Starting phenix.real_space_refine
on Wed Mar  4 01:52:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6zgd_11202/03_2026/6zgd_11202.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zgd_11202/03_2026/6zgd_11202.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zgd_11202/03_2026/6zgd_11202.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zgd_11202/03_2026/6zgd_11202.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6zgd_11202/03_2026/6zgd_11202.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zgd_11202/03_2026/6zgd_11202.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    6745      2.51       5
     N    1685      2.21       5
     O    1725      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10175
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2035
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 96}
          Link IDs: {'PTRANS': 17, 'TRANS': 270}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 308
          Unresolved non-hydrogen angles: 395
          Unresolved non-hydrogen dihedrals: 238
          Unresolved non-hydrogen chiralities: 36
          Planarities with less than four sites: {'ASP:plan': 12, 'GLU:plan': 12, 'ASN:plan1': 5, 'TYR:plan': 2, 'TRP:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 3, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 166
    Chain: "B"
      Number of atoms: 2035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2035
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 96}
          Link IDs: {'PTRANS': 17, 'TRANS': 270}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 308
          Unresolved non-hydrogen angles: 395
          Unresolved non-hydrogen dihedrals: 238
          Unresolved non-hydrogen chiralities: 36
          Planarities with less than four sites: {'ASP:plan': 12, 'GLU:plan': 12, 'ASN:plan1': 5, 'TYR:plan': 2, 'TRP:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 3, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 166
    Chain: "C"
      Number of atoms: 2035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2035
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 96}
          Link IDs: {'PTRANS': 17, 'TRANS': 270}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 308
          Unresolved non-hydrogen angles: 395
          Unresolved non-hydrogen dihedrals: 238
          Unresolved non-hydrogen chiralities: 36
          Planarities with less than four sites: {'ASP:plan': 12, 'GLU:plan': 12, 'ASN:plan1': 5, 'TYR:plan': 2, 'TRP:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 3, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 166
    Chain: "D"
      Number of atoms: 2035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2035
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 96}
          Link IDs: {'PTRANS': 17, 'TRANS': 270}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 308
          Unresolved non-hydrogen angles: 395
          Unresolved non-hydrogen dihedrals: 238
          Unresolved non-hydrogen chiralities: 36
          Planarities with less than four sites: {'ASP:plan': 12, 'GLU:plan': 12, 'ASN:plan1': 5, 'TYR:plan': 2, 'TRP:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 3, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 166
    Chain: "E"
      Number of atoms: 2035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2035
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 96}
          Link IDs: {'PTRANS': 17, 'TRANS': 270}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 308
          Unresolved non-hydrogen angles: 395
          Unresolved non-hydrogen dihedrals: 238
          Unresolved non-hydrogen chiralities: 36
          Planarities with less than four sites: {'ASP:plan': 12, 'GLU:plan': 12, 'ASN:plan1': 5, 'TYR:plan': 2, 'TRP:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 3, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 166
  Time building chain proxies: 2.42, per 1000 atoms: 0.24
  Number of scatterers: 10175
  At special positions: 0
  Unit cell: (89.38, 87.74, 112.34, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O    1725      8.00
     N    1685      7.00
     C    6745      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.87
  Conformation dependent library (CDL) restraints added in 469.7 milliseconds
  

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2840

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 15 sheets defined
      38.5% alpha, 25.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 152 through 156
    Processing helix  chain 'A' and resid 196 through 201
    Processing helix  chain 'A' and resid 201 through 214
      removed outlier: 3.714A  pdb=" N   MET A 205 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 244
      removed outlier: 4.300A  pdb=" N   THR A 226 " --> pdb=" O   GLU A 222 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   THR A 231 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 282
      removed outlier: 3.887A  pdb=" N   PHE A 260 " --> pdb=" O   GLY A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 314
      Proline residue:  A 300  - end of helix
    Processing helix  chain 'B' and resid 152 through 156
    Processing helix  chain 'B' and resid 196 through 201
    Processing helix  chain 'B' and resid 201 through 214
      removed outlier: 3.714A  pdb=" N   MET B 205 " --> pdb=" O   ILE B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 244
      removed outlier: 4.299A  pdb=" N   THR B 226 " --> pdb=" O   GLU B 222 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   THR B 231 " --> pdb=" O   LEU B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 282
      removed outlier: 3.887A  pdb=" N   PHE B 260 " --> pdb=" O   GLY B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 314
      Proline residue:  B 300  - end of helix
    Processing helix  chain 'C' and resid 152 through 156
    Processing helix  chain 'C' and resid 196 through 201
    Processing helix  chain 'C' and resid 201 through 214
      removed outlier: 3.714A  pdb=" N   MET C 205 " --> pdb=" O   ILE C 201 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 244
      removed outlier: 4.300A  pdb=" N   THR C 226 " --> pdb=" O   GLU C 222 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   THR C 231 " --> pdb=" O   LEU C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 253 through 282
      removed outlier: 3.887A  pdb=" N   PHE C 260 " --> pdb=" O   GLY C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 284 through 314
      Proline residue:  C 300  - end of helix
    Processing helix  chain 'D' and resid 152 through 156
    Processing helix  chain 'D' and resid 196 through 201
    Processing helix  chain 'D' and resid 201 through 214
      removed outlier: 3.714A  pdb=" N   MET D 205 " --> pdb=" O   ILE D 201 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 220 through 244
      removed outlier: 4.299A  pdb=" N   THR D 226 " --> pdb=" O   GLU D 222 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   THR D 231 " --> pdb=" O   LEU D 227 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 253 through 282
      removed outlier: 3.887A  pdb=" N   PHE D 260 " --> pdb=" O   GLY D 256 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 284 through 314
      Proline residue:  D 300  - end of helix
    Processing helix  chain 'E' and resid 152 through 156
    Processing helix  chain 'E' and resid 196 through 201
    Processing helix  chain 'E' and resid 201 through 214
      removed outlier: 3.714A  pdb=" N   MET E 205 " --> pdb=" O   ILE E 201 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 220 through 244
      removed outlier: 4.299A  pdb=" N   THR E 226 " --> pdb=" O   GLU E 222 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   THR E 231 " --> pdb=" O   LEU E 227 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 253 through 282
      removed outlier: 3.887A  pdb=" N   PHE E 260 " --> pdb=" O   GLY E 256 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 284 through 314
      Proline residue:  E 300  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 94
      removed outlier: 5.265A  pdb=" N   ALA A  87 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   SER A 107 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   VAL A  89 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
      removed outlier: 5.640A  pdb=" N   ARG A 105 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE A  37 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   THR A  36 " --> pdb=" O   SER A  29 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   SER A  29 " --> pdb=" O   THR A  36 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LYS A  38 " --> pdb=" O   CYS A  27 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   CYS A  27 " --> pdb=" O   LYS A  38 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ASN A  40 " --> pdb=" O   ILE A  25 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ILE A  25 " --> pdb=" O   ASN A  40 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   PHE A  42 " --> pdb=" O   TYR A  23 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL A  18 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78
    Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 128
      removed outlier: 6.472A  pdb=" N   LYS A 183 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   VAL A 169 " --> pdb=" O   LYS A 183 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   ASP A 185 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ALA A 167 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   GLN A 187 " --> pdb=" O   PHE A 165 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   PHE A 165 " --> pdb=" O   GLN A 187 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ARG A 189 " --> pdb=" O   GLU A 163 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 86 through 94
      removed outlier: 5.265A  pdb=" N   ALA B  87 " --> pdb=" O   SER B 107 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   SER B 107 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   VAL B  89 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
      removed outlier: 5.640A  pdb=" N   ARG B 105 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE B  37 " --> pdb=" O   VAL B 110 " (cutoff:3.500A)
      removed outlier: 7.737A  pdb=" N   THR B  36 " --> pdb=" O   SER B  29 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   SER B  29 " --> pdb=" O   THR B  36 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LYS B  38 " --> pdb=" O   CYS B  27 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   CYS B  27 " --> pdb=" O   LYS B  38 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ASN B  40 " --> pdb=" O   ILE B  25 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ILE B  25 " --> pdb=" O   ASN B  40 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   PHE B  42 " --> pdb=" O   TYR B  23 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL B  18 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78
    Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 128
      removed outlier: 6.473A  pdb=" N   LYS B 183 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   VAL B 169 " --> pdb=" O   LYS B 183 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ASP B 185 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   ALA B 167 " --> pdb=" O   ASP B 185 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   GLN B 187 " --> pdb=" O   PHE B 165 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   PHE B 165 " --> pdb=" O   GLN B 187 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ARG B 189 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 86 through 94
      removed outlier: 5.265A  pdb=" N   ALA C  87 " --> pdb=" O   SER C 107 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   SER C 107 " --> pdb=" O   ALA C  87 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   VAL C  89 " --> pdb=" O   ARG C 105 " (cutoff:3.500A)
      removed outlier: 5.640A  pdb=" N   ARG C 105 " --> pdb=" O   VAL C  89 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE C  37 " --> pdb=" O   VAL C 110 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   THR C  36 " --> pdb=" O   SER C  29 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   SER C  29 " --> pdb=" O   THR C  36 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LYS C  38 " --> pdb=" O   CYS C  27 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   CYS C  27 " --> pdb=" O   LYS C  38 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ASN C  40 " --> pdb=" O   ILE C  25 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ILE C  25 " --> pdb=" O   ASN C  40 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   PHE C  42 " --> pdb=" O   TYR C  23 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL C  18 " --> pdb=" O   VAL C 141 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 78
    Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 128
      removed outlier: 6.472A  pdb=" N   LYS C 183 " --> pdb=" O   VAL C 169 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   VAL C 169 " --> pdb=" O   LYS C 183 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ASP C 185 " --> pdb=" O   ALA C 167 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ALA C 167 " --> pdb=" O   ASP C 185 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   GLN C 187 " --> pdb=" O   PHE C 165 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   PHE C 165 " --> pdb=" O   GLN C 187 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ARG C 189 " --> pdb=" O   GLU C 163 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 94
      removed outlier: 5.265A  pdb=" N   ALA D  87 " --> pdb=" O   SER D 107 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   SER D 107 " --> pdb=" O   ALA D  87 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   VAL D  89 " --> pdb=" O   ARG D 105 " (cutoff:3.500A)
      removed outlier: 5.641A  pdb=" N   ARG D 105 " --> pdb=" O   VAL D  89 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   PHE D  37 " --> pdb=" O   VAL D 110 " (cutoff:3.500A)
      removed outlier: 7.737A  pdb=" N   THR D  36 " --> pdb=" O   SER D  29 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   SER D  29 " --> pdb=" O   THR D  36 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LYS D  38 " --> pdb=" O   CYS D  27 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   CYS D  27 " --> pdb=" O   LYS D  38 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ASN D  40 " --> pdb=" O   ILE D  25 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ILE D  25 " --> pdb=" O   ASN D  40 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   PHE D  42 " --> pdb=" O   TYR D  23 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL D  18 " --> pdb=" O   VAL D 141 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78
    Processing sheet with id=AB3, first strand: chain 'D' and resid 125 through 128
      removed outlier: 6.472A  pdb=" N   LYS D 183 " --> pdb=" O   VAL D 169 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   VAL D 169 " --> pdb=" O   LYS D 183 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ASP D 185 " --> pdb=" O   ALA D 167 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   ALA D 167 " --> pdb=" O   ASP D 185 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   GLN D 187 " --> pdb=" O   PHE D 165 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   PHE D 165 " --> pdb=" O   GLN D 187 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ARG D 189 " --> pdb=" O   GLU D 163 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 86 through 94
      removed outlier: 5.265A  pdb=" N   ALA E  87 " --> pdb=" O   SER E 107 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   SER E 107 " --> pdb=" O   ALA E  87 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   VAL E  89 " --> pdb=" O   ARG E 105 " (cutoff:3.500A)
      removed outlier: 5.640A  pdb=" N   ARG E 105 " --> pdb=" O   VAL E  89 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE E  37 " --> pdb=" O   VAL E 110 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   THR E  36 " --> pdb=" O   SER E  29 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   SER E  29 " --> pdb=" O   THR E  36 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LYS E  38 " --> pdb=" O   CYS E  27 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   CYS E  27 " --> pdb=" O   LYS E  38 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   ASN E  40 " --> pdb=" O   ILE E  25 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ILE E  25 " --> pdb=" O   ASN E  40 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   PHE E  42 " --> pdb=" O   TYR E  23 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   VAL E  18 " --> pdb=" O   VAL E 141 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 78
    Processing sheet with id=AB6, first strand: chain 'E' and resid 125 through 128
      removed outlier: 6.472A  pdb=" N   LYS E 183 " --> pdb=" O   VAL E 169 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   VAL E 169 " --> pdb=" O   LYS E 183 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ASP E 185 " --> pdb=" O   ALA E 167 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   ALA E 167 " --> pdb=" O   ASP E 185 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   GLN E 187 " --> pdb=" O   PHE E 165 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   PHE E 165 " --> pdb=" O   GLN E 187 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ARG E 189 " --> pdb=" O   GLU E 163 " (cutoff:3.500A)

    560 hydrogen bonds defined for protein.
    1635 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.11

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3180
        1.34 -     1.46: 2421
        1.46 -     1.57: 4819
        1.57 -     1.69: 0
        1.69 -     1.81: 35
  Bond restraints: 10455
  Sorted by residual:
  bond pdb=" CG1 ILE A 233 "
       pdb=" CD1 ILE A 233 "
    ideal  model  delta    sigma   weight residual
    1.513  1.448  0.065 3.90e-02 6.57e+02 2.78e+00
  bond pdb=" CG1 ILE C 233 "
       pdb=" CD1 ILE C 233 "
    ideal  model  delta    sigma   weight residual
    1.513  1.448  0.065 3.90e-02 6.57e+02 2.74e+00
  bond pdb=" CG1 ILE E 233 "
       pdb=" CD1 ILE E 233 "
    ideal  model  delta    sigma   weight residual
    1.513  1.448  0.065 3.90e-02 6.57e+02 2.74e+00
  bond pdb=" CG1 ILE B 233 "
       pdb=" CD1 ILE B 233 "
    ideal  model  delta    sigma   weight residual
    1.513  1.449  0.064 3.90e-02 6.57e+02 2.71e+00
  bond pdb=" CG1 ILE D 233 "
       pdb=" CD1 ILE D 233 "
    ideal  model  delta    sigma   weight residual
    1.513  1.449  0.064 3.90e-02 6.57e+02 2.68e+00
  ... (remaining 10450 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 13575
        1.14 -     2.29: 671
        2.29 -     3.43: 124
        3.43 -     4.58: 20
        4.58 -     5.72: 30
  Bond angle restraints: 14420
  Sorted by residual:
  angle pdb=" N   VAL D 155 "
        pdb=" CA  VAL D 155 "
        pdb=" C   VAL D 155 "
      ideal   model   delta    sigma   weight residual
     111.91  109.26    2.65 8.90e-01 1.26e+00 8.90e+00
  angle pdb=" N   VAL B 155 "
        pdb=" CA  VAL B 155 "
        pdb=" C   VAL B 155 "
      ideal   model   delta    sigma   weight residual
     111.91  109.27    2.64 8.90e-01 1.26e+00 8.82e+00
  angle pdb=" N   VAL C 155 "
        pdb=" CA  VAL C 155 "
        pdb=" C   VAL C 155 "
      ideal   model   delta    sigma   weight residual
     111.91  109.28    2.63 8.90e-01 1.26e+00 8.75e+00
  angle pdb=" N   VAL E 155 "
        pdb=" CA  VAL E 155 "
        pdb=" C   VAL E 155 "
      ideal   model   delta    sigma   weight residual
     111.91  109.30    2.61 8.90e-01 1.26e+00 8.58e+00
  angle pdb=" N   VAL A 155 "
        pdb=" CA  VAL A 155 "
        pdb=" C   VAL A 155 "
      ideal   model   delta    sigma   weight residual
     111.91  109.31    2.60 8.90e-01 1.26e+00 8.56e+00
  ... (remaining 14415 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.11: 5273
       10.11 -    20.23: 491
       20.23 -    30.34: 226
       30.34 -    40.46: 35
       40.46 -    50.57: 25
  Dihedral angle restraints: 6050
    sinusoidal: 1730
      harmonic: 4320
  Sorted by residual:
  dihedral pdb=" CA  PRO E   9 "
           pdb=" C   PRO E   9 "
           pdb=" N   PRO E  10 "
           pdb=" CA  PRO E  10 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.38  -20.62     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  PRO A   9 "
           pdb=" C   PRO A   9 "
           pdb=" N   PRO A  10 "
           pdb=" CA  PRO A  10 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.40  -20.60     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  PRO C   9 "
           pdb=" C   PRO C   9 "
           pdb=" N   PRO C  10 "
           pdb=" CA  PRO C  10 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.41  -20.59     0      5.00e+00 4.00e-02 1.70e+01
  ... (remaining 6047 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1285
       0.046 -    0.092: 333
       0.092 -    0.137: 132
       0.137 -    0.183: 5
       0.183 -    0.229: 5
  Chirality restraints: 1760
  Sorted by residual:
  chirality pdb=" CA  PHE A 299 "
            pdb=" N   PHE A 299 "
            pdb=" C   PHE A 299 "
            pdb=" CB  PHE A 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  PHE B 299 "
            pdb=" N   PHE B 299 "
            pdb=" C   PHE B 299 "
            pdb=" CB  PHE B 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CA  PHE C 299 "
            pdb=" N   PHE C 299 "
            pdb=" C   PHE C 299 "
            pdb=" CB  PHE C 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 1757 not shown)

  Planarity restraints: 1825
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 198 "   -0.045 5.00e-02 4.00e+02   6.86e-02 7.53e+00
        pdb=" N   PRO B 199 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO B 199 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 199 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 198 "    0.045 5.00e-02 4.00e+02   6.85e-02 7.51e+00
        pdb=" N   PRO D 199 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO D 199 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO D 199 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 198 "   -0.045 5.00e-02 4.00e+02   6.84e-02 7.48e+00
        pdb=" N   PRO A 199 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO A 199 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 199 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 1822 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 182
        2.69 -     3.24: 10400
        3.24 -     3.79: 15383
        3.79 -     4.35: 17375
        4.35 -     4.90: 30233
  Nonbonded interactions: 73573
  Sorted by model distance:
  nonbonded pdb=" O   LEU E 209 "
            pdb=" OG  SER E 212 "
     model   vdw
     2.137 3.040
  nonbonded pdb=" O   LEU D 209 "
            pdb=" OG  SER D 212 "
     model   vdw
     2.137 3.040
  nonbonded pdb=" O   LEU C 209 "
            pdb=" OG  SER C 212 "
     model   vdw
     2.137 3.040
  nonbonded pdb=" O   LEU B 209 "
            pdb=" OG  SER B 212 "
     model   vdw
     2.138 3.040
  nonbonded pdb=" O   LEU A 209 "
            pdb=" OG  SER A 212 "
     model   vdw
     2.138 3.040
  ... (remaining 73568 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'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.210
  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:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.550
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  10455  Z= 0.247
  Angle     :  0.622   5.723  14420  Z= 0.352
  Chirality :  0.048   0.229   1760
  Planarity :  0.006   0.069   1825
  Dihedral  : 10.928  50.574   3210
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  0.00 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.21), residues: 1400
  helix:  0.93 (0.21), residues: 515
  sheet: -1.41 (0.26), residues: 335
  loop : -1.88 (0.25), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 287 
 TYR   0.011   0.002   TYR D 251 
 PHE   0.025   0.002   PHE E 299 
 TRP   0.013   0.002   TRP D 160 
 HIS   0.005   0.002   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00586 (10455)
  covalent geometry    : angle       0.62183 (14420)
  hydrogen bonds       : bond        0.10907 (  560)
  hydrogen bonds       : angle       6.73060 ( 1635)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 284
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A   38 LYS cc_start: 0.7893 (mttm) cc_final: 0.7588 (ttmm)
REVERT: A  117 ARG cc_start: 0.7693 (mtm180) cc_final: 0.7303 (mmm-85)
REVERT: A  287 ARG cc_start: 0.8701 (mtp85) cc_final: 0.8472 (mmm-85)
REVERT: B  117 ARG cc_start: 0.7648 (mtm180) cc_final: 0.7333 (mmm-85)
REVERT: B  238 PHE cc_start: 0.9275 (t80) cc_final: 0.8904 (t80)
REVERT: B  287 ARG cc_start: 0.8783 (mtp85) cc_final: 0.8487 (mmm-85)
REVERT: C  117 ARG cc_start: 0.7847 (mtm180) cc_final: 0.7432 (mmm-85)
REVERT: C  287 ARG cc_start: 0.8755 (mtp85) cc_final: 0.8493 (mmm-85)
REVERT: D   38 LYS cc_start: 0.7831 (mttm) cc_final: 0.7578 (ttmm)
REVERT: D  187 GLN cc_start: 0.7847 (mt0) cc_final: 0.7621 (tt0)
REVERT: D  239 ASN cc_start: 0.8713 (t0) cc_final: 0.8485 (t0)
REVERT: E  287 ARG cc_start: 0.8734 (mtp85) cc_final: 0.8465 (mmm-85)
  outliers start: 5
  outliers final: 0
  residues processed: 284
  average time/residue: 0.0991
  time to fit residues: 38.7189
Evaluate side-chains
  202 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    0.1980
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.0570
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.5298

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.147165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.108876 restraints weight = 16925.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.111909 restraints weight = 10118.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.113985 restraints weight = 7158.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.115191 restraints weight = 5692.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.116242 restraints weight = 4896.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10455  Z= 0.121
  Angle     :  0.553   5.655  14420  Z= 0.292
  Chirality :  0.046   0.158   1760
  Planarity :  0.005   0.045   1825
  Dihedral  :  4.190  18.414   1525
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.74 (0.22), residues: 1400
  helix:  1.43 (0.22), residues: 500
  sheet: -1.00 (0.26), residues: 345
  loop : -1.95 (0.25), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 287 
 TYR   0.008   0.001   TYR A 251 
 PHE   0.016   0.001   PHE C  37 
 TRP   0.021   0.002   TRP D 213 
 HIS   0.005   0.001   HIS D 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (10455)
  covalent geometry    : angle       0.55256 (14420)
  hydrogen bonds       : bond        0.03258 (  560)
  hydrogen bonds       : angle       4.80157 ( 1635)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 274
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7635 (mttm) cc_final: 0.7326 (ttmm)
REVERT: A  117 ARG cc_start: 0.7633 (mtm180) cc_final: 0.7240 (mmm-85)
REVERT: A  274 THR cc_start: 0.9430 (p) cc_final: 0.8976 (m)
REVERT: A  287 ARG cc_start: 0.8797 (mtp85) cc_final: 0.8551 (mmm-85)
REVERT: B  200 ASN cc_start: 0.8592 (t0) cc_final: 0.8299 (t0)
REVERT: B  261 MET cc_start: 0.7956 (mmt) cc_final: 0.7674 (mmm)
REVERT: C  192 ARG cc_start: 0.9215 (tpp80) cc_final: 0.8950 (mmm-85)
REVERT: C  200 ASN cc_start: 0.8396 (t0) cc_final: 0.8015 (t0)
REVERT: C  261 MET cc_start: 0.7941 (mmt) cc_final: 0.7595 (mmm)
REVERT: C  287 ARG cc_start: 0.8817 (mtp85) cc_final: 0.8541 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8109 (t0) cc_final: 0.7886 (t0)
REVERT: D   38 LYS cc_start: 0.7602 (mttm) cc_final: 0.7309 (ttmm)
REVERT: D  187 GLN cc_start: 0.8176 (mt0) cc_final: 0.7948 (mt0)
REVERT: D  307 ASN cc_start: 0.8072 (t0) cc_final: 0.7845 (t0)
REVERT: E  200 ASN cc_start: 0.8673 (t0) cc_final: 0.8465 (t0)
REVERT: E  287 ARG cc_start: 0.8858 (mtp85) cc_final: 0.8568 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 274
  average time/residue: 0.0975
  time to fit residues: 37.3823
Evaluate side-chains
  207 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 96 optimal weight:   20.0000
   chunk 52 optimal weight:    2.9990
   chunk 9 optimal weight:    0.3980
   chunk 53 optimal weight:    2.9990
   chunk 125 optimal weight:    6.9990
   chunk 86 optimal weight:    0.0060
   chunk 129 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0010
   chunk 63 optimal weight:    9.9990
   chunk 122 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   overall best weight:    1.2806

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

Flipped N/Q/H residues before XYZ refinement:
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.146199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.109234 restraints weight = 17117.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.112242 restraints weight = 10227.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.114318 restraints weight = 7245.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.115561 restraints weight = 5724.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.116226 restraints weight = 4905.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10455  Z= 0.145
  Angle     :  0.546   5.669  14420  Z= 0.293
  Chirality :  0.046   0.152   1760
  Planarity :  0.005   0.039   1825
  Dihedral  :  4.085  17.880   1525
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.22), residues: 1400
  helix:  1.48 (0.22), residues: 500
  sheet: -1.01 (0.27), residues: 345
  loop : -1.81 (0.25), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 287 
 TYR   0.007   0.001   TYR B 186 
 PHE   0.015   0.001   PHE A  37 
 TRP   0.015   0.002   TRP B 213 
 HIS   0.005   0.002   HIS B 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (10455)
  covalent geometry    : angle       0.54568 (14420)
  hydrogen bonds       : bond        0.03182 (  560)
  hydrogen bonds       : angle       4.53309 ( 1635)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7857 (mttm) cc_final: 0.7474 (ttmm)
REVERT: A  102 TYR cc_start: 0.8413 (t80) cc_final: 0.8170 (t80)
REVERT: A  117 ARG cc_start: 0.7677 (mtm180) cc_final: 0.7236 (mmm-85)
REVERT: A  252 MET cc_start: 0.7281 (ptt) cc_final: 0.7074 (ptt)
REVERT: A  287 ARG cc_start: 0.8855 (mtp85) cc_final: 0.8598 (mmm-85)
REVERT: B  192 ARG cc_start: 0.9140 (mtt-85) cc_final: 0.8758 (mmm-85)
REVERT: B  200 ASN cc_start: 0.8548 (t0) cc_final: 0.8289 (t0)
REVERT: B  261 MET cc_start: 0.7881 (mmt) cc_final: 0.7666 (mmm)
REVERT: C  200 ASN cc_start: 0.8366 (t0) cc_final: 0.8036 (t0)
REVERT: C  287 ARG cc_start: 0.8841 (mtp85) cc_final: 0.8537 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8072 (t0) cc_final: 0.7866 (t0)
REVERT: D   38 LYS cc_start: 0.7783 (mttm) cc_final: 0.7427 (ttmm)
REVERT: D  187 GLN cc_start: 0.8150 (mt0) cc_final: 0.7870 (mt0)
REVERT: D  200 ASN cc_start: 0.8358 (t0) cc_final: 0.8138 (t0)
REVERT: D  239 ASN cc_start: 0.8608 (t0) cc_final: 0.8155 (t0)
REVERT: D  307 ASN cc_start: 0.8103 (t0) cc_final: 0.7826 (t0)
REVERT: E  287 ARG cc_start: 0.8832 (mtp85) cc_final: 0.8496 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 269
  average time/residue: 0.1061
  time to fit residues: 39.3578
Evaluate side-chains
  209 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 60 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9980
   chunk 110 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 84 optimal weight:   10.0000
   chunk 99 optimal weight:   20.0000
   chunk 80 optimal weight:    3.9990
   chunk 39 optimal weight:   20.0000
   chunk 34 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   overall best weight:    5.9988

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

Flipped N/Q/H residues before XYZ refinement:
** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.135781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.097800 restraints weight = 17904.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.100239 restraints weight = 11366.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.101992 restraints weight = 8437.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.102877 restraints weight = 6917.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.103690 restraints weight = 6109.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.085  10455  Z= 0.468
  Angle     :  0.767   7.532  14420  Z= 0.432
  Chirality :  0.053   0.216   1760
  Planarity :  0.007   0.053   1825
  Dihedral  :  4.842  19.026   1525
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.90 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.22), residues: 1400
  helix:  0.67 (0.22), residues: 495
  sheet: -1.19 (0.27), residues: 320
  loop : -2.09 (0.26), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 192 
 TYR   0.016   0.003   TYR B 263 
 PHE   0.026   0.003   PHE E 238 
 TRP   0.027   0.003   TRP E 160 
 HIS   0.008   0.004   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.01079 (10455)
  covalent geometry    : angle       0.76701 (14420)
  hydrogen bonds       : bond        0.04740 (  560)
  hydrogen bonds       : angle       5.53357 ( 1635)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7996 (mttm) cc_final: 0.7342 (mtpp)
REVERT: A  200 ASN cc_start: 0.8825 (t0) cc_final: 0.8451 (t0)
REVERT: A  252 MET cc_start: 0.7378 (ptt) cc_final: 0.7144 (ptt)
REVERT: A  287 ARG cc_start: 0.8902 (mtp85) cc_final: 0.8686 (mmm-85)
REVERT: B  200 ASN cc_start: 0.8929 (t0) cc_final: 0.8605 (t0)
REVERT: C   42 PHE cc_start: 0.7472 (p90) cc_final: 0.7243 (p90)
REVERT: C  200 ASN cc_start: 0.8758 (t0) cc_final: 0.8375 (t0)
REVERT: C  274 THR cc_start: 0.9695 (m) cc_final: 0.9310 (t)
REVERT: C  287 ARG cc_start: 0.8957 (mtp85) cc_final: 0.8703 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8233 (t0) cc_final: 0.8015 (t0)
REVERT: C  312 PHE cc_start: 0.8613 (t80) cc_final: 0.8154 (t80)
REVERT: D   38 LYS cc_start: 0.7966 (mttm) cc_final: 0.7295 (mtpp)
REVERT: D   42 PHE cc_start: 0.7473 (p90) cc_final: 0.6769 (p90)
REVERT: D  187 GLN cc_start: 0.8027 (mt0) cc_final: 0.7798 (mt0)
REVERT: D  200 ASN cc_start: 0.8761 (t0) cc_final: 0.8296 (t0)
REVERT: D  274 THR cc_start: 0.9713 (m) cc_final: 0.9253 (t)
REVERT: D  307 ASN cc_start: 0.8253 (t0) cc_final: 0.8043 (t0)
REVERT: D  312 PHE cc_start: 0.8676 (t80) cc_final: 0.8300 (t80)
REVERT: E   42 PHE cc_start: 0.7215 (p90) cc_final: 0.6974 (p90)
REVERT: E  287 ARG cc_start: 0.8916 (mtp85) cc_final: 0.8622 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 232
  average time/residue: 0.1098
  time to fit residues: 34.7789
Evaluate side-chains
  191 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 60 optimal weight:   20.0000
   chunk 71 optimal weight:   20.0000
   chunk 6 optimal weight:    0.0770
   chunk 102 optimal weight:    0.5980
   chunk 3 optimal weight:   10.0000
   chunk 101 optimal weight:    0.9990
   chunk 57 optimal weight:   20.0000
   chunk 20 optimal weight:    0.5980
   chunk 116 optimal weight:   10.0000
   chunk 93 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.6542

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

Flipped N/Q/H residues before XYZ refinement:
A 187 GLN
C 187 GLN
D 200 ASN
E 200 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.147495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.110474 restraints weight = 16850.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.113196 restraints weight = 10600.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.114758 restraints weight = 7758.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.116171 restraints weight = 6362.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.116590 restraints weight = 5544.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  10455  Z= 0.131
  Angle     :  0.574   6.102  14420  Z= 0.304
  Chirality :  0.047   0.187   1760
  Planarity :  0.005   0.055   1825
  Dihedral  :  4.338  17.704   1525
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.00 (0.22), residues: 1400
  helix:  1.16 (0.22), residues: 495
  sheet: -1.23 (0.26), residues: 350
  loop : -1.95 (0.26), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 287 
 TYR   0.010   0.001   TYR E 186 
 PHE   0.015   0.002   PHE C  37 
 TRP   0.017   0.002   TRP B 213 
 HIS   0.005   0.001   HIS B 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (10455)
  covalent geometry    : angle       0.57449 (14420)
  hydrogen bonds       : bond        0.03282 (  560)
  hydrogen bonds       : angle       4.65196 ( 1635)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.8028 (mttm) cc_final: 0.7363 (mtpp)
REVERT: A  200 ASN cc_start: 0.8554 (t0) cc_final: 0.8184 (t0)
REVERT: A  287 ARG cc_start: 0.8799 (mtp85) cc_final: 0.8536 (mmm-85)
REVERT: B  200 ASN cc_start: 0.8674 (t0) cc_final: 0.8403 (t0)
REVERT: B  239 ASN cc_start: 0.8988 (t0) cc_final: 0.8311 (t0)
REVERT: B  243 GLU cc_start: 0.7141 (mm-30) cc_final: 0.5698 (mm-30)
REVERT: C  200 ASN cc_start: 0.8475 (t0) cc_final: 0.8084 (t0)
REVERT: C  287 ARG cc_start: 0.8807 (mtp85) cc_final: 0.8501 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8047 (t0) cc_final: 0.7767 (t0)
REVERT: D   38 LYS cc_start: 0.7987 (mttm) cc_final: 0.7314 (mtpp)
REVERT: D  200 ASN cc_start: 0.8325 (t0) cc_final: 0.7912 (t0)
REVERT: D  274 THR cc_start: 0.9603 (m) cc_final: 0.8949 (t)
REVERT: D  307 ASN cc_start: 0.8025 (t0) cc_final: 0.7756 (t0)
REVERT: E  287 ARG cc_start: 0.8795 (mtp85) cc_final: 0.8502 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 0.0968
  time to fit residues: 35.0327
Evaluate side-chains
  207 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 86 optimal weight:    0.0170
   chunk 10 optimal weight:    9.9990
   chunk 59 optimal weight:   10.0000
   chunk 30 optimal weight:    0.0170
   chunk 25 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 111 optimal weight:    4.9990
   chunk 96 optimal weight:   20.0000
   chunk 54 optimal weight:   10.0000
   overall best weight:    1.1460

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

Flipped N/Q/H residues before XYZ refinement:
A 187 GLN
C 187 GLN
E 187 GLN
E 200 ASN
** E 239 ASN ** 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 = 0.3740 r_free = 0.3740 target = 0.145023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.105290 restraints weight = 17783.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.108266 restraints weight = 10610.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.110372 restraints weight = 7548.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.111147 restraints weight = 6005.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.112394 restraints weight = 5361.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10455  Z= 0.141
  Angle     :  0.557   6.334  14420  Z= 0.294
  Chirality :  0.046   0.168   1760
  Planarity :  0.005   0.059   1825
  Dihedral  :  4.192  17.473   1525
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.22), residues: 1400
  helix:  1.35 (0.22), residues: 500
  sheet: -1.04 (0.26), residues: 350
  loop : -1.93 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 287 
 TYR   0.007   0.001   TYR C 186 
 PHE   0.016   0.001   PHE B 238 
 TRP   0.017   0.002   TRP A 213 
 HIS   0.005   0.002   HIS C 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (10455)
  covalent geometry    : angle       0.55682 (14420)
  hydrogen bonds       : bond        0.03177 (  560)
  hydrogen bonds       : angle       4.50162 ( 1635)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7875 (mttm) cc_final: 0.7254 (mtpp)
REVERT: A  200 ASN cc_start: 0.8551 (t0) cc_final: 0.8197 (t0)
REVERT: A  287 ARG cc_start: 0.8859 (mtp85) cc_final: 0.8613 (mmm-85)
REVERT: B  200 ASN cc_start: 0.8707 (t0) cc_final: 0.8327 (t0)
REVERT: C  200 ASN cc_start: 0.8478 (t0) cc_final: 0.8059 (t0)
REVERT: C  287 ARG cc_start: 0.8898 (mtp85) cc_final: 0.8632 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8093 (t0) cc_final: 0.7820 (t0)
REVERT: D   38 LYS cc_start: 0.7814 (mttm) cc_final: 0.7184 (mtpp)
REVERT: D  200 ASN cc_start: 0.8328 (t0) cc_final: 0.7921 (t0)
REVERT: D  239 ASN cc_start: 0.8699 (t0) cc_final: 0.8330 (t0)
REVERT: D  307 ASN cc_start: 0.8121 (t0) cc_final: 0.7819 (t0)
REVERT: E  200 ASN cc_start: 0.8513 (t0) cc_final: 0.8182 (t0)
REVERT: E  287 ARG cc_start: 0.8906 (mtp85) cc_final: 0.8651 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 249
  average time/residue: 0.0998
  time to fit residues: 34.7195
Evaluate side-chains
  203 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 77 optimal weight:    0.6980
   chunk 37 optimal weight:    5.9990
   chunk 16 optimal weight:    9.9990
   chunk 33 optimal weight:    0.0980
   chunk 109 optimal weight:    9.9990
   chunk 87 optimal weight:    7.9990
   chunk 20 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   chunk 63 optimal weight:    9.9990
   chunk 88 optimal weight:    9.9990
   chunk 68 optimal weight:   20.0000
   overall best weight:    1.6582

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

Flipped N/Q/H residues before XYZ refinement:
B 127 HIS
C 127 HIS
C 187 GLN
C 200 ASN
D 200 ASN
E 200 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.144002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.104108 restraints weight = 17661.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.106928 restraints weight = 10625.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.108917 restraints weight = 7656.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.110076 restraints weight = 6137.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.110076 restraints weight = 5305.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.2747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10455  Z= 0.167
  Angle     :  0.566   6.486  14420  Z= 0.302
  Chirality :  0.046   0.165   1760
  Planarity :  0.005   0.064   1825
  Dihedral  :  4.174  18.543   1525
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.22), residues: 1400
  helix:  1.42 (0.22), residues: 500
  sheet: -1.00 (0.27), residues: 350
  loop : -1.92 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 287 
 TYR   0.008   0.001   TYR A 186 
 PHE   0.016   0.001   PHE B 238 
 TRP   0.015   0.002   TRP D 213 
 HIS   0.007   0.002   HIS C 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (10455)
  covalent geometry    : angle       0.56635 (14420)
  hydrogen bonds       : bond        0.03244 (  560)
  hydrogen bonds       : angle       4.54514 ( 1635)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7893 (mttm) cc_final: 0.7264 (mtpp)
REVERT: A  200 ASN cc_start: 0.8620 (t0) cc_final: 0.8237 (t0)
REVERT: A  287 ARG cc_start: 0.8903 (mtp85) cc_final: 0.8665 (mmm-85)
REVERT: B   88 ASP cc_start: 0.8445 (t0) cc_final: 0.8233 (t0)
REVERT: B  187 GLN cc_start: 0.8241 (mt0) cc_final: 0.8033 (mt0)
REVERT: B  200 ASN cc_start: 0.8784 (t0) cc_final: 0.8394 (t0)
REVERT: B  239 ASN cc_start: 0.8986 (t0) cc_final: 0.8403 (t0)
REVERT: C  200 ASN cc_start: 0.8397 (t0) cc_final: 0.7972 (t0)
REVERT: C  287 ARG cc_start: 0.8927 (mtp85) cc_final: 0.8671 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8129 (t0) cc_final: 0.7853 (t0)
REVERT: D   38 LYS cc_start: 0.7765 (mttm) cc_final: 0.7148 (mtpp)
REVERT: D  200 ASN cc_start: 0.8502 (t0) cc_final: 0.7924 (t0)
REVERT: D  307 ASN cc_start: 0.8137 (t0) cc_final: 0.7851 (t0)
REVERT: E  200 ASN cc_start: 0.8553 (t160) cc_final: 0.8212 (t0)
REVERT: E  287 ARG cc_start: 0.8943 (mtp85) cc_final: 0.8700 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 0.0948
  time to fit residues: 31.0677
Evaluate side-chains
  201 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 129 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0970
   chunk 69 optimal weight:    7.9990
   chunk 131 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 111 optimal weight:    7.9990
   chunk 80 optimal weight:    3.9990
   chunk 73 optimal weight:    0.4980
   chunk 5 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 12 optimal weight:   20.0000
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
C 187 GLN
D 127 HIS
** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 200 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.147619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.108046 restraints weight = 17423.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.110948 restraints weight = 10285.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.112997 restraints weight = 7345.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.114233 restraints weight = 5878.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.114984 restraints weight = 5082.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10455  Z= 0.118
  Angle     :  0.557   7.314  14420  Z= 0.288
  Chirality :  0.046   0.199   1760
  Planarity :  0.005   0.055   1825
  Dihedral  :  4.061  18.824   1525
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.22), residues: 1400
  helix:  1.20 (0.22), residues: 530
  sheet: -0.83 (0.27), residues: 345
  loop : -1.70 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 287 
 TYR   0.010   0.001   TYR A 102 
 PHE   0.012   0.001   PHE E  37 
 TRP   0.019   0.002   TRP D 213 
 HIS   0.005   0.001   HIS E 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (10455)
  covalent geometry    : angle       0.55720 (14420)
  hydrogen bonds       : bond        0.03014 (  560)
  hydrogen bonds       : angle       4.35035 ( 1635)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7833 (mttm) cc_final: 0.7224 (mtpp)
REVERT: A  200 ASN cc_start: 0.8471 (t0) cc_final: 0.8124 (t0)
REVERT: A  287 ARG cc_start: 0.8905 (mtp85) cc_final: 0.8663 (mmm-85)
REVERT: B  200 ASN cc_start: 0.8619 (t0) cc_final: 0.8202 (t0)
REVERT: C  200 ASN cc_start: 0.8281 (t0) cc_final: 0.7864 (t0)
REVERT: C  248 LYS cc_start: 0.7077 (mmtt) cc_final: 0.6463 (mmmt)
REVERT: C  287 ARG cc_start: 0.8884 (mtp85) cc_final: 0.8604 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8094 (t0) cc_final: 0.7786 (t0)
REVERT: D   38 LYS cc_start: 0.7767 (mttm) cc_final: 0.7116 (mtpp)
REVERT: D  200 ASN cc_start: 0.8420 (t0) cc_final: 0.7869 (t0)
REVERT: D  307 ASN cc_start: 0.8076 (t0) cc_final: 0.7729 (t0)
REVERT: E  200 ASN cc_start: 0.8460 (t160) cc_final: 0.8111 (t0)
REVERT: E  287 ARG cc_start: 0.8899 (mtp85) cc_final: 0.8647 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 252
  average time/residue: 0.0964
  time to fit residues: 34.2864
Evaluate side-chains
  205 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 38 optimal weight:    9.9990
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 82 optimal weight:   20.0000
   chunk 46 optimal weight:    2.9990
   chunk 124 optimal weight:   20.0000
   chunk 83 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 61 optimal weight:    8.9990
   chunk 136 optimal weight:    0.7980
   chunk 44 optimal weight:    7.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
C 187 GLN
D 127 HIS
D 187 GLN
E 200 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.144459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.105160 restraints weight = 17442.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.107960 restraints weight = 10581.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.109911 restraints weight = 7585.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.110754 restraints weight = 6091.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.111970 restraints weight = 5405.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10455  Z= 0.179
  Angle     :  0.573   7.826  14420  Z= 0.305
  Chirality :  0.047   0.211   1760
  Planarity :  0.005   0.051   1825
  Dihedral  :  4.105  18.368   1525
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.22), residues: 1400
  helix:  1.30 (0.21), residues: 495
  sheet: -0.89 (0.27), residues: 345
  loop : -1.93 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 287 
 TYR   0.009   0.001   TYR D 278 
 PHE   0.022   0.002   PHE C 299 
 TRP   0.016   0.002   TRP B 160 
 HIS   0.010   0.002   HIS C 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (10455)
  covalent geometry    : angle       0.57302 (14420)
  hydrogen bonds       : bond        0.03328 (  560)
  hydrogen bonds       : angle       4.50020 ( 1635)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7893 (mttm) cc_final: 0.7296 (mtpp)
REVERT: A  200 ASN cc_start: 0.8604 (t0) cc_final: 0.8255 (t0)
REVERT: A  224 ASN cc_start: 0.8822 (m-40) cc_final: 0.8217 (t0)
REVERT: A  287 ARG cc_start: 0.8887 (mtp85) cc_final: 0.8639 (mmm-85)
REVERT: B   88 ASP cc_start: 0.8632 (t70) cc_final: 0.8431 (t0)
REVERT: B  200 ASN cc_start: 0.8740 (t0) cc_final: 0.8370 (t0)
REVERT: B  239 ASN cc_start: 0.9022 (t0) cc_final: 0.8547 (t0)
REVERT: C  200 ASN cc_start: 0.8421 (t0) cc_final: 0.8003 (t0)
REVERT: C  224 ASN cc_start: 0.8654 (m-40) cc_final: 0.8068 (t0)
REVERT: C  243 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6943 (mm-30)
REVERT: C  287 ARG cc_start: 0.8884 (mtp85) cc_final: 0.8622 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8124 (t0) cc_final: 0.7831 (t0)
REVERT: D   38 LYS cc_start: 0.7791 (mttm) cc_final: 0.7130 (mtpp)
REVERT: D  187 GLN cc_start: 0.8455 (mt0) cc_final: 0.7919 (tt0)
REVERT: D  200 ASN cc_start: 0.8531 (t0) cc_final: 0.8023 (t0)
REVERT: D  274 THR cc_start: 0.9587 (m) cc_final: 0.9114 (m)
REVERT: D  307 ASN cc_start: 0.8125 (t0) cc_final: 0.7792 (t0)
REVERT: E  200 ASN cc_start: 0.8527 (t160) cc_final: 0.8220 (t0)
REVERT: E  287 ARG cc_start: 0.8902 (mtp85) cc_final: 0.8645 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 0.0949
  time to fit residues: 31.3278
Evaluate side-chains
  192 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 116 optimal weight:   10.0000
   chunk 131 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 128 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 114 optimal weight:   30.0000
   chunk 125 optimal weight:    1.9990
   chunk 124 optimal weight:    6.9990
   chunk 85 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
D 187 GLN
E 200 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.144489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.105766 restraints weight = 17139.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.108583 restraints weight = 10452.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.110498 restraints weight = 7527.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.111620 restraints weight = 6062.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.112686 restraints weight = 5258.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10455  Z= 0.170
  Angle     :  0.578   8.297  14420  Z= 0.306
  Chirality :  0.047   0.205   1760
  Planarity :  0.005   0.062   1825
  Dihedral  :  4.132  17.836   1525
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.22), residues: 1400
  helix:  1.29 (0.22), residues: 495
  sheet: -0.93 (0.27), residues: 345
  loop : -1.92 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 287 
 TYR   0.009   0.001   TYR D 278 
 PHE   0.022   0.002   PHE C 299 
 TRP   0.024   0.002   TRP C 213 
 HIS   0.009   0.002   HIS C 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (10455)
  covalent geometry    : angle       0.57801 (14420)
  hydrogen bonds       : bond        0.03304 (  560)
  hydrogen bonds       : angle       4.52752 ( 1635)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7943 (mttm) cc_final: 0.7310 (mtpp)
REVERT: A  200 ASN cc_start: 0.8628 (t0) cc_final: 0.8324 (t0)
REVERT: A  224 ASN cc_start: 0.8812 (m-40) cc_final: 0.8191 (t0)
REVERT: A  287 ARG cc_start: 0.8877 (mtp85) cc_final: 0.8623 (mmm-85)
REVERT: B   88 ASP cc_start: 0.8649 (t70) cc_final: 0.8446 (t0)
REVERT: B  200 ASN cc_start: 0.8733 (t0) cc_final: 0.8354 (t0)
REVERT: B  239 ASN cc_start: 0.8970 (t0) cc_final: 0.8500 (t0)
REVERT: C  200 ASN cc_start: 0.8419 (t0) cc_final: 0.7985 (t0)
REVERT: C  224 ASN cc_start: 0.8650 (m-40) cc_final: 0.8055 (t0)
REVERT: C  287 ARG cc_start: 0.8862 (mtp85) cc_final: 0.8596 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8059 (t0) cc_final: 0.7769 (t0)
REVERT: D   38 LYS cc_start: 0.7798 (mttm) cc_final: 0.7131 (mtpp)
REVERT: D  187 GLN cc_start: 0.8385 (mt0) cc_final: 0.7795 (tt0)
REVERT: D  200 ASN cc_start: 0.8587 (t0) cc_final: 0.8063 (t0)
REVERT: D  307 ASN cc_start: 0.8084 (t0) cc_final: 0.7752 (t0)
REVERT: E  200 ASN cc_start: 0.8515 (t160) cc_final: 0.8236 (t0)
REVERT: E  287 ARG cc_start: 0.8896 (mtp85) cc_final: 0.8631 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.0964
  time to fit residues: 31.1503
Evaluate side-chains
  194 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 68 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 114 optimal weight:   30.0000
   chunk 139 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 11 optimal weight:   20.0000
   chunk 55 optimal weight:    3.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.151574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.113178 restraints weight = 17469.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.116555 restraints weight = 9602.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.118811 restraints weight = 6536.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.119753 restraints weight = 5115.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.120893 restraints weight = 4492.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  10455  Z= 0.237
  Angle     :  0.614   8.336  14420  Z= 0.331
  Chirality :  0.048   0.214   1760
  Planarity :  0.005   0.058   1825
  Dihedral  :  4.326  18.279   1525
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.22), residues: 1400
  helix:  1.15 (0.21), residues: 495
  sheet: -1.05 (0.27), residues: 345
  loop : -1.91 (0.27), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 287 
 TYR   0.013   0.002   TYR D 278 
 PHE   0.026   0.002   PHE C 299 
 TRP   0.028   0.003   TRP C 213 
 HIS   0.012   0.003   HIS C 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 (10455)
  covalent geometry    : angle       0.61437 (14420)
  hydrogen bonds       : bond        0.03695 (  560)
  hydrogen bonds       : angle       4.80070 ( 1635)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1607.24 seconds
wall clock time: 28 minutes 18.45 seconds (1698.45 seconds total)