 'TRANS': 344}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2839
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 2839
          Classifications: {'peptide': 366}
          Link IDs: {'PTRANS': 21, 'TRANS': 344}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 2839
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 2839
          Classifications: {'peptide': 366}
          Link IDs: {'PTRANS': 21, 'TRANS': 344}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 2839
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 2839
          Classifications: {'peptide': 366}
          Link IDs: {'PTRANS': 21, 'TRANS': 344}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 10.03, per 1000 atoms: 0.58
  Number of scatterers: 17232
  At special positions: 0
  Unit cell: (120.91, 118.77, 105.93, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S     102     16.00
     P      18     15.00
     Mg      6     11.99
     O    3192      8.00
     N    2946      7.00
     C   10968      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.96
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3972

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 60 sheets defined
      23.2% alpha, 14.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 27
    Processing helix  chain 'A' and resid 30 through 33
    Processing helix  chain 'A' and resid 41 through 53
    Processing helix  chain 'A' and resid 68 through 73
    Processing helix  chain 'A' and resid 74 through 77
    Processing helix  chain 'A' and resid 95 through 101
      removed outlier: 3.749A  pdb=" N   ALA A  99 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 106
    Processing helix  chain 'A' and resid 148 through 153
    Processing helix  chain 'A' and resid 189 through 194
      removed outlier: 3.934A  pdb=" N   ARG A 193 " --> pdb=" O   SER A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 213
      removed outlier: 3.693A  pdb=" N   ALA A 208 " --> pdb=" O   GLU A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 245
      Proline residue:  A 242  - end of helix
    Processing helix  chain 'B' and resid 22 through 27
    Processing helix  chain 'B' and resid 30 through 33
    Processing helix  chain 'B' and resid 41 through 53
    Processing helix  chain 'B' and resid 68 through 73
    Processing helix  chain 'B' and resid 74 through 77
    Processing helix  chain 'B' and resid 95 through 101
      removed outlier: 3.743A  pdb=" N   ALA B  99 " --> pdb=" O   ALA B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 106
    Processing helix  chain 'B' and resid 148 through 153
    Processing helix  chain 'B' and resid 189 through 194
      removed outlier: 3.988A  pdb=" N   ARG B 193 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 213
      removed outlier: 3.742A  pdb=" N   ALA B 208 " --> pdb=" O   GLU B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 245
      Proline residue:  B 242  - end of helix
    Processing helix  chain 'C' and resid 22 through 27
    Processing helix  chain 'C' and resid 30 through 33
    Processing helix  chain 'C' and resid 41 through 53
    Processing helix  chain 'C' and resid 68 through 73
    Processing helix  chain 'C' and resid 74 through 77
    Processing helix  chain 'C' and resid 95 through 101
      removed outlier: 3.758A  pdb=" N   ALA C  99 " --> pdb=" O   ALA C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 106
    Processing helix  chain 'C' and resid 148 through 153
    Processing helix  chain 'C' and resid 189 through 194
      removed outlier: 4.019A  pdb=" N   ARG C 193 " --> pdb=" O   SER C 189 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 213
      removed outlier: 3.740A  pdb=" N   ALA C 208 " --> pdb=" O   GLU C 204 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 229 through 245
      Proline residue:  C 242  - end of helix
    Processing helix  chain 'D' and resid 22 through 27
    Processing helix  chain 'D' and resid 30 through 33
    Processing helix  chain 'D' and resid 41 through 53
    Processing helix  chain 'D' and resid 68 through 73
    Processing helix  chain 'D' and resid 74 through 77
    Processing helix  chain 'D' and resid 95 through 101
      removed outlier: 3.719A  pdb=" N   ALA D  99 " --> pdb=" O   ALA D  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 106
    Processing helix  chain 'D' and resid 148 through 153
    Processing helix  chain 'D' and resid 189 through 194
      removed outlier: 3.933A  pdb=" N   ARG D 193 " --> pdb=" O   SER D 189 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 204 through 213
      removed outlier: 3.721A  pdb=" N   ALA D 208 " --> pdb=" O   GLU D 204 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 229 through 245
      Proline residue:  D 242  - end of helix
    Processing helix  chain 'E' and resid 22 through 27
    Processing helix  chain 'E' and resid 30 through 33
    Processing helix  chain 'E' and resid 41 through 53
    Processing helix  chain 'E' and resid 68 through 73
    Processing helix  chain 'E' and resid 74 through 77
    Processing helix  chain 'E' and resid 95 through 101
      removed outlier: 3.743A  pdb=" N   ALA E  99 " --> pdb=" O   ALA E  95 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 101 through 106
    Processing helix  chain 'E' and resid 148 through 153
    Processing helix  chain 'E' and resid 189 through 194
      removed outlier: 3.987A  pdb=" N   ARG E 193 " --> pdb=" O   SER E 189 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 204 through 213
      removed outlier: 3.744A  pdb=" N   ALA E 208 " --> pdb=" O   GLU E 204 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 229 through 245
      Proline residue:  E 242  - end of helix
    Processing helix  chain 'F' and resid 22 through 27
    Processing helix  chain 'F' and resid 30 through 33
    Processing helix  chain 'F' and resid 41 through 53
    Processing helix  chain 'F' and resid 68 through 73
    Processing helix  chain 'F' and resid 74 through 77
    Processing helix  chain 'F' and resid 95 through 101
      removed outlier: 3.739A  pdb=" N   ALA F  99 " --> pdb=" O   ALA F  95 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 101 through 106
    Processing helix  chain 'F' and resid 148 through 153
    Processing helix  chain 'F' and resid 189 through 194
      removed outlier: 3.990A  pdb=" N   ARG F 193 " --> pdb=" O   SER F 189 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 204 through 213
      removed outlier: 3.723A  pdb=" N   ALA F 208 " --> pdb=" O   GLU F 204 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 229 through 245
      Proline residue:  F 242  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83
    Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36
    Processing sheet with id=AA3, first strand: chain 'A' and resid 119 through 121
    Processing sheet with id=AA4, first strand: chain 'A' and resid 178 through 180
      removed outlier: 4.898A  pdb=" N   GLN A 145 " --> pdb=" O   LEU A 220 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 155 through 156
    Processing sheet with id=AA6, first strand: chain 'A' and resid 268 through 269
      removed outlier: 6.519A  pdb=" N   THR A 268 " --> pdb=" O   ILE A 287 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   VAL A 286 " --> pdb=" O   ILE A 305 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   MET A 321 " --> pdb=" O   ILE A 339 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   HIS A 338 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 273 through 275
      removed outlier: 6.518A  pdb=" N   LEU A 274 " --> pdb=" O   ILE A 293 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   SER A 292 " --> pdb=" O   ILE A 310 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   ALA A 309 " --> pdb=" O   VAL A 327 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 280 through 281
      removed outlier: 6.759A  pdb=" N   LYS A 280 " --> pdb=" O   ILE A 299 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   VAL A 298 " --> pdb=" O   VAL A 316 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 350 through 351
      removed outlier: 6.570A  pdb=" N   GLU A 350 " --> pdb=" O   VAL A 368 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 360 through 362
      removed outlier: 6.724A  pdb=" N   LYS A 361 " --> pdb=" O   ILE A 378 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 82 through 83
    Processing sheet with id=AB3, first strand: chain 'B' and resid 35 through 36
    Processing sheet with id=AB4, first strand: chain 'B' and resid 119 through 121
    Processing sheet with id=AB5, first strand: chain 'B' and resid 178 through 180
      removed outlier: 4.893A  pdb=" N   GLN B 145 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 155 through 156
    Processing sheet with id=AB7, first strand: chain 'B' and resid 268 through 269
      removed outlier: 6.400A  pdb=" N   THR B 268 " --> pdb=" O   ILE B 287 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   VAL B 286 " --> pdb=" O   ILE B 305 " (cutoff:3.500A)
      removed outlier: 6.079A  pdb=" N   ARG B 304 " --> pdb=" O   VAL B 322 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   MET B 321 " --> pdb=" O   ILE B 339 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   HIS B 338 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'B' and resid 273 through 275
      removed outlier: 6.520A  pdb=" N   LEU B 274 " --> pdb=" O   ILE B 293 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   SER B 292 " --> pdb=" O   ILE B 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'B' and resid 280 through 281
      removed outlier: 6.724A  pdb=" N   LYS B 280 " --> pdb=" O   ILE B 299 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   VAL B 298 " --> pdb=" O   VAL B 316 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'B' and resid 350 through 351
      removed outlier: 6.551A  pdb=" N   GLU B 350 " --> pdb=" O   VAL B 368 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1
    Processing sheet with id=AC2, first strand: chain 'B' and resid 360 through 362
      removed outlier: 6.527A  pdb=" N   LYS B 361 " --> pdb=" O   ILE B 378 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2
    Processing sheet with id=AC3, first strand: chain 'C' and resid 82 through 83
    Processing sheet with id=AC4, first strand: chain 'C' and resid 35 through 36
    Processing sheet with id=AC5, first strand: chain 'C' and resid 119 through 121
    Processing sheet with id=AC6, first strand: chain 'C' and resid 178 through 180
    Processing sheet with id=AC7, first strand: chain 'C' and resid 155 through 156
    Processing sheet with id=AC8, first strand: chain 'C' and resid 268 through 269
      removed outlier: 6.371A  pdb=" N   THR C 268 " --> pdb=" O   ILE C 287 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   VAL C 286 " --> pdb=" O   ILE C 305 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   ARG C 304 " --> pdb=" O   VAL C 322 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   MET C 321 " --> pdb=" O   ILE C 339 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   HIS C 338 " --> pdb=" O   LEU C 357 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC8
    Processing sheet with id=AC9, first strand: chain 'C' and resid 273 through 275
      removed outlier: 6.529A  pdb=" N   LEU C 274 " --> pdb=" O   ILE C 293 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   SER C 292 " --> pdb=" O   ILE C 310 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ALA C 309 " --> pdb=" O   VAL C 327 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC9
    Processing sheet with id=AD1, first strand: chain 'C' and resid 280 through 281
      removed outlier: 6.751A  pdb=" N   LYS C 280 " --> pdb=" O   ILE C 299 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   VAL C 298 " --> pdb=" O   VAL C 316 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD1
    Processing sheet with id=AD2, first strand: chain 'C' and resid 350 through 351
      removed outlier: 6.523A  pdb=" N   GLU C 350 " --> pdb=" O   VAL C 368 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD2
    Processing sheet with id=AD3, first strand: chain 'C' and resid 360 through 362
      removed outlier: 6.697A  pdb=" N   LYS C 361 " --> pdb=" O   ILE C 378 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD3
    Processing sheet with id=AD4, first strand: chain 'D' and resid 82 through 83
    Processing sheet with id=AD5, first strand: chain 'D' and resid 35 through 36
    Processing sheet with id=AD6, first strand: chain 'D' and resid 119 through 121
    Processing sheet with id=AD7, first strand: chain 'D' and resid 178 through 180
      removed outlier: 4.866A  pdb=" N   GLN D 145 " --> pdb=" O   LEU D 220 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'D' and resid 155 through 156
    Processing sheet with id=AD9, first strand: chain 'D' and resid 268 through 269
      removed outlier: 6.525A  pdb=" N   THR D 268 " --> pdb=" O   ILE D 287 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   VAL D 286 " --> pdb=" O   ILE D 305 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   MET D 321 " --> pdb=" O   ILE D 339 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   HIS D 338 " --> pdb=" O   LEU D 357 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'D' and resid 273 through 275
      removed outlier: 6.516A  pdb=" N   LEU D 274 " --> pdb=" O   ILE D 293 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   SER D 292 " --> pdb=" O   ILE D 310 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ALA D 309 " --> pdb=" O   VAL D 327 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE1
    Processing sheet with id=AE2, first strand: chain 'D' and resid 280 through 281
      removed outlier: 6.756A  pdb=" N   LYS D 280 " --> pdb=" O   ILE D 299 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE2
    Processing sheet with id=AE3, first strand: chain 'D' and resid 350 through 351
      removed outlier: 6.562A  pdb=" N   GLU D 350 " --> pdb=" O   VAL D 368 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE3
    Processing sheet with id=AE4, first strand: chain 'D' and resid 360 through 362
      removed outlier: 6.723A  pdb=" N   LYS D 361 " --> pdb=" O   ILE D 378 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE4
    Processing sheet with id=AE5, first strand: chain 'E' and resid 82 through 83
    Processing sheet with id=AE6, first strand: chain 'E' and resid 35 through 36
    Processing sheet with id=AE7, first strand: chain 'E' and resid 119 through 121
    Processing sheet with id=AE8, first strand: chain 'E' and resid 178 through 180
      removed outlier: 4.906A  pdb=" N   GLN E 145 " --> pdb=" O   LEU E 220 " (cutoff:3.500A)
    Processing sheet with id=AE9, first strand: chain 'E' and resid 155 through 156
    Processing sheet with id=AF1, first strand: chain 'E' and resid 268 through 269
      removed outlier: 6.445A  pdb=" N   THR E 268 " --> pdb=" O   ILE E 287 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   VAL E 286 " --> pdb=" O   ILE E 305 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   ARG E 304 " --> pdb=" O   VAL E 322 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   MET E 321 " --> pdb=" O   ILE E 339 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   HIS E 338 " --> pdb=" O   LEU E 357 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AF1
    Processing sheet with id=AF2, first strand: chain 'E' and resid 273 through 275
      removed outlier: 6.494A  pdb=" N   LEU E 274 " --> pdb=" O   ILE E 293 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   SER E 292 " --> pdb=" O   ILE E 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AF2
    Processing sheet with id=AF3, first strand: chain 'E' and resid 280 through 281
      removed outlier: 6.760A  pdb=" N   LYS E 280 " --> pdb=" O   ILE E 299 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   VAL E 298 " --> pdb=" O   VAL E 316 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   LYS E 315 " --> pdb=" O   ILE E 333 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AF3
    Processing sheet with id=AF4, first strand: chain 'E' and resid 350 through 351
      removed outlier: 6.549A  pdb=" N   GLU E 350 " --> pdb=" O   VAL E 368 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AF4
    Processing sheet with id=AF5, first strand: chain 'E' and resid 360 through 362
      removed outlier: 6.527A  pdb=" N   LYS E 361 " --> pdb=" O   ILE E 378 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AF5
    Processing sheet with id=AF6, first strand: chain 'F' and resid 82 through 83
    Processing sheet with id=AF7, first strand: chain 'F' and resid 35 through 36
    Processing sheet with id=AF8, first strand: chain 'F' and resid 119 through 121
    Processing sheet with id=AF9, first strand: chain 'F' and resid 178 through 180
    Processing sheet with id=AG1, first strand: chain 'F' and resid 155 through 156
    Processing sheet with id=AG2, first strand: chain 'F' and resid 268 through 269
      removed outlier: 6.410A  pdb=" N   THR F 268 " --> pdb=" O   ILE F 287 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   VAL F 286 " --> pdb=" O   ILE F 305 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   ARG F 304 " --> pdb=" O   VAL F 322 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   MET F 321 " --> pdb=" O   ILE F 339 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   HIS F 338 " --> pdb=" O   LEU F 357 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AG2
    Processing sheet with id=AG3, first strand: chain 'F' and resid 273 through 275
      removed outlier: 6.531A  pdb=" N   LEU F 274 " --> pdb=" O   ILE F 293 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   SER F 292 " --> pdb=" O   ILE F 310 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   ALA F 309 " --> pdb=" O   VAL F 327 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AG3
    Processing sheet with id=AG4, first strand: chain 'F' and resid 280 through 281
      removed outlier: 6.546A  pdb=" N   LYS F 280 " --> pdb=" O   ILE F 299 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   VAL F 298 " --> pdb=" O   VAL F 316 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AG4
    Processing sheet with id=AG5, first strand: chain 'F' and resid 350 through 351
      removed outlier: 6.504A  pdb=" N   GLU F 350 " --> pdb=" O   VAL F 368 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AG5
    Processing sheet with id=AG6, first strand: chain 'F' and resid 360 through 362
      removed outlier: 6.649A  pdb=" N   LYS F 361 " --> pdb=" O   ILE F 378 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AG6

    360 hydrogen bonds defined for protein.
    990 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: 5.95

  Time building geometry restraints manager: 4.74 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2977
        1.32 -     1.44: 4309
        1.44 -     1.57: 10114
        1.57 -     1.69: 30
        1.69 -     1.81: 174
  Bond restraints: 17604
  Sorted by residual:
  bond pdb=" C5  GTP B 401 "
       pdb=" C6  GTP B 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.466 -0.076 2.00e-02 2.50e+03 1.45e+01
  bond pdb=" C5  GTP E 401 "
       pdb=" C6  GTP E 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.466 -0.076 2.00e-02 2.50e+03 1.44e+01
  bond pdb=" C5  GTP F 401 "
       pdb=" C6  GTP F 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.466 -0.076 2.00e-02 2.50e+03 1.44e+01
  bond pdb=" C5  GTP C 401 "
       pdb=" C6  GTP C 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.465 -0.075 2.00e-02 2.50e+03 1.41e+01
  bond pdb=" C5  GTP A 401 "
       pdb=" C6  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.465 -0.075 2.00e-02 2.50e+03 1.40e+01
  ... (remaining 17599 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.64: 23450
        2.64 -     5.29: 341
        5.29 -     7.93: 66
        7.93 -    10.58: 15
       10.58 -    13.22: 2
  Bond angle restraints: 23874
  Sorted by residual:
  angle pdb=" N   ILE C 201 "
        pdb=" CA  ILE C 201 "
        pdb=" C   ILE C 201 "
      ideal   model   delta    sigma   weight residual
     109.37   96.15   13.22 1.35e+00 5.49e-01 9.59e+01
  angle pdb=" N   GLU F 202 "
        pdb=" CA  GLU F 202 "
        pdb=" C   GLU F 202 "
      ideal   model   delta    sigma   weight residual
     111.36  118.36   -7.00 1.09e+00 8.42e-01 4.12e+01
  angle pdb=" N   GLU E 202 "
        pdb=" CA  GLU E 202 "
        pdb=" C   GLU E 202 "
      ideal   model   delta    sigma   weight residual
     111.28  117.28   -6.00 1.09e+00 8.42e-01 3.03e+01
  angle pdb=" N   GLU B 202 "
        pdb=" CA  GLU B 202 "
        pdb=" C   GLU B 202 "
      ideal   model   delta    sigma   weight residual
     111.36  117.29   -5.93 1.09e+00 8.42e-01 2.96e+01
  angle pdb=" N   SER C 200 "
        pdb=" CA  SER C 200 "
        pdb=" C   SER C 200 "
      ideal   model   delta    sigma   weight residual
     107.70  118.86  -11.16 2.09e+00 2.29e-01 2.85e+01
  ... (remaining 23869 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.20: 10291
       34.20 -    68.40: 221
       68.40 -   102.61: 6
      102.61 -   136.81: 6
      136.81 -   171.01: 12
  Dihedral angle restraints: 10536
    sinusoidal: 4332
      harmonic: 6204
  Sorted by residual:
  dihedral pdb=" C5' GTP C 401 "
           pdb=" O5' GTP C 401 "
           pdb=" PA  GTP C 401 "
           pdb=" O3A GTP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -101.74  171.01     1      2.00e+01 2.50e-03 4.77e+01
  dihedral pdb=" C5' GTP F 401 "
           pdb=" O5' GTP F 401 "
           pdb=" PA  GTP F 401 "
           pdb=" O3A GTP F 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -100.85  170.12     1      2.00e+01 2.50e-03 4.76e+01
  dihedral pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" O3A GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -100.44  169.71     1      2.00e+01 2.50e-03 4.76e+01
  ... (remaining 10533 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 2399
       0.098 -    0.197: 234
       0.197 -    0.295: 17
       0.295 -    0.394: 0
       0.394 -    0.492: 2
  Chirality restraints: 2652
  Sorted by residual:
  chirality pdb=" CA  ILE C 201 "
            pdb=" N   ILE C 201 "
            pdb=" C   ILE C 201 "
            pdb=" CB  ILE C 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.93   -0.49 2.00e-01 2.50e+01 6.06e+00
  chirality pdb=" CA  GLU F 202 "
            pdb=" N   GLU F 202 "
            pdb=" C   GLU F 202 "
            pdb=" CB  GLU F 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.63e+00
  chirality pdb=" CA  GLU C 202 "
            pdb=" N   GLU C 202 "
            pdb=" C   GLU C 202 "
            pdb=" CB  GLU C 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.84e+00
  ... (remaining 2649 not shown)

  Planarity restraints: 3054
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 199 "   -0.017 2.00e-02 2.50e+03   3.40e-02 1.16e+01
        pdb=" C   ALA C 199 "    0.059 2.00e-02 2.50e+03
        pdb=" O   ALA C 199 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   SER C 200 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 110 "   -0.050 5.00e-02 4.00e+02   7.64e-02 9.33e+00
        pdb=" N   PRO B 111 "    0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO B 111 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO B 111 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 110 "    0.050 5.00e-02 4.00e+02   7.61e-02 9.27e+00
        pdb=" N   PRO E 111 "   -0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO E 111 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO E 111 "    0.041 5.00e-02 4.00e+02
  ... (remaining 3051 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1259
        2.74 -     3.28: 17444
        3.28 -     3.82: 28339
        3.82 -     4.36: 35864
        4.36 -     4.90: 61851
  Nonbonded interactions: 144757
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 325 "
            pdb=" O   SER B 343 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OG  SER C 325 "
            pdb=" O   SER C 343 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" OG  SER E 325 "
            pdb=" O   SER E 343 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OG  SER F 325 "
            pdb=" O   SER F 343 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OD1 ASP B 226 "
            pdb="MG    MG B 402 "
     model   vdw
     2.217 2.170
  ... (remaining 144752 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.010
  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:          0.640
  Check model and map are aligned:         0.120
  Set scattering table:                    0.140
  Process input model:                     39.700
  Find NCS groups from input model:        0.680
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
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      :  0.005   0.076  17604  Z= 0.242
  Angle     :  0.783  13.220  23874  Z= 0.400
  Chirality :  0.056   0.492   2652
  Planarity :  0.006   0.076   3054
  Dihedral  : 16.308 171.012   6564
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  8.20 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  0.60 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.05 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.18), residues: 2172
  helix:  1.02 (0.30), residues: 318
  sheet:  0.22 (0.35), residues: 234
  loop : -1.33 (0.15), residues: 1620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 149 
 HIS   0.009   0.002   HIS E 338 
 PHE   0.014   0.001   PHE D  85 
 TYR   0.007   0.001   TYR C 233 
 ARG   0.003   0.000   ARG E  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17699 (  360)
  hydrogen bonds       : angle       7.26939 (  990)
  covalent geometry    : bond        0.00459 (17604)
  covalent geometry    : angle       0.78335 (23874)

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

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

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 228
  time to evaluate  : 1.729 
Fit side-chains
   revert: symmetry clash
REVERT: A  187 ASN cc_start: 0.6731 (m-40) cc_final: 0.6464 (m110)
REVERT: C  144 SER cc_start: 0.8463 (t) cc_final: 0.8082 (p)
REVERT: C  201 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7757 (mt)
REVERT: D  187 ASN cc_start: 0.6743 (m-40) cc_final: 0.6490 (m110)
REVERT: F  102 ARG cc_start: 0.7791 (ptm160) cc_final: 0.7023 (ttm110)
REVERT: F  144 SER cc_start: 0.8449 (t) cc_final: 0.8077 (p)
  outliers start: 6
  outliers final: 4
  residues processed: 233
  average time/residue: 0.2753
  time to fit residues: 99.1048
Evaluate side-chains
  211 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 206
  time to evaluate  : 1.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain C residue  201 ILE
Chi-restraints excluded: chain E residue  201 ILE
Chi-restraints excluded: chain F residue  201 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 182 optimal weight:    1.9990
   chunk 163 optimal weight:    0.9990
   chunk 90 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 110 optimal weight:    2.9990
   chunk 87 optimal weight:    0.2980
   chunk 169 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 102 optimal weight:    3.9990
   chunk 126 optimal weight:    2.9990
   chunk 196 optimal weight:    0.0370
   overall best weight:    1.2664

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

Flipped N/Q/H residues before XYZ refinement:
A 132 HIS
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 132 HIS
C 107 GLN
C 132 HIS
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 132 HIS
** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 132 HIS
E 261 HIS
F 107 GLN
F 132 HIS
** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.193939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.143251 restraints weight = 17194.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 2.02
r_work: 0.3371 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.0881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  17604  Z= 0.168
  Angle     :  0.645   7.313  23874  Z= 0.323
  Chirality :  0.053   0.283   2652
  Planarity :  0.006   0.052   3054
  Dihedral  : 15.193 169.403   2440
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  8.09 %
    Favored  : 91.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.18), residues: 2172
  helix:  0.12 (0.27), residues: 390
  sheet:  0.39 (0.37), residues: 204
  loop : -1.36 (0.15), residues: 1578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 336 
 HIS   0.006   0.002   HIS B 261 
 PHE   0.012   0.001   PHE D  85 
 TYR   0.013   0.002   TYR E 152 
 ARG   0.003   0.000   ARG C 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05230 (  360)
  hydrogen bonds       : angle       6.37635 (  990)
  covalent geometry    : bond        0.00411 (17604)
  covalent geometry    : angle       0.64455 (23874)

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

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

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 203
  time to evaluate  : 1.974 
Fit side-chains
REVERT: A  212 GLU cc_start: 0.6348 (tt0) cc_final: 0.5870 (tt0)
REVERT: B   56 GLU cc_start: 0.7822 (tp30) cc_final: 0.7527 (mm-30)
REVERT: C   41 MET cc_start: 0.8187 (mtt) cc_final: 0.7886 (mtt)
REVERT: D  212 GLU cc_start: 0.6333 (tt0) cc_final: 0.5940 (tt0)
REVERT: F  202 GLU cc_start: 0.7506 (mp0) cc_final: 0.7149 (mp0)
  outliers start: 15
  outliers final: 7
  residues processed: 212
  average time/residue: 0.3329
  time to fit residues: 105.4111
Evaluate side-chains
  201 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 194
  time to evaluate  : 1.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain E residue  201 ILE
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain F residue   41 MET
Chi-restraints excluded: chain F residue  200 SER
Chi-restraints excluded: chain F residue  201 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 215 optimal weight:    0.0370
   chunk 95 optimal weight:    1.9990
   chunk 178 optimal weight:    1.9990
   chunk 93 optimal weight:    0.6980
   chunk 107 optimal weight:    1.9990
   chunk 130 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0980
   chunk 86 optimal weight:    0.9990
   chunk 152 optimal weight:    0.8980
   chunk 54 optimal weight:    9.9990
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
A 132 HIS
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 132 HIS
** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 261 HIS
F 132 HIS
** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.197280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.146568 restraints weight = 17122.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 1.98
r_work: 0.3419 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.1093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  17604  Z= 0.109
  Angle     :  0.572   6.639  23874  Z= 0.287
  Chirality :  0.050   0.181   2652
  Planarity :  0.005   0.048   3054
  Dihedral  : 14.920 177.198   2438
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 10.86 %
    Favored  : 87.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.18), residues: 2172
  helix:  0.23 (0.27), residues: 390
  sheet:  0.26 (0.39), residues: 174
  loop : -1.36 (0.15), residues: 1608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 149 
 HIS   0.007   0.001   HIS E 261 
 PHE   0.009   0.001   PHE A 167 
 TYR   0.011   0.001   TYR B 233 
 ARG   0.002   0.000   ARG E  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04355 (  360)
  hydrogen bonds       : angle       6.11631 (  990)
  covalent geometry    : bond        0.00254 (17604)
  covalent geometry    : angle       0.57185 (23874)

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

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

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 204
  time to evaluate  : 1.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 VAL cc_start: 0.6342 (OUTLIER) cc_final: 0.6108 (t)
REVERT: A  212 GLU cc_start: 0.6440 (tt0) cc_final: 0.6102 (tt0)
REVERT: B   87 VAL cc_start: 0.6361 (OUTLIER) cc_final: 0.6121 (t)
REVERT: C   87 VAL cc_start: 0.6202 (OUTLIER) cc_final: 0.5949 (t)
REVERT: C  202 GLU cc_start: 0.7908 (pm20) cc_final: 0.7645 (pm20)
REVERT: D   87 VAL cc_start: 0.6314 (OUTLIER) cc_final: 0.6051 (t)
REVERT: D  212 GLU cc_start: 0.6364 (tt0) cc_final: 0.6068 (tt0)
REVERT: E   87 VAL cc_start: 0.6439 (OUTLIER) cc_final: 0.6194 (t)
REVERT: F  202 GLU cc_start: 0.7507 (mp0) cc_final: 0.7045 (mp0)
  outliers start: 31
  outliers final: 14
  residues processed: 226
  average time/residue: 0.3597
  time to fit residues: 123.9306
Evaluate side-chains
  204 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 1.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain B residue  292 SER
Chi-restraints excluded: chain C residue   87 VAL
Chi-restraints excluded: chain C residue  292 SER
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  201 ILE
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain E residue  261 HIS
Chi-restraints excluded: chain F residue  200 SER
Chi-restraints excluded: chain F residue  201 ILE
Chi-restraints excluded: chain F residue  292 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 109 optimal weight:    0.8980
   chunk 98 optimal weight:    0.8980
   chunk 149 optimal weight:    1.9990
   chunk 184 optimal weight:    1.9990
   chunk 135 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 50 optimal weight:   10.0000
   chunk 191 optimal weight:    0.6980
   chunk 168 optimal weight:    3.9990
   chunk 200 optimal weight:   10.0000
   chunk 72 optimal weight:    7.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 132 HIS
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 132 HIS
B 261 HIS
C 132 HIS
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 132 HIS
** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 132 HIS
F 132 HIS
** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.195349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.145641 restraints weight = 17218.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 2.39
r_work: 0.3337 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  17604  Z= 0.145
  Angle     :  0.586   6.005  23874  Z= 0.293
  Chirality :  0.051   0.177   2652
  Planarity :  0.005   0.047   3054
  Dihedral  : 14.791 179.791   2438
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 11.83 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.18), residues: 2172
  helix:  0.29 (0.27), residues: 390
  sheet: -0.06 (0.33), residues: 264
  loop : -1.50 (0.16), residues: 1518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 336 
 HIS   0.019   0.002   HIS E 261 
 PHE   0.010   0.001   PHE E 167 
 TYR   0.013   0.002   TYR C 233 
 ARG   0.001   0.000   ARG B 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04449 (  360)
  hydrogen bonds       : angle       6.05794 (  990)
  covalent geometry    : bond        0.00363 (17604)
  covalent geometry    : angle       0.58557 (23874)

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

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

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 190
  time to evaluate  : 2.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 VAL cc_start: 0.6295 (OUTLIER) cc_final: 0.6084 (t)
REVERT: A  212 GLU cc_start: 0.6391 (tt0) cc_final: 0.6081 (tt0)
REVERT: B   56 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7098 (mm-30)
REVERT: B   87 VAL cc_start: 0.6239 (OUTLIER) cc_final: 0.6008 (t)
REVERT: C  157 TYR cc_start: 0.6008 (m-80) cc_final: 0.5789 (m-80)
REVERT: C  202 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7177 (pm20)
REVERT: D   87 VAL cc_start: 0.6273 (OUTLIER) cc_final: 0.6061 (t)
REVERT: D  212 GLU cc_start: 0.6371 (tt0) cc_final: 0.6096 (tt0)
REVERT: D  221 GLU cc_start: 0.8017 (pm20) cc_final: 0.7329 (mm-30)
REVERT: E   87 VAL cc_start: 0.6210 (OUTLIER) cc_final: 0.5969 (t)
REVERT: F  157 TYR cc_start: 0.6015 (m-80) cc_final: 0.5795 (m-80)
REVERT: F  202 GLU cc_start: 0.7513 (mp0) cc_final: 0.7130 (mp0)
  outliers start: 50
  outliers final: 30
  residues processed: 227
  average time/residue: 0.3450
  time to fit residues: 120.8991
Evaluate side-chains
  218 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 183
  time to evaluate  : 1.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain B residue  261 HIS
Chi-restraints excluded: chain B residue  292 SER
Chi-restraints excluded: chain C residue   41 MET
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  292 SER
Chi-restraints excluded: chain C residue  338 HIS
Chi-restraints excluded: chain D residue   87 VAL
Chi-restraints excluded: chain D residue  185 ILE
Chi-restraints excluded: chain D residue  200 SER
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  140 THR
Chi-restraints excluded: chain E residue  201 ILE
Chi-restraints excluded: chain E residue  235 LEU
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain E residue  292 SER
Chi-restraints excluded: chain F residue    9 MET
Chi-restraints excluded: chain F residue  140 THR
Chi-restraints excluded: chain F residue  168 VAL
Chi-restraints excluded: chain F residue  200 SER
Chi-restraints excluded: chain F residue  201 ILE
Chi-restraints excluded: chain F residue  292 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 131 optimal weight:    2.9990
   chunk 147 optimal weight:    3.9990
   chunk 112 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 56 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   chunk 114 optimal weight:    2.9990
   chunk 150 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 132 HIS
A 331 ASN
B 132 HIS
** B 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 132 HIS
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 338 HIS
D 132 HIS
D 331 ASN
E 132 HIS
E 261 HIS
F 132 HIS
** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 331 ASN
F 338 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.188098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.130727 restraints weight = 17524.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.92
r_work: 0.3295 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050  17604  Z= 0.261
  Angle     :  0.681   5.965  23874  Z= 0.343
  Chirality :  0.055   0.185   2652
  Planarity :  0.005   0.047   3054
  Dihedral  : 14.759 179.791   2436
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 12.27 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.17), residues: 2172
  helix:  0.16 (0.26), residues: 390
  sheet: -0.39 (0.32), residues: 264
  loop : -1.74 (0.15), residues: 1518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 336 
 HIS   0.031   0.002   HIS B 261 
 PHE   0.012   0.002   PHE E 167 
 TYR   0.017   0.002   TYR C 233 
 ARG   0.005   0.000   ARG B 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05476 (  360)
  hydrogen bonds       : angle       6.17599 (  990)
  covalent geometry    : bond        0.00664 (17604)
  covalent geometry    : angle       0.68139 (23874)

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

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

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 187
  time to evaluate  : 2.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  212 GLU cc_start: 0.6269 (tt0) cc_final: 0.5973 (tt0)
REVERT: A  237 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8144 (ttp)
REVERT: B   87 VAL cc_start: 0.6189 (OUTLIER) cc_final: 0.5939 (t)
REVERT: C  157 TYR cc_start: 0.6092 (OUTLIER) cc_final: 0.5794 (m-80)
REVERT: C  202 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6726 (pm20)
REVERT: D  212 GLU cc_start: 0.6304 (tt0) cc_final: 0.5894 (tt0)
REVERT: D  237 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8155 (ttp)
REVERT: E   87 VAL cc_start: 0.6162 (OUTLIER) cc_final: 0.5908 (t)
REVERT: E  201 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6685 (tt)
REVERT: F  157 TYR cc_start: 0.6068 (OUTLIER) cc_final: 0.5778 (m-80)
REVERT: F  261 HIS cc_start: 0.6453 (t-90) cc_final: 0.6195 (t-90)
  outliers start: 60
  outliers final: 38
  residues processed: 234
  average time/residue: 0.2990
  time to fit residues: 109.6300
Evaluate side-chains
  230 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 184
  time to evaluate  : 1.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  292 SER
Chi-restraints excluded: chain A residue  338 HIS
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  292 SER
Chi-restraints excluded: chain C residue    9 MET
Chi-restraints excluded: chain C residue   41 MET
Chi-restraints excluded: chain C residue   55 THR
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  157 TYR
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  292 SER
Chi-restraints excluded: chain C residue  322 VAL
Chi-restraints excluded: chain C residue  338 HIS
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  185 ILE
Chi-restraints excluded: chain D residue  200 SER
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  237 MET
Chi-restraints excluded: chain D residue  292 SER
Chi-restraints excluded: chain D residue  338 HIS
Chi-restraints excluded: chain E residue   54 VAL
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  132 HIS
Chi-restraints excluded: chain E residue  140 THR
Chi-restraints excluded: chain E residue  201 ILE
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain E residue  261 HIS
Chi-restraints excluded: chain E residue  292 SER
Chi-restraints excluded: chain F residue    9 MET
Chi-restraints excluded: chain F residue  140 THR
Chi-restraints excluded: chain F residue  157 TYR
Chi-restraints excluded: chain F residue  168 VAL
Chi-restraints excluded: chain F residue  200 SER
Chi-restraints excluded: chain F residue  201 ILE
Chi-restraints excluded: chain F residue  292 SER
Chi-restraints excluded: chain F residue  338 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 114 optimal weight:    0.8980
   chunk 184 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 207 optimal weight:    0.2980
   chunk 13 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 177 optimal weight:    0.9990
   chunk 156 optimal weight:    9.9990
   chunk 23 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 120 optimal weight:    0.0870
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
A 132 HIS
A 261 HIS
B 132 HIS
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 338 HIS
** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 261 HIS
** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 338 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.193623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.143704 restraints weight = 17406.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 2.54
r_work: 0.3317 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.1592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  17604  Z= 0.115
  Angle     :  0.580   6.026  23874  Z= 0.294
  Chirality :  0.050   0.305   2652
  Planarity :  0.005   0.048   3054
  Dihedral  : 14.505 178.912   2436
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 13.52 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.17), residues: 2172
  helix:  0.28 (0.27), residues: 390
  sheet: -0.71 (0.35), residues: 204
  loop : -1.66 (0.15), residues: 1578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E 149 
 HIS   0.020   0.002   HIS F 338 
 PHE   0.011   0.001   PHE E 131 
 TYR   0.012   0.001   TYR B 233 
 ARG   0.007   0.000   ARG E 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04335 (  360)
  hydrogen bonds       : angle       6.02335 (  990)
  covalent geometry    : bond        0.00262 (17604)
  covalent geometry    : angle       0.58043 (23874)

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

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

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 188
  time to evaluate  : 2.013 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  212 GLU cc_start: 0.6299 (tt0) cc_final: 0.6008 (tt0)
REVERT: B   87 VAL cc_start: 0.6181 (OUTLIER) cc_final: 0.5953 (t)
REVERT: B  221 GLU cc_start: 0.7996 (pm20) cc_final: 0.7365 (mm-30)
REVERT: D  212 GLU cc_start: 0.6334 (tt0) cc_final: 0.6070 (tt0)
REVERT: D  221 GLU cc_start: 0.8016 (pm20) cc_final: 0.7476 (mm-30)
REVERT: E   87 VAL cc_start: 0.6237 (OUTLIER) cc_final: 0.6012 (t)
REVERT: E  266 ARG cc_start: 0.7656 (mmm-85) cc_final: 0.7393 (mmm160)
REVERT: F  202 GLU cc_start: 0.7610 (mp0) cc_final: 0.7026 (mp0)
  outliers start: 47
  outliers final: 34
  residues processed: 229
  average time/residue: 0.3176
  time to fit residues: 112.9291
Evaluate side-chains
  216 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 180
  time to evaluate  : 2.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  338 HIS
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  132 HIS
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  235 LEU
Chi-restraints excluded: chain B residue  292 SER
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain C residue   41 MET
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  168 VAL
Chi-restraints excluded: chain C residue  292 SER
Chi-restraints excluded: chain C residue  322 VAL
Chi-restraints excluded: chain C residue  338 HIS
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  185 ILE
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  235 LEU
Chi-restraints excluded: chain D residue  338 HIS
Chi-restraints excluded: chain E residue   54 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  140 THR
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain E residue  292 SER
Chi-restraints excluded: chain F residue   55 THR
Chi-restraints excluded: chain F residue  122 THR
Chi-restraints excluded: chain F residue  140 THR
Chi-restraints excluded: chain F residue  168 VAL
Chi-restraints excluded: chain F residue  201 ILE
Chi-restraints excluded: chain F residue  292 SER
Chi-restraints excluded: chain F residue  338 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 191 optimal weight:    5.9990
   chunk 52 optimal weight:   20.0000
   chunk 6 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 4 optimal weight:    3.9990
   chunk 121 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 211 optimal weight:    0.0070
   chunk 31 optimal weight:    0.8980
   overall best weight:    1.5804

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

Flipped N/Q/H residues before XYZ refinement:
A 132 HIS
** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 261 HIS
C 132 HIS
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 338 HIS
D 132 HIS
E 132 HIS
F 132 HIS
** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 338 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.190705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.140080 restraints weight = 17457.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 2.71
r_work: 0.3261 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  17604  Z= 0.186
  Angle     :  0.619   6.120  23874  Z= 0.311
  Chirality :  0.053   0.309   2652
  Planarity :  0.005   0.048   3054
  Dihedral  : 14.387 178.647   2434
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.22 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.17), residues: 2172
  helix:  0.27 (0.27), residues: 390
  sheet: -0.55 (0.33), residues: 234
  loop : -1.74 (0.15), residues: 1548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 336 
 HIS   0.015   0.002   HIS F 338 
 PHE   0.012   0.001   PHE D 167 
 TYR   0.014   0.002   TYR B 233 
 ARG   0.003   0.000   ARG E  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04789 (  360)
  hydrogen bonds       : angle       6.03278 (  990)
  covalent geometry    : bond        0.00470 (17604)
  covalent geometry    : angle       0.61948 (23874)

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

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

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 181
  time to evaluate  : 1.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  212 GLU cc_start: 0.6316 (tt0) cc_final: 0.6047 (tt0)
REVERT: B   87 VAL cc_start: 0.6208 (OUTLIER) cc_final: 0.5951 (t)
REVERT: B  221 GLU cc_start: 0.8082 (pm20) cc_final: 0.7449 (mm-30)
REVERT: D  212 GLU cc_start: 0.6363 (tt0) cc_final: 0.6097 (tt0)
REVERT: D  221 GLU cc_start: 0.8054 (pm20) cc_final: 0.7429 (mm-30)
REVERT: E   87 VAL cc_start: 0.6123 (OUTLIER) cc_final: 0.5862 (t)
REVERT: E  266 ARG cc_start: 0.7701 (mmm-85) cc_final: 0.7473 (mmm160)
REVERT: F  202 GLU cc_start: 0.7586 (mp0) cc_final: 0.7002 (mp0)
  outliers start: 50
  outliers final: 39
  residues processed: 222
  average time/residue: 0.2723
  time to fit residues: 93.3956
Evaluate side-chains
  222 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 181
  time to evaluate  : 1.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  313 ASN
Chi-restraints excluded: chain A residue  338 HIS
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  261 HIS
Chi-restraints excluded: chain B residue  292 SER
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain C residue    9 MET
Chi-restraints excluded: chain C residue   41 MET
Chi-restraints excluded: chain C residue   55 THR
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  292 SER
Chi-restraints excluded: chain C residue  322 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  185 ILE
Chi-restraints excluded: chain D residue  200 SER
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  313 ASN
Chi-restraints excluded: chain D residue  338 HIS
Chi-restraints excluded: chain E residue   54 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  140 THR
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain E residue  292 SER
Chi-restraints excluded: chain E residue  322 VAL
Chi-restraints excluded: chain F residue    9 MET
Chi-restraints excluded: chain F residue   55 THR
Chi-restraints excluded: chain F residue  122 THR
Chi-restraints excluded: chain F residue  140 THR
Chi-restraints excluded: chain F residue  200 SER
Chi-restraints excluded: chain F residue  201 ILE
Chi-restraints excluded: chain F residue  292 SER
Chi-restraints excluded: chain F residue  338 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 80 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9980
   chunk 84 optimal weight:    6.9990
   chunk 114 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 20 optimal weight:   10.0000
   chunk 156 optimal weight:    9.9990
   chunk 112 optimal weight:    0.9990
   chunk 129 optimal weight:    0.7980
   chunk 105 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 132 HIS
B 261 HIS
C 132 HIS
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 132 HIS
** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 261 HIS
F 132 HIS
** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 338 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.191696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.142404 restraints weight = 17275.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 2.66
r_work: 0.3280 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  17604  Z= 0.148
  Angle     :  0.594   5.888  23874  Z= 0.299
  Chirality :  0.052   0.303   2652
  Planarity :  0.005   0.047   3054
  Dihedral  : 14.264 176.910   2434
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 14.44 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.17), residues: 2172
  helix:  0.27 (0.27), residues: 390
  sheet: -0.55 (0.33), residues: 234
  loop : -1.73 (0.15), residues: 1548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.019   0.002   HIS F 338 
 PHE   0.011   0.001   PHE B 167 
 TYR   0.013   0.001   TYR B 233 
 ARG   0.006   0.000   ARG B 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04548 (  360)
  hydrogen bonds       : angle       5.98541 (  990)
  covalent geometry    : bond        0.00369 (17604)
  covalent geometry    : angle       0.59371 (23874)

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

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

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 186
  time to evaluate  : 1.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  212 GLU cc_start: 0.6369 (tt0) cc_final: 0.6099 (tt0)
REVERT: A  237 MET cc_start: 0.8395 (ttp) cc_final: 0.8159 (ttp)
REVERT: B   87 VAL cc_start: 0.6259 (OUTLIER) cc_final: 0.6037 (t)
REVERT: B  221 GLU cc_start: 0.8079 (pm20) cc_final: 0.7460 (mm-30)
REVERT: D  212 GLU cc_start: 0.6400 (tt0) cc_final: 0.6142 (tt0)
REVERT: E   87 VAL cc_start: 0.6171 (OUTLIER) cc_final: 0.5902 (t)
REVERT: F  202 GLU cc_start: 0.7581 (mp0) cc_final: 0.6969 (mp0)
  outliers start: 47
  outliers final: 39
  residues processed: 224
  average time/residue: 0.2771
  time to fit residues: 96.4335
Evaluate side-chains
  226 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 185
  time to evaluate  : 1.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  313 ASN
Chi-restraints excluded: chain A residue  338 HIS
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  261 HIS
Chi-restraints excluded: chain B residue  292 SER
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain C residue    9 MET
Chi-restraints excluded: chain C residue   41 MET
Chi-restraints excluded: chain C residue   55 THR
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  292 SER
Chi-restraints excluded: chain C residue  322 VAL
Chi-restraints excluded: chain C residue  338 HIS
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  185 ILE
Chi-restraints excluded: chain D residue  200 SER
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  313 ASN
Chi-restraints excluded: chain D residue  338 HIS
Chi-restraints excluded: chain E residue   54 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  140 THR
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain E residue  261 HIS
Chi-restraints excluded: chain E residue  292 SER
Chi-restraints excluded: chain E residue  322 VAL
Chi-restraints excluded: chain F residue    9 MET
Chi-restraints excluded: chain F residue   55 THR
Chi-restraints excluded: chain F residue  140 THR
Chi-restraints excluded: chain F residue  200 SER
Chi-restraints excluded: chain F residue  201 ILE
Chi-restraints excluded: chain F residue  292 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 147 optimal weight:    3.9990
   chunk 207 optimal weight:    2.9990
   chunk 154 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 113 optimal weight:    0.7980
   chunk 56 optimal weight:    6.9990
   chunk 173 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 114 optimal weight:    0.9980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 261 HIS
** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.195945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.147407 restraints weight = 17620.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 3.08
r_work: 0.3351 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.1753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  17604  Z= 0.136
  Angle     :  0.586   5.892  23874  Z= 0.295
  Chirality :  0.051   0.280   2652
  Planarity :  0.005   0.047   3054
  Dihedral  : 14.134 175.283   2434
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 14.17 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.17), residues: 2172
  helix:  0.29 (0.27), residues: 390
  sheet: -0.83 (0.34), residues: 204
  loop : -1.72 (0.15), residues: 1578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 336 
 HIS   0.018   0.001   HIS B 261 
 PHE   0.011   0.001   PHE B 167 
 TYR   0.013   0.001   TYR B 233 
 ARG   0.006   0.000   ARG E 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04423 (  360)
  hydrogen bonds       : angle       5.93455 (  990)
  covalent geometry    : bond        0.00335 (17604)
  covalent geometry    : angle       0.58576 (23874)

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

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

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 183
  time to evaluate  : 2.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  212 GLU cc_start: 0.6424 (tt0) cc_final: 0.6166 (tt0)
REVERT: A  237 MET cc_start: 0.8410 (ttp) cc_final: 0.8198 (ttp)
REVERT: B   87 VAL cc_start: 0.6270 (OUTLIER) cc_final: 0.6029 (t)
REVERT: B  221 GLU cc_start: 0.8093 (pm20) cc_final: 0.7531 (mm-30)
REVERT: D  212 GLU cc_start: 0.6433 (tt0) cc_final: 0.6190 (tt0)
REVERT: E   87 VAL cc_start: 0.6233 (OUTLIER) cc_final: 0.5983 (t)
REVERT: E  221 GLU cc_start: 0.8015 (pm20) cc_final: 0.7472 (mm-30)
REVERT: F  202 GLU cc_start: 0.7652 (mp0) cc_final: 0.7058 (mp0)
  outliers start: 49
  outliers final: 44
  residues processed: 222
  average time/residue: 0.2828
  time to fit residues: 97.2977
Evaluate side-chains
  229 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 183
  time to evaluate  : 1.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  313 ASN
Chi-restraints excluded: chain A residue  338 HIS
Chi-restraints excluded: chain B residue   41 MET
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  292 SER
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain C residue    9 MET
Chi-restraints excluded: chain C residue   41 MET
Chi-restraints excluded: chain C residue   55 THR
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  292 SER
Chi-restraints excluded: chain C residue  322 VAL
Chi-restraints excluded: chain C residue  338 HIS
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  185 ILE
Chi-restraints excluded: chain D residue  200 SER
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  292 SER
Chi-restraints excluded: chain D residue  313 ASN
Chi-restraints excluded: chain D residue  338 HIS
Chi-restraints excluded: chain E residue   54 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  140 THR
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain E residue  261 HIS
Chi-restraints excluded: chain E residue  292 SER
Chi-restraints excluded: chain E residue  322 VAL
Chi-restraints excluded: chain F residue    9 MET
Chi-restraints excluded: chain F residue   55 THR
Chi-restraints excluded: chain F residue  122 THR
Chi-restraints excluded: chain F residue  140 THR
Chi-restraints excluded: chain F residue  185 ILE
Chi-restraints excluded: chain F residue  200 SER
Chi-restraints excluded: chain F residue  201 ILE
Chi-restraints excluded: chain F residue  292 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 184 optimal weight:    3.9990
   chunk 130 optimal weight:    2.9990
   chunk 92 optimal weight:   10.0000
   chunk 147 optimal weight:    2.9990
   chunk 158 optimal weight:    3.9990
   chunk 156 optimal weight:   10.0000
   chunk 161 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 155 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 132 HIS
** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 261 HIS
C 132 HIS
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 132 HIS
E 261 HIS
F 132 HIS
** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.192789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.146206 restraints weight = 17631.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 2.64
r_work: 0.3320 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  17604  Z= 0.197
  Angle     :  0.630   5.783  23874  Z= 0.317
  Chirality :  0.053   0.339   2652
  Planarity :  0.005   0.047   3054
  Dihedral  : 14.154 176.182   2434
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.77 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.17), residues: 2172
  helix:  0.28 (0.27), residues: 390
  sheet: -0.66 (0.32), residues: 234
  loop : -1.80 (0.15), residues: 1548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 336 
 HIS   0.010   0.002   HIS E 261 
 PHE   0.012   0.001   PHE E 167 
 TYR   0.015   0.002   TYR C 233 
 ARG   0.007   0.000   ARG E 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04901 (  360)
  hydrogen bonds       : angle       5.95038 (  990)
  covalent geometry    : bond        0.00498 (17604)
  covalent geometry    : angle       0.63019 (23874)

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

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

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4344 Ramachandran restraints generated.
    2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 190
  time to evaluate  : 2.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  212 GLU cc_start: 0.6524 (tt0) cc_final: 0.6291 (tt0)
REVERT: A  237 MET cc_start: 0.8578 (ttp) cc_final: 0.8374 (ttp)
REVERT: B   87 VAL cc_start: 0.6283 (OUTLIER) cc_final: 0.6035 (t)
REVERT: D  212 GLU cc_start: 0.6523 (tt0) cc_final: 0.6307 (tt0)
REVERT: D  221 GLU cc_start: 0.7985 (pm20) cc_final: 0.7641 (mm-30)
REVERT: D  237 MET cc_start: 0.8568 (ttp) cc_final: 0.8364 (ttp)
REVERT: E   87 VAL cc_start: 0.6062 (OUTLIER) cc_final: 0.5788 (t)
REVERT: E  221 GLU cc_start: 0.8010 (pm20) cc_final: 0.7596 (mm-30)
REVERT: F  202 GLU cc_start: 0.7735 (mp0) cc_final: 0.7155 (mp0)
  outliers start: 51
  outliers final: 43
  residues processed: 231
  average time/residue: 0.3054
  time to fit residues: 107.7728
Evaluate side-chains
  231 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 186
  time to evaluate  : 1.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  313 ASN
Chi-restraints excluded: chain A residue  338 HIS
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  261 HIS
Chi-restraints excluded: chain B residue  292 SER
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain C residue    9 MET
Chi-restraints excluded: chain C residue   41 MET
Chi-restraints excluded: chain C residue   55 THR
Chi-restraints excluded: chain C residue  122 THR
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  292 SER
Chi-restraints excluded: chain C residue  322 VAL
Chi-restraints excluded: chain C residue  338 HIS
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  185 ILE
Chi-restraints excluded: chain D residue  200 SER
Chi-restraints excluded: chain D residue  201 ILE
Chi-restraints excluded: chain D residue  292 SER
Chi-restraints excluded: chain D residue  313 ASN
Chi-restraints excluded: chain D residue  338 HIS
Chi-restraints excluded: chain E residue   54 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   87 VAL
Chi-restraints excluded: chain E residue  140 THR
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain E residue  261 HIS
Chi-restraints excluded: chain E residue  292 SER
Chi-restraints excluded: chain E residue  322 VAL
Chi-restraints excluded: chain F residue    9 MET
Chi-restraints excluded: chain F residue   55 THR
Chi-restraints excluded: chain F residue  122 THR
Chi-restraints excluded: chain F residue  140 THR
Chi-restraints excluded: chain F residue  185 ILE
Chi-restraints excluded: chain F residue  200 SER
Chi-restraints excluded: chain F residue  201 ILE
Chi-restraints excluded: chain F residue  292 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 15 optimal weight:    0.3980
   chunk 173 optimal weight:    0.2980
   chunk 125 optimal weight:    5.9990
   chunk 144 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 66 optimal weight:    0.9990
   chunk 131 optimal weight:    0.4980
   chunk 94 optimal weight:    0.9990
   chunk 133 optimal weight:    0.0770
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 261 HIS
** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.197669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.150161 restraints weight = 17542.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 2.88
r_work: 0.3388 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  17604  Z= 0.109
  Angle     :  0.574   6.049  23874  Z= 0.291
  Chirality :  0.050   0.305   2652
  Planarity :  0.005   0.047   3054
  Dihedral  : 13.930 172.347   2434
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 15.15 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.17), residues: 2172
  helix:  0.30 (0.27), residues: 390
  sheet: -0.83 (0.34), residues: 204
  loop : -1.72 (0.15), residues: 1578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 149 
 HIS   0.019   0.002   HIS B 261 
 PHE   0.010   0.001   PHE B 167 
 TYR   0.011   0.001   TYR B 233 
 ARG   0.005   0.000   ARG E 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04178 (  360)
  hydrogen bonds       : angle       5.83544 (  990)
  covalent geometry    : bond        0.00255 (17604)
  covalent geometry    : angle       0.57443 (23874)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8899.92 seconds
wall clock time: 155 minutes 58.81 seconds (9358.81 seconds total)