Starting phenix.real_space_refine
on Fri Feb 14 08:32:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6zgd_11202/02_2025/6zgd_11202.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zgd_11202/02_2025/6zgd_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6zgd_11202/02_2025/6zgd_11202.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zgd_11202/02_2025/6zgd_11202.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zgd_11202/02_2025/6zgd_11202.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zgd_11202/02_2025/6zgd_11202.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4}
          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: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4}
          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: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4}
          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: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4}
          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: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 166
  Time building chain proxies: 6.12, per 1000 atoms: 0.60
  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: 2.78
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 1.10
  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: 3.20

  Time building geometry restraints manager: 3.22 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

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:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     26.050
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.570
-------------------------------------------------------------------------------
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= 0.391
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (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
 TRP   0.013   0.002   TRP D 160 
 HIS   0.005   0.002   HIS A 235 
 PHE   0.025   0.002   PHE E 299 
 TYR   0.011   0.002   TYR D 251 
 ARG   0.007   0.001   ARG C 287 

*********************** 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  : 1.113 
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: 0.8492 (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: 0.2449
  time to fit residues: 94.1131
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  : 1.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    7.9990
   chunk 106 optimal weight:    0.6980
   chunk 58 optimal weight:   20.0000
   chunk 36 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   chunk 56 optimal weight:   10.0000
   chunk 109 optimal weight:    3.9990
   chunk 42 optimal weight:   30.0000
   chunk 66 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 127 optimal weight:   20.0000
   overall best weight:    3.3388

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

Flipped N/Q/H residues before XYZ refinement:
A  80 ASN
** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 ASN
D  80 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.139692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.101152 restraints weight = 17554.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.103610 restraints weight = 11466.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.105327 restraints weight = 8601.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068  10455  Z= 0.438
  Angle     :  0.628   5.635  14420  Z= 0.347
  Chirality :  0.049   0.189   1760
  Planarity :  0.006   0.051   1825
  Dihedral  :  4.500  19.533   1525
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.22), residues: 1400
  helix:  0.99 (0.22), residues: 495
  sheet: -1.10 (0.27), residues: 320
  loop : -2.11 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 160 
 HIS   0.007   0.002   HIS D 235 
 PHE   0.023   0.002   PHE C 238 
 TYR   0.009   0.002   TYR A 251 
 ARG   0.005   0.001   ARG D 287 

*********************** 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
  251 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 1.095 
Fit side-chains
REVERT: A   38 LYS cc_start: 0.8006 (mttm) cc_final: 0.7583 (ttmm)
REVERT: A  200 ASN cc_start: 0.8696 (t0) cc_final: 0.8485 (t0)
REVERT: B  200 ASN cc_start: 0.8781 (t0) cc_final: 0.8530 (t0)
REVERT: B  238 PHE cc_start: 0.9314 (t80) cc_final: 0.9086 (t80)
REVERT: B  239 ASN cc_start: 0.8902 (t0) cc_final: 0.8503 (t0)
REVERT: C  200 ASN cc_start: 0.8630 (t0) cc_final: 0.8306 (t0)
REVERT: C  261 MET cc_start: 0.7985 (mmt) cc_final: 0.7694 (mmm)
REVERT: C  287 ARG cc_start: 0.8873 (mtp85) cc_final: 0.8604 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8204 (t0) cc_final: 0.8000 (t0)
REVERT: D   38 LYS cc_start: 0.7895 (mttm) cc_final: 0.7555 (ttmm)
REVERT: D  243 GLU cc_start: 0.7478 (tp30) cc_final: 0.7236 (tp30)
REVERT: D  307 ASN cc_start: 0.8161 (t0) cc_final: 0.7941 (t0)
REVERT: E  192 ARG cc_start: 0.9230 (mtt-85) cc_final: 0.9012 (tpp80)
REVERT: E  287 ARG cc_start: 0.8896 (mtp85) cc_final: 0.8624 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 251
  average time/residue: 0.2303
  time to fit residues: 79.6297
Evaluate side-chains
  197 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 99 optimal weight:    6.9990
   chunk 118 optimal weight:    0.0980
   chunk 3 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 124 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9980
   chunk 92 optimal weight:    9.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3754 r_free = 0.3754 target = 0.146209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.111973 restraints weight = 17007.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.112158 restraints weight = 11417.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.113297 restraints weight = 8663.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10455  Z= 0.240
  Angle     :  0.561   5.583  14420  Z= 0.300
  Chirality :  0.046   0.167   1760
  Planarity :  0.005   0.044   1825
  Dihedral  :  4.250  18.079   1525
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.22), residues: 1400
  helix:  1.42 (0.22), residues: 500
  sheet: -1.12 (0.27), residues: 340
  loop : -1.95 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 213 
 HIS   0.005   0.001   HIS B 235 
 PHE   0.016   0.001   PHE C  37 
 TYR   0.008   0.001   TYR D 251 
 ARG   0.006   0.000   ARG D 287 

*********************** 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
  255 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7975 (mttm) cc_final: 0.7604 (ttmm)
REVERT: A  200 ASN cc_start: 0.8612 (t0) cc_final: 0.8391 (t0)
REVERT: B  200 ASN cc_start: 0.8629 (t0) cc_final: 0.8300 (t0)
REVERT: C  192 ARG cc_start: 0.9263 (tpp80) cc_final: 0.9001 (tpp80)
REVERT: C  200 ASN cc_start: 0.8512 (t0) cc_final: 0.8070 (t0)
REVERT: C  287 ARG cc_start: 0.8910 (mtp85) cc_final: 0.8642 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8178 (t0) cc_final: 0.7903 (t0)
REVERT: D   38 LYS cc_start: 0.7859 (mttm) cc_final: 0.7487 (ttmm)
REVERT: D  307 ASN cc_start: 0.8163 (t0) cc_final: 0.7870 (t0)
REVERT: E  192 ARG cc_start: 0.9180 (mtt-85) cc_final: 0.8964 (tpp80)
REVERT: E  200 ASN cc_start: 0.8725 (t0) cc_final: 0.8505 (t0)
REVERT: E  287 ARG cc_start: 0.8905 (mtp85) cc_final: 0.8619 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 255
  average time/residue: 0.2290
  time to fit residues: 80.7124
Evaluate side-chains
  214 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 34 optimal weight:   20.0000
   chunk 96 optimal weight:   20.0000
   chunk 102 optimal weight:    0.6980
   chunk 68 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   chunk 60 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 76 optimal weight:    0.7980
   chunk 117 optimal weight:    9.9990
   chunk 128 optimal weight:    6.9990
   overall best weight:    5.2986

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.135619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.097500 restraints weight = 17632.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.099891 restraints weight = 11282.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.101587 restraints weight = 8412.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.081  10455  Z= 0.646
  Angle     :  0.743   7.191  14420  Z= 0.416
  Chirality :  0.051   0.174   1760
  Planarity :  0.007   0.059   1825
  Dihedral  :  4.954  19.420   1525
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.22), residues: 1400
  helix:  0.69 (0.22), residues: 500
  sheet: -1.31 (0.26), residues: 325
  loop : -2.20 (0.27), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP B 160 
 HIS   0.008   0.004   HIS A 235 
 PHE   0.026   0.003   PHE E 238 
 TYR   0.025   0.002   TYR D 278 
 ARG   0.006   0.001   ARG B 287 

*********************** 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
  224 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7994 (mttm) cc_final: 0.7303 (mtpp)
REVERT: A   42 PHE cc_start: 0.7488 (p90) cc_final: 0.7197 (p90)
REVERT: A  200 ASN cc_start: 0.8889 (t0) cc_final: 0.8591 (t0)
REVERT: B   42 PHE cc_start: 0.7477 (p90) cc_final: 0.7248 (p90)
REVERT: B  200 ASN cc_start: 0.8911 (t0) cc_final: 0.8572 (t0)
REVERT: B  239 ASN cc_start: 0.9184 (t0) cc_final: 0.8809 (t0)
REVERT: C   42 PHE cc_start: 0.7471 (p90) cc_final: 0.7205 (p90)
REVERT: C  200 ASN cc_start: 0.8745 (t0) cc_final: 0.8384 (t0)
REVERT: C  224 ASN cc_start: 0.8856 (m-40) cc_final: 0.8116 (t0)
REVERT: C  287 ARG cc_start: 0.8954 (mtp85) cc_final: 0.8724 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8268 (t0) cc_final: 0.8046 (t0)
REVERT: D   38 LYS cc_start: 0.7876 (mttm) cc_final: 0.7210 (mtpp)
REVERT: D  200 ASN cc_start: 0.8722 (t0) cc_final: 0.8254 (t0)
REVERT: D  274 THR cc_start: 0.9735 (m) cc_final: 0.9268 (t)
REVERT: D  307 ASN cc_start: 0.8259 (t0) cc_final: 0.8035 (t0)
REVERT: D  312 PHE cc_start: 0.8685 (t80) cc_final: 0.8297 (t80)
REVERT: E   42 PHE cc_start: 0.7272 (p90) cc_final: 0.6994 (p90)
REVERT: E  200 ASN cc_start: 0.8973 (t0) cc_final: 0.8614 (t0)
REVERT: E  274 THR cc_start: 0.9573 (p) cc_final: 0.9254 (t)
REVERT: E  287 ARG cc_start: 0.8943 (mtp85) cc_final: 0.8670 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 224
  average time/residue: 0.2300
  time to fit residues: 71.1469
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  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 124 optimal weight:    8.9990
   chunk 95 optimal weight:   30.0000
   chunk 114 optimal weight:   30.0000
   chunk 117 optimal weight:    5.9990
   chunk 63 optimal weight:    6.9990
   chunk 71 optimal weight:   20.0000
   chunk 37 optimal weight:    1.9990
   chunk 136 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
C 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.143943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.104760 restraints weight = 17340.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.107561 restraints weight = 10582.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.109501 restraints weight = 7644.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  10455  Z= 0.254
  Angle     :  0.576   6.978  14420  Z= 0.308
  Chirality :  0.047   0.183   1760
  Planarity :  0.005   0.054   1825
  Dihedral  :  4.415  18.377   1525
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.22), residues: 1400
  helix:  1.22 (0.22), residues: 500
  sheet: -1.09 (0.26), residues: 325
  loop : -2.17 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 213 
 HIS   0.006   0.002   HIS C 235 
 PHE   0.015   0.001   PHE C  37 
 TYR   0.009   0.001   TYR C 186 
 ARG   0.005   0.000   ARG B 287 

*********************** 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
  244 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 1.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7927 (mttm) cc_final: 0.7277 (mtpp)
REVERT: A  200 ASN cc_start: 0.8699 (t0) cc_final: 0.8448 (t0)
REVERT: B  200 ASN cc_start: 0.8748 (t0) cc_final: 0.8479 (t0)
REVERT: B  239 ASN cc_start: 0.8995 (t0) cc_final: 0.8520 (t0)
REVERT: C  200 ASN cc_start: 0.8362 (t0) cc_final: 0.8015 (t0)
REVERT: C  224 ASN cc_start: 0.8808 (m-40) cc_final: 0.8069 (t0)
REVERT: C  248 LYS cc_start: 0.7141 (mmmt) cc_final: 0.6018 (mmtt)
REVERT: C  287 ARG cc_start: 0.9009 (mtp85) cc_final: 0.8779 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8200 (t0) cc_final: 0.7918 (t0)
REVERT: D   38 LYS cc_start: 0.7840 (mttm) cc_final: 0.7184 (mtpp)
REVERT: D  200 ASN cc_start: 0.8429 (t0) cc_final: 0.7951 (t0)
REVERT: D  307 ASN cc_start: 0.8182 (t0) cc_final: 0.7932 (t0)
REVERT: E  200 ASN cc_start: 0.8807 (t0) cc_final: 0.8531 (t0)
REVERT: E  287 ARG cc_start: 0.8968 (mtp85) cc_final: 0.8740 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 244
  average time/residue: 0.2403
  time to fit residues: 80.1932
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  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 122 optimal weight:    9.9990
   chunk 12 optimal weight:   20.0000
   chunk 2 optimal weight:   20.0000
   chunk 115 optimal weight:   10.0000
   chunk 47 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 91 optimal weight:   10.0000
   chunk 74 optimal weight:    0.8980
   chunk 125 optimal weight:    8.9990
   chunk 52 optimal weight:    2.9990
   chunk 126 optimal weight:    0.9990
   overall best weight:    1.5186

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.144087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.104275 restraints weight = 17536.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.107181 restraints weight = 10681.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.109142 restraints weight = 7699.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10455  Z= 0.258
  Angle     :  0.568   7.333  14420  Z= 0.301
  Chirality :  0.046   0.174   1760
  Planarity :  0.005   0.050   1825
  Dihedral  :  4.283  17.768   1525
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.22), residues: 1400
  helix:  1.38 (0.22), residues: 500
  sheet: -1.26 (0.26), residues: 350
  loop : -1.94 (0.27), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 160 
 HIS   0.006   0.002   HIS D 235 
 PHE   0.018   0.001   PHE A 238 
 TYR   0.008   0.001   TYR D 221 
 ARG   0.006   0.000   ARG B 287 

*********************** 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
  238 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7931 (mttm) cc_final: 0.7270 (mtpp)
REVERT: A  200 ASN cc_start: 0.8700 (t0) cc_final: 0.8425 (t0)
REVERT: B  200 ASN cc_start: 0.8747 (t0) cc_final: 0.8448 (t0)
REVERT: B  239 ASN cc_start: 0.8883 (t0) cc_final: 0.8555 (t0)
REVERT: B  274 THR cc_start: 0.9270 (p) cc_final: 0.8934 (t)
REVERT: C  200 ASN cc_start: 0.8282 (t0) cc_final: 0.7971 (t0)
REVERT: C  224 ASN cc_start: 0.8830 (m-40) cc_final: 0.8148 (t0)
REVERT: C  248 LYS cc_start: 0.6981 (mmmt) cc_final: 0.6546 (mmtt)
REVERT: C  287 ARG cc_start: 0.8993 (mtp85) cc_final: 0.8753 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8170 (t0) cc_final: 0.7883 (t0)
REVERT: D   38 LYS cc_start: 0.7838 (mttm) cc_final: 0.7168 (mtpp)
REVERT: D  200 ASN cc_start: 0.8200 (t0) cc_final: 0.7789 (t0)
REVERT: D  274 THR cc_start: 0.9679 (m) cc_final: 0.9053 (t)
REVERT: D  307 ASN cc_start: 0.8171 (t0) cc_final: 0.7918 (t0)
REVERT: E  200 ASN cc_start: 0.8751 (t0) cc_final: 0.8415 (t0)
REVERT: E  274 THR cc_start: 0.9471 (p) cc_final: 0.9109 (t)
REVERT: E  287 ARG cc_start: 0.8979 (mtp85) cc_final: 0.8744 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.2353
  time to fit residues: 77.5688
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  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 64 optimal weight:    8.9990
   chunk 57 optimal weight:    7.9990
   chunk 92 optimal weight:    0.9980
   chunk 120 optimal weight:    9.9990
   chunk 84 optimal weight:   10.0000
   chunk 134 optimal weight:    0.9990
   chunk 112 optimal weight:    9.9990
   chunk 79 optimal weight:    0.7980
   chunk 119 optimal weight:    9.9990
   chunk 34 optimal weight:    7.9990
   chunk 107 optimal weight:    1.9990
   overall best weight:    2.5586

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.141808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.101639 restraints weight = 17871.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.104170 restraints weight = 11076.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.105998 restraints weight = 8095.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  10455  Z= 0.354
  Angle     :  0.604   7.671  14420  Z= 0.326
  Chirality :  0.048   0.210   1760
  Planarity :  0.006   0.058   1825
  Dihedral  :  4.399  17.919   1525
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.22), residues: 1400
  helix:  1.27 (0.22), residues: 500
  sheet: -1.05 (0.27), residues: 325
  loop : -2.12 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 213 
 HIS   0.006   0.003   HIS E 235 
 PHE   0.017   0.002   PHE A 238 
 TYR   0.010   0.001   TYR A 186 
 ARG   0.006   0.000   ARG B 287 

*********************** 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
  226 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 1.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7904 (mttm) cc_final: 0.7263 (mtpp)
REVERT: A  200 ASN cc_start: 0.8766 (t0) cc_final: 0.8472 (t0)
REVERT: A  238 PHE cc_start: 0.9270 (t80) cc_final: 0.8970 (t80)
REVERT: A  274 THR cc_start: 0.9601 (m) cc_final: 0.9031 (t)
REVERT: B  200 ASN cc_start: 0.8814 (t0) cc_final: 0.8421 (t0)
REVERT: B  239 ASN cc_start: 0.9081 (t0) cc_final: 0.8721 (t0)
REVERT: C  200 ASN cc_start: 0.8349 (t0) cc_final: 0.8057 (t0)
REVERT: C  224 ASN cc_start: 0.8864 (m-40) cc_final: 0.8157 (t0)
REVERT: C  287 ARG cc_start: 0.9003 (mtp85) cc_final: 0.8769 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8207 (t0) cc_final: 0.7952 (t0)
REVERT: D   38 LYS cc_start: 0.7815 (mttm) cc_final: 0.7168 (mtpp)
REVERT: D  200 ASN cc_start: 0.8576 (t0) cc_final: 0.7963 (t0)
REVERT: D  307 ASN cc_start: 0.8206 (t0) cc_final: 0.7938 (t0)
REVERT: E  200 ASN cc_start: 0.8831 (t0) cc_final: 0.8517 (t0)
REVERT: E  287 ARG cc_start: 0.8991 (mtp85) cc_final: 0.8764 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 226
  average time/residue: 0.2317
  time to fit residues: 72.5172
Evaluate side-chains
  200 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 60 optimal weight:    9.9990
   chunk 96 optimal weight:   20.0000
   chunk 97 optimal weight:    6.9990
   chunk 111 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0670
   chunk 135 optimal weight:    0.9980
   chunk 69 optimal weight:    0.1980
   chunk 113 optimal weight:    7.9990
   overall best weight:    1.0520

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.145952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.106648 restraints weight = 17257.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.109524 restraints weight = 10392.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.111536 restraints weight = 7432.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10455  Z= 0.218
  Angle     :  0.565   7.183  14420  Z= 0.296
  Chirality :  0.047   0.201   1760
  Planarity :  0.005   0.057   1825
  Dihedral  :  4.234  17.310   1525
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.22), residues: 1400
  helix:  1.34 (0.22), residues: 500
  sheet: -1.11 (0.27), residues: 350
  loop : -2.04 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 213 
 HIS   0.005   0.002   HIS A 235 
 PHE   0.017   0.001   PHE C 299 
 TYR   0.010   0.001   TYR E 186 
 ARG   0.006   0.000   ARG D 287 

*********************** 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
  239 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 1.175 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7877 (mttm) cc_final: 0.7249 (mtpp)
REVERT: A  200 ASN cc_start: 0.8648 (t0) cc_final: 0.8356 (t0)
REVERT: B  200 ASN cc_start: 0.8674 (t0) cc_final: 0.8399 (t0)
REVERT: B  239 ASN cc_start: 0.8983 (t0) cc_final: 0.8562 (t0)
REVERT: C  224 ASN cc_start: 0.8786 (m-40) cc_final: 0.8129 (t0)
REVERT: C  287 ARG cc_start: 0.8964 (mtp85) cc_final: 0.8712 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8140 (t0) cc_final: 0.7848 (t0)
REVERT: D   38 LYS cc_start: 0.7834 (mttm) cc_final: 0.7182 (mtpp)
REVERT: D  200 ASN cc_start: 0.8470 (t0) cc_final: 0.7892 (t0)
REVERT: D  307 ASN cc_start: 0.8118 (t0) cc_final: 0.7836 (t0)
REVERT: E  200 ASN cc_start: 0.8718 (t0) cc_final: 0.8448 (t0)
REVERT: E  224 ASN cc_start: 0.8669 (m-40) cc_final: 0.8410 (m-40)
REVERT: E  287 ARG cc_start: 0.8977 (mtp85) cc_final: 0.8739 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.2399
  time to fit residues: 78.7824
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  : 1.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 90 optimal weight:   10.0000
   chunk 2 optimal weight:    0.0070
   chunk 76 optimal weight:    0.5980
   chunk 108 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 62 optimal weight:   20.0000
   chunk 84 optimal weight:    9.9990
   chunk 64 optimal weight:    0.8980
   chunk 123 optimal weight:   30.0000
   chunk 87 optimal weight:    7.9990
   chunk 118 optimal weight:    0.9990
   overall best weight:    0.6598

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.147422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.108279 restraints weight = 17394.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.111336 restraints weight = 10311.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.113451 restraints weight = 7280.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.3117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10455  Z= 0.191
  Angle     :  0.559   7.774  14420  Z= 0.290
  Chirality :  0.046   0.175   1760
  Planarity :  0.005   0.061   1825
  Dihedral  :  4.122  16.740   1525
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.22), residues: 1400
  helix:  1.38 (0.22), residues: 500
  sheet: -0.95 (0.27), residues: 350
  loop : -2.02 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 213 
 HIS   0.006   0.002   HIS D 235 
 PHE   0.015   0.001   PHE C 299 
 TYR   0.010   0.001   TYR D 251 
 ARG   0.007   0.000   ARG D 287 

*********************** 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
  241 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 1.389 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7883 (mttm) cc_final: 0.7257 (mtpp)
REVERT: A  200 ASN cc_start: 0.8535 (t0) cc_final: 0.8320 (t0)
REVERT: B  187 GLN cc_start: 0.8158 (mt0) cc_final: 0.7893 (tt0)
REVERT: B  200 ASN cc_start: 0.8635 (t0) cc_final: 0.8303 (t0)
REVERT: B  239 ASN cc_start: 0.8868 (t0) cc_final: 0.8418 (t0)
REVERT: B  261 MET cc_start: 0.7828 (mmt) cc_final: 0.7549 (mmm)
REVERT: C  200 ASN cc_start: 0.8469 (t0) cc_final: 0.8201 (t0)
REVERT: C  224 ASN cc_start: 0.8830 (m-40) cc_final: 0.8259 (t0)
REVERT: C  287 ARG cc_start: 0.8945 (mtp85) cc_final: 0.8684 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8125 (t0) cc_final: 0.7824 (t0)
REVERT: D   38 LYS cc_start: 0.7811 (mttm) cc_final: 0.7165 (mtpp)
REVERT: D  200 ASN cc_start: 0.8267 (t0) cc_final: 0.7743 (t0)
REVERT: D  307 ASN cc_start: 0.8081 (t0) cc_final: 0.7764 (t0)
REVERT: E  200 ASN cc_start: 0.8635 (t0) cc_final: 0.8410 (t0)
REVERT: E  224 ASN cc_start: 0.8661 (m-40) cc_final: 0.8425 (m-40)
REVERT: E  287 ARG cc_start: 0.8967 (mtp85) cc_final: 0.8728 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 241
  average time/residue: 0.2412
  time to fit residues: 80.6908
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  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 1 optimal weight:   10.0000
   chunk 139 optimal weight:    1.9990
   chunk 115 optimal weight:    9.9990
   chunk 70 optimal weight:   20.0000
   chunk 113 optimal weight:    6.9990
   chunk 42 optimal weight:    0.0270
   chunk 23 optimal weight:    0.5980
   chunk 91 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0470
   chunk 134 optimal weight:    0.0980
   overall best weight:    0.3536

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

Flipped N/Q/H residues before XYZ refinement:
D 127 HIS
D 187 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.149944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.112211 restraints weight = 17197.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.114633 restraints weight = 10714.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.116668 restraints weight = 7894.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10455  Z= 0.171
  Angle     :  0.562   8.287  14420  Z= 0.288
  Chirality :  0.046   0.182   1760
  Planarity :  0.005   0.048   1825
  Dihedral  :  4.013  20.412   1525
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.22), residues: 1400
  helix:  1.21 (0.22), residues: 530
  sheet: -0.53 (0.28), residues: 365
  loop : -2.02 (0.26), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP D 213 
 HIS   0.007   0.002   HIS D 127 
 PHE   0.013   0.001   PHE C 299 
 TYR   0.010   0.001   TYR D 263 
 ARG   0.007   0.000   ARG D 287 

********************** 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
  252 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 1.233 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7914 (mttm) cc_final: 0.7304 (mtpp)
REVERT: A  200 ASN cc_start: 0.8483 (t0) cc_final: 0.8273 (t0)
REVERT: B  187 GLN cc_start: 0.8199 (mt0) cc_final: 0.7918 (tt0)
REVERT: B  200 ASN cc_start: 0.8586 (t0) cc_final: 0.8229 (t0)
REVERT: B  239 ASN cc_start: 0.8844 (t0) cc_final: 0.8405 (t0)
REVERT: B  261 MET cc_start: 0.7725 (mmt) cc_final: 0.7519 (mmm)
REVERT: C  200 ASN cc_start: 0.8422 (t0) cc_final: 0.8086 (t0)
REVERT: C  224 ASN cc_start: 0.8782 (m-40) cc_final: 0.8222 (t0)
REVERT: C  287 ARG cc_start: 0.8917 (mtp85) cc_final: 0.8633 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8057 (t0) cc_final: 0.7753 (t0)
REVERT: D   38 LYS cc_start: 0.7787 (mttm) cc_final: 0.7183 (mtpp)
REVERT: D  200 ASN cc_start: 0.8312 (t0) cc_final: 0.7735 (t0)
REVERT: D  307 ASN cc_start: 0.8017 (t0) cc_final: 0.7639 (t0)
REVERT: E  192 ARG cc_start: 0.9171 (mtt-85) cc_final: 0.8835 (mmm-85)
REVERT: E  200 ASN cc_start: 0.8518 (t0) cc_final: 0.8153 (t0)
REVERT: E  216 PHE cc_start: 0.8449 (m-80) cc_final: 0.8204 (m-80)
REVERT: E  224 ASN cc_start: 0.8606 (m-40) cc_final: 0.8324 (m-40)
REVERT: E  287 ARG cc_start: 0.8927 (mtp85) cc_final: 0.8669 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 252
  average time/residue: 0.2235
  time to fit residues: 78.2902
Evaluate side-chains
  217 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   chunk 95 optimal weight:   20.0000
   chunk 56 optimal weight:    9.9990
   chunk 124 optimal weight:    6.9990
   chunk 129 optimal weight:    0.2980
   chunk 97 optimal weight:    8.9990
   chunk 133 optimal weight:    0.7980
   chunk 71 optimal weight:   20.0000
   chunk 134 optimal weight:    0.0170
   overall best weight:    0.5218

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.150713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.112449 restraints weight = 17169.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.115006 restraints weight = 10876.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.116867 restraints weight = 7998.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.3572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10455  Z= 0.175
  Angle     :  0.554   8.373  14420  Z= 0.284
  Chirality :  0.045   0.173   1760
  Planarity :  0.005   0.041   1825
  Dihedral  :  3.939  21.686   1525
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.22), residues: 1400
  helix:  1.20 (0.22), residues: 530
  sheet: -0.42 (0.28), residues: 365
  loop : -1.94 (0.26), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP C 213 
 HIS   0.005   0.002   HIS E 235 
 PHE   0.013   0.001   PHE B  37 
 TYR   0.009   0.001   TYR B 263 
 ARG   0.007   0.000   ARG D 287 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3066.19 seconds
wall clock time: 55 minutes 21.02 seconds (3321.02 seconds total)