Starting phenix.real_space_refine
on Thu Mar 14 14:44:21 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsj_0498/03_2024/6nsj_0498_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsj_0498/03_2024/6nsj_0498.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsj_0498/03_2024/6nsj_0498_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsj_0498/03_2024/6nsj_0498_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsj_0498/03_2024/6nsj_0498_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsj_0498/03_2024/6nsj_0498.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsj_0498/03_2024/6nsj_0498.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsj_0498/03_2024/6nsj_0498_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nsj_0498/03_2024/6nsj_0498_updated.pdb"
  }
  resolution = 2.7
  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=   0.011
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: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      30      5.16       5
     C    6234      2.51       5
     N    1332      2.21       5
     O    1494      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 9096
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 1449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1449
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 8, 'TRANS': 173}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1449
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 8, 'TRANS': 173}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1449
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 8, 'TRANS': 173}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1449
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 8, 'TRANS': 173}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1449
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 8, 'TRANS': 173}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1449
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 8, 'TRANS': 173}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 67
          Unusual residues: {'XP4': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 67
          Unusual residues: {'XP4': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "C"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 67
          Unusual residues: {'XP4': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "D"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 67
          Unusual residues: {'XP4': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "E"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 67
          Unusual residues: {'XP4': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "F"
      Number of atoms: 67
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 67
          Unusual residues: {'XP4': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'XP4:plan-2': 1, 'XP4:plan-1': 1}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 5.48, per 1000 atoms: 0.60
  Number of scatterers: 9096
  At special positions: 0
  Unit cell: (101.65, 95.23, 59.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P       6     15.00
     O    1494      8.00
     N    1332      7.00
     C    6234      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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.13
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2004

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      42 helices and 0 sheets defined
      74.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 19
    Processing helix  chain 'A' and resid 28 through 53
      removed outlier: 4.180A  pdb=" N   VAL A  31 " --> pdb=" O   SER A  28 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   MET A  32 " --> pdb=" O   THR A  29 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL A  36 " --> pdb=" O   ASN A  33 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLY A  37 " --> pdb=" O   PHE A  34 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLY A  38 " --> pdb=" O   PHE A  35 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER A  40 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE A  41 " --> pdb=" O   GLY A  38 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   VAL A  42 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   CYS A  43 " --> pdb=" O   SER A  40 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN A  44 " --> pdb=" O   ILE A  41 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   VAL A  46 " --> pdb=" O   CYS A  43 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   THR A  49 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   TYR A  50 " --> pdb=" O   VAL A  47 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   SER A  51 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU A  53 " --> pdb=" O   TYR A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 96
      removed outlier: 4.497A  pdb=" N   LEU A  83 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   PHE A  84 " --> pdb=" O   THR A  80 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   GLY A  85 " --> pdb=" O   GLY A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 124
      removed outlier: 4.771A  pdb=" N   VAL A 116 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
      Proline residue:  A 117  - end of helix
    Processing helix  chain 'A' and resid 138 through 160
      removed outlier: 3.937A  pdb=" N   TRP A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   ALA A 143 " --> pdb=" O   GLY A 139 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   ALA A 156 " --> pdb=" O   LEU A 152 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   PHE A 157 " --> pdb=" O   TRP A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 180
      removed outlier: 3.748A  pdb=" N   TRP A 172 " --> pdb=" O   LYS A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 191
    Processing helix  chain 'B' and resid 2 through 22
      removed outlier: 3.581A  pdb=" N   LEU B  21 " --> pdb=" O   GLY B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 53
      removed outlier: 4.098A  pdb=" N   VAL B  31 " --> pdb=" O   SER B  28 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   MET B  32 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   VAL B  36 " --> pdb=" O   ASN B  33 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLY B  37 " --> pdb=" O   PHE B  34 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLY B  38 " --> pdb=" O   PHE B  35 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU B  39 " --> pdb=" O   VAL B  36 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE B  41 " --> pdb=" O   GLY B  38 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL B  42 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   CYS B  43 " --> pdb=" O   SER B  40 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ASN B  44 " --> pdb=" O   ILE B  41 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   VAL B  46 " --> pdb=" O   CYS B  43 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   THR B  49 " --> pdb=" O   VAL B  46 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   TYR B  50 " --> pdb=" O   VAL B  47 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   SER B  51 " --> pdb=" O   ILE B  48 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU B  53 " --> pdb=" O   TYR B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 97
      removed outlier: 4.228A  pdb=" N   LEU B  83 " --> pdb=" O   ALA B  79 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   PHE B  84 " --> pdb=" O   THR B  80 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY B  85 " --> pdb=" O   GLY B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 124
      removed outlier: 4.734A  pdb=" N   VAL B 116 " --> pdb=" O   ALA B 112 " (cutoff:3.500A)
      Proline residue:  B 117  - end of helix
    Processing helix  chain 'B' and resid 138 through 160
      removed outlier: 3.932A  pdb=" N   TRP B 142 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   ALA B 143 " --> pdb=" O   GLY B 139 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   ALA B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   PHE B 157 " --> pdb=" O   TRP B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 180
      removed outlier: 3.700A  pdb=" N   TRP B 172 " --> pdb=" O   LYS B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 191
    Processing helix  chain 'C' and resid 2 through 22
      removed outlier: 3.978A  pdb=" N   LEU C  21 " --> pdb=" O   GLY C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 53
      removed outlier: 3.876A  pdb=" N   ALA C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   VAL C  31 " --> pdb=" O   LYS C  27 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   MET C  32 " --> pdb=" O   SER C  28 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   ASN C  33 " --> pdb=" O   THR C  29 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   VAL C  47 " --> pdb=" O   CYS C  43 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 97
      removed outlier: 4.387A  pdb=" N   LEU C  83 " --> pdb=" O   ALA C  79 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   PHE C  84 " --> pdb=" O   THR C  80 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLY C  85 " --> pdb=" O   GLY C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 124
      removed outlier: 4.765A  pdb=" N   VAL C 116 " --> pdb=" O   ALA C 112 " (cutoff:3.500A)
      Proline residue:  C 117  - end of helix
    Processing helix  chain 'C' and resid 138 through 160
      removed outlier: 3.969A  pdb=" N   TRP C 142 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   ALA C 143 " --> pdb=" O   GLY C 139 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ALA C 156 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   PHE C 157 " --> pdb=" O   TRP C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 180
      removed outlier: 3.694A  pdb=" N   TRP C 172 " --> pdb=" O   LYS C 168 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 184 through 191
    Processing helix  chain 'D' and resid 2 through 19
    Processing helix  chain 'D' and resid 28 through 53
      removed outlier: 4.181A  pdb=" N   VAL D  31 " --> pdb=" O   SER D  28 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   MET D  32 " --> pdb=" O   THR D  29 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL D  36 " --> pdb=" O   ASN D  33 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLY D  37 " --> pdb=" O   PHE D  34 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLY D  38 " --> pdb=" O   PHE D  35 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU D  39 " --> pdb=" O   VAL D  36 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER D  40 " --> pdb=" O   GLY D  37 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE D  41 " --> pdb=" O   GLY D  38 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   VAL D  42 " --> pdb=" O   LEU D  39 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   CYS D  43 " --> pdb=" O   SER D  40 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ASN D  44 " --> pdb=" O   ILE D  41 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   VAL D  46 " --> pdb=" O   CYS D  43 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   THR D  49 " --> pdb=" O   VAL D  46 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   TYR D  50 " --> pdb=" O   VAL D  47 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   SER D  51 " --> pdb=" O   ILE D  48 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   LEU D  53 " --> pdb=" O   TYR D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 76 through 96
      removed outlier: 4.503A  pdb=" N   LEU D  83 " --> pdb=" O   ALA D  79 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   PHE D  84 " --> pdb=" O   THR D  80 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLY D  85 " --> pdb=" O   GLY D  81 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 124
      removed outlier: 4.772A  pdb=" N   VAL D 116 " --> pdb=" O   ALA D 112 " (cutoff:3.500A)
      Proline residue:  D 117  - end of helix
    Processing helix  chain 'D' and resid 138 through 160
      removed outlier: 3.935A  pdb=" N   TRP D 142 " --> pdb=" O   GLU D 138 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   ALA D 143 " --> pdb=" O   GLY D 139 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   ALA D 156 " --> pdb=" O   LEU D 152 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   PHE D 157 " --> pdb=" O   TRP D 153 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 168 through 180
      removed outlier: 3.747A  pdb=" N   TRP D 172 " --> pdb=" O   LYS D 168 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 184 through 191
    Processing helix  chain 'E' and resid 2 through 22
      removed outlier: 3.578A  pdb=" N   LEU E  21 " --> pdb=" O   GLY E  17 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 53
      removed outlier: 4.098A  pdb=" N   VAL E  31 " --> pdb=" O   SER E  28 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   MET E  32 " --> pdb=" O   THR E  29 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   VAL E  36 " --> pdb=" O   ASN E  33 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLY E  37 " --> pdb=" O   PHE E  34 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLY E  38 " --> pdb=" O   PHE E  35 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU E  39 " --> pdb=" O   VAL E  36 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE E  41 " --> pdb=" O   GLY E  38 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL E  42 " --> pdb=" O   LEU E  39 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   CYS E  43 " --> pdb=" O   SER E  40 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ASN E  44 " --> pdb=" O   ILE E  41 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   VAL E  46 " --> pdb=" O   CYS E  43 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   THR E  49 " --> pdb=" O   VAL E  46 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   TYR E  50 " --> pdb=" O   VAL E  47 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   SER E  51 " --> pdb=" O   ILE E  48 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU E  53 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 76 through 97
      removed outlier: 4.236A  pdb=" N   LEU E  83 " --> pdb=" O   ALA E  79 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   PHE E  84 " --> pdb=" O   THR E  80 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLY E  85 " --> pdb=" O   GLY E  81 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 102 through 124
      removed outlier: 4.736A  pdb=" N   VAL E 116 " --> pdb=" O   ALA E 112 " (cutoff:3.500A)
      Proline residue:  E 117  - end of helix
    Processing helix  chain 'E' and resid 138 through 160
      removed outlier: 3.940A  pdb=" N   TRP E 142 " --> pdb=" O   GLU E 138 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   ALA E 143 " --> pdb=" O   GLY E 139 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   ALA E 156 " --> pdb=" O   LEU E 152 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   PHE E 157 " --> pdb=" O   TRP E 153 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 169 through 180
    Processing helix  chain 'E' and resid 184 through 191
    Processing helix  chain 'F' and resid 2 through 22
      removed outlier: 3.978A  pdb=" N   LEU F  21 " --> pdb=" O   GLY F  17 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 26 through 53
      removed outlier: 3.875A  pdb=" N   ALA F  30 " --> pdb=" O   PRO F  26 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   VAL F  31 " --> pdb=" O   LYS F  27 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   MET F  32 " --> pdb=" O   SER F  28 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   ASN F  33 " --> pdb=" O   THR F  29 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   VAL F  47 " --> pdb=" O   CYS F  43 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 76 through 97
      removed outlier: 4.387A  pdb=" N   LEU F  83 " --> pdb=" O   ALA F  79 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   PHE F  84 " --> pdb=" O   THR F  80 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLY F  85 " --> pdb=" O   GLY F  81 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 102 through 124
      removed outlier: 4.768A  pdb=" N   VAL F 116 " --> pdb=" O   ALA F 112 " (cutoff:3.500A)
      Proline residue:  F 117  - end of helix
    Processing helix  chain 'F' and resid 138 through 160
      removed outlier: 3.968A  pdb=" N   TRP F 142 " --> pdb=" O   GLU F 138 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   ALA F 143 " --> pdb=" O   GLY F 139 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   ALA F 156 " --> pdb=" O   LEU F 152 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   PHE F 157 " --> pdb=" O   TRP F 153 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 168 through 180
      removed outlier: 3.695A  pdb=" N   TRP F 172 " --> pdb=" O   LYS F 168 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 184 through 191

    500 hydrogen bonds defined for protein.
    1410 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.25

  Time building geometry restraints manager: 3.47 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1266
        1.31 -     1.43: 2834
        1.43 -     1.56: 5242
        1.56 -     1.68: 6
        1.68 -     1.80: 48
  Bond restraints: 9396
  Sorted by residual:
  bond pdb=" N   TRP B 183 "
       pdb=" CA  TRP B 183 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.20e-02 6.94e+03 8.39e+00
  bond pdb=" N   TRP E 183 "
       pdb=" CA  TRP E 183 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.20e-02 6.94e+03 8.32e+00
  bond pdb=" N   TRP A 183 "
       pdb=" CA  TRP A 183 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.23e-02 6.61e+03 7.93e+00
  bond pdb=" N   TRP D 183 "
       pdb=" CA  TRP D 183 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.23e-02 6.61e+03 7.60e+00
  bond pdb=" N   TRP C 183 "
       pdb=" CA  TRP C 183 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.033 1.23e-02 6.61e+03 7.41e+00
  ... (remaining 9391 not shown)

  Histogram of bond angle deviations from ideal:
       99.52 -   106.49: 327
      106.49 -   113.46: 5326
      113.46 -   120.43: 3964
      120.43 -   127.40: 2970
      127.40 -   134.37: 217
  Bond angle restraints: 12804
  Sorted by residual:
  angle pdb=" N   MET A 127 "
        pdb=" CA  MET A 127 "
        pdb=" C   MET A 127 "
      ideal   model   delta    sigma   weight residual
     108.96   99.52    9.44 1.59e+00 3.96e-01 3.53e+01
  angle pdb=" N   MET D 127 "
        pdb=" CA  MET D 127 "
        pdb=" C   MET D 127 "
      ideal   model   delta    sigma   weight residual
     108.96   99.68    9.28 1.59e+00 3.96e-01 3.41e+01
  angle pdb=" C   MET A 127 "
        pdb=" CA  MET A 127 "
        pdb=" CB  MET A 127 "
      ideal   model   delta    sigma   weight residual
     110.22  117.20   -6.98 1.67e+00 3.59e-01 1.74e+01
  angle pdb=" N   TRP F 153 "
        pdb=" CA  TRP F 153 "
        pdb=" C   TRP F 153 "
      ideal   model   delta    sigma   weight residual
     113.18  108.60    4.58 1.21e+00 6.83e-01 1.44e+01
  angle pdb=" C   MET D 127 "
        pdb=" CA  MET D 127 "
        pdb=" CB  MET D 127 "
      ideal   model   delta    sigma   weight residual
     110.22  116.54   -6.32 1.67e+00 3.59e-01 1.43e+01
  ... (remaining 12799 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.91: 4447
       11.91 -    23.82: 446
       23.82 -    35.72: 169
       35.72 -    47.63: 88
       47.63 -    59.54: 40
  Dihedral angle restraints: 5190
    sinusoidal: 2058
      harmonic: 3132
  Sorted by residual:
  dihedral pdb=" CA  MET F 127 "
           pdb=" C   MET F 127 "
           pdb=" N   LEU F 128 "
           pdb=" CA  LEU F 128 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.38  -29.62     0      5.00e+00 4.00e-02 3.51e+01
  dihedral pdb=" CA  MET C 127 "
           pdb=" C   MET C 127 "
           pdb=" N   LEU C 128 "
           pdb=" CA  LEU C 128 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.62  -29.38     0      5.00e+00 4.00e-02 3.45e+01
  dihedral pdb=" CA  MET E 127 "
           pdb=" C   MET E 127 "
           pdb=" N   LEU E 128 "
           pdb=" CA  LEU E 128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.76  -28.24     0      5.00e+00 4.00e-02 3.19e+01
  ... (remaining 5187 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 760
       0.041 -    0.082: 479
       0.082 -    0.122: 135
       0.122 -    0.163: 37
       0.163 -    0.204: 29
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CB  VAL C  12 "
            pdb=" CA  VAL C  12 "
            pdb=" CG1 VAL C  12 "
            pdb=" CG2 VAL C  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CB  VAL F  12 "
            pdb=" CA  VAL F  12 "
            pdb=" CG1 VAL F  12 "
            pdb=" CG2 VAL F  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.83e-01
  chirality pdb=" CA  ARG F 102 "
            pdb=" N   ARG F 102 "
            pdb=" C   ARG F 102 "
            pdb=" CB  ARG F 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.47e-01
  ... (remaining 1437 not shown)

  Planarity restraints: 1470
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 182 "    0.014 2.00e-02 2.50e+03   2.90e-02 8.38e+00
        pdb=" C   ALA B 182 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   ALA B 182 "    0.018 2.00e-02 2.50e+03
        pdb=" N   TRP B 183 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA E 182 "    0.014 2.00e-02 2.50e+03   2.88e-02 8.30e+00
        pdb=" C   ALA E 182 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   ALA E 182 "    0.018 2.00e-02 2.50e+03
        pdb=" N   TRP E 183 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D 182 "    0.012 2.00e-02 2.50e+03   2.34e-02 5.49e+00
        pdb=" C   ALA D 182 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   ALA D 182 "    0.015 2.00e-02 2.50e+03
        pdb=" N   TRP D 183 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1467 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 2826
        2.85 -     3.36: 8798
        3.36 -     3.88: 14692
        3.88 -     4.39: 17631
        4.39 -     4.90: 29703
  Nonbonded interactions: 73650
  Sorted by model distance:
  nonbonded pdb=" O   ARG D 102 "
            pdb=" OG  SER D 105 "
     model   vdw
     2.340 2.440
  nonbonded pdb=" O   ARG A 102 "
            pdb=" OG  SER A 105 "
     model   vdw
     2.340 2.440
  nonbonded pdb=" O   GLU E 177 "
            pdb=" OG1 THR E 181 "
     model   vdw
     2.360 2.440
  nonbonded pdb=" O   GLU B 177 "
            pdb=" OG1 THR B 181 "
     model   vdw
     2.360 2.440
  nonbonded pdb=" O   GLU C 177 "
            pdb=" OG1 THR C 181 "
     model   vdw
     2.364 2.440
  ... (remaining 73645 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 195 or resid 201 or (resid 203 and (name C10 or  \ 
name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or nam \ 
e O5 or name O6 ))))
  selection = (chain 'B' and (resid 1 through 195 or resid 201 or (resid 203 and (name C10 or  \ 
name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or nam \ 
e O5 or name O6 ))))
  selection = (chain 'C' and (resid 1 through 195 or resid 201 or (resid 203 and (name C10 or  \ 
name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or nam \ 
e O5 or name O6 ))))
  selection = (chain 'D' and (resid 1 through 195 or resid 201 or (resid 203 and (name C10 or  \ 
name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or nam \ 
e O5 or name O6 ))))
  selection = (chain 'E' and (resid 1 through 195 or resid 201 or (resid 203 and (name C10 or  \ 
name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or nam \ 
e O5 or name O6 ))))
  selection = (chain 'F' and (resid 1 through 195 or (resid 201 and (name C18 or name C19 or n \ 
ame C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 o \ 
r name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or name O \ 
7 or name O8 )) or resid 203))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.240
  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:          1.400
  Check model and map are aligned:         0.140
  Set scattering table:                    0.110
  Process input model:                     26.380
  Find NCS groups from input model:        0.860
  Set up NCS constraints:                  0.060
  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:11.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.061   9396  Z= 0.514
  Angle     :  1.121  10.256  12804  Z= 0.591
  Chirality :  0.060   0.204   1440
  Planarity :  0.008   0.051   1470
  Dihedral  : 13.933  59.540   3186
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  :  5.66 %
    Favored  : 92.16 %
  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: -4.40 (0.17), residues: 1068
  helix: -2.78 (0.11), residues: 804
  sheet:  None (None), residues: 0
  loop : -2.54 (0.33), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D 142 
 HIS   0.009   0.002   HIS D  95 
 PHE   0.025   0.004   PHE C  86 
 TYR   0.022   0.003   TYR A  88 
 ARG   0.004   0.002   ARG E 102 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 SER cc_start: 0.7946 (m) cc_final: 0.7698 (t)
REVERT: A  146 TRP cc_start: 0.8006 (OUTLIER) cc_final: 0.7671 (m-10)
REVERT: B   75 PHE cc_start: 0.6916 (OUTLIER) cc_final: 0.6299 (t80)
REVERT: B  125 SER cc_start: 0.7684 (m) cc_final: 0.7412 (t)
REVERT: B  134 LEU cc_start: 0.4186 (OUTLIER) cc_final: 0.3984 (tt)
REVERT: B  177 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7608 (mt-10)
REVERT: C  124 TYR cc_start: 0.6483 (m-80) cc_final: 0.5883 (m-10)
REVERT: D  125 SER cc_start: 0.7927 (m) cc_final: 0.7700 (t)
REVERT: D  146 TRP cc_start: 0.8008 (OUTLIER) cc_final: 0.7681 (m-10)
REVERT: E   75 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6282 (t80)
REVERT: E  125 SER cc_start: 0.7614 (m) cc_final: 0.7333 (t)
REVERT: E  177 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7535 (mt-10)
REVERT: F  124 TYR cc_start: 0.6458 (m-80) cc_final: 0.5861 (m-10)
  outliers start: 20
  outliers final: 4
  residues processed: 153
  average time/residue: 0.9173
  time to fit residues: 152.5858
Evaluate side-chains
  108 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 TRP
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  146 TRP
Chi-restraints excluded: chain C residue  146 TRP
Chi-restraints excluded: chain D residue  146 TRP
Chi-restraints excluded: chain E residue   75 PHE
Chi-restraints excluded: chain E residue  146 TRP
Chi-restraints excluded: chain F residue  146 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
B  95 HIS
B 131 HIS
C 131 HIS
E  95 HIS
F 131 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7241
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9396  Z= 0.148
  Angle     :  0.546   5.932  12804  Z= 0.274
  Chirality :  0.040   0.142   1440
  Planarity :  0.004   0.028   1470
  Dihedral  : 13.235  57.444   1440
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 12.96 %
    Favored  : 84.64 %
  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: -1.36 (0.23), residues: 1068
  helix: -0.37 (0.16), residues: 804
  sheet:  None (None), residues: 0
  loop : -2.23 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E 142 
 HIS   0.003   0.000   HIS B  95 
 PHE   0.017   0.002   PHE F 110 
 TYR   0.013   0.001   TYR F   8 
 ARG   0.002   0.001   ARG F 102 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.944 
Fit side-chains
REVERT: A  125 SER cc_start: 0.7658 (m) cc_final: 0.7380 (t)
REVERT: A  146 TRP cc_start: 0.7867 (OUTLIER) cc_final: 0.7416 (m-10)
REVERT: B  125 SER cc_start: 0.7425 (m) cc_final: 0.7143 (t)
REVERT: B  126 ASP cc_start: 0.4600 (p0) cc_final: 0.3901 (t0)
REVERT: B  134 LEU cc_start: 0.4126 (OUTLIER) cc_final: 0.3866 (tt)
REVERT: B  146 TRP cc_start: 0.7623 (OUTLIER) cc_final: 0.6566 (m-90)
REVERT: C  126 ASP cc_start: 0.4775 (p0) cc_final: 0.3908 (t0)
REVERT: C  127 MET cc_start: 0.2753 (OUTLIER) cc_final: 0.1732 (ttm)
REVERT: D  125 SER cc_start: 0.7657 (m) cc_final: 0.7387 (t)
REVERT: D  127 MET cc_start: 0.3145 (ttm) cc_final: 0.2082 (ppp)
REVERT: D  146 TRP cc_start: 0.7880 (OUTLIER) cc_final: 0.7397 (m-10)
REVERT: E  126 ASP cc_start: 0.4535 (p0) cc_final: 0.3827 (t0)
REVERT: E  146 TRP cc_start: 0.7528 (OUTLIER) cc_final: 0.6469 (m-90)
REVERT: F  126 ASP cc_start: 0.4766 (p0) cc_final: 0.3901 (t0)
  outliers start: 22
  outliers final: 3
  residues processed: 121
  average time/residue: 0.8652
  time to fit residues: 114.5898
Evaluate side-chains
  103 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 TRP
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  146 TRP
Chi-restraints excluded: chain C residue  127 MET
Chi-restraints excluded: chain C residue  146 TRP
Chi-restraints excluded: chain D residue  146 TRP
Chi-restraints excluded: chain D residue  168 LYS
Chi-restraints excluded: chain E residue  146 TRP
Chi-restraints excluded: chain F residue  146 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 30 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0060
   chunk 27 optimal weight:    3.9990
   chunk 98 optimal weight:    6.9990
   chunk 106 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 78 optimal weight:    7.9990
   overall best weight:    1.3200

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   9396  Z= 0.162
  Angle     :  0.521   7.928  12804  Z= 0.258
  Chirality :  0.039   0.134   1440
  Planarity :  0.003   0.027   1470
  Dihedral  : 11.746  54.585   1436
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 12.42 %
    Favored  : 84.10 %
  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: -0.17 (0.25), residues: 1068
  helix:  0.53 (0.18), residues: 804
  sheet:  None (None), residues: 0
  loop : -1.96 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 142 
 HIS   0.002   0.001   HIS D  95 
 PHE   0.016   0.001   PHE F 110 
 TYR   0.019   0.001   TYR F   8 
 ARG   0.002   0.001   ARG B 102 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 101
  time to evaluate  : 0.902 
Fit side-chains
REVERT: A  125 SER cc_start: 0.7575 (m) cc_final: 0.7334 (t)
REVERT: B   75 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.6642 (t80)
REVERT: B  125 SER cc_start: 0.7248 (m) cc_final: 0.6968 (t)
REVERT: B  126 ASP cc_start: 0.4589 (p0) cc_final: 0.3937 (t0)
REVERT: B  134 LEU cc_start: 0.4102 (OUTLIER) cc_final: 0.3840 (tt)
REVERT: B  146 TRP cc_start: 0.7599 (OUTLIER) cc_final: 0.6582 (m-90)
REVERT: C   75 PHE cc_start: 0.6834 (OUTLIER) cc_final: 0.6281 (t80)
REVERT: C  126 ASP cc_start: 0.4517 (p0) cc_final: 0.3736 (t0)
REVERT: D  125 SER cc_start: 0.7565 (m) cc_final: 0.7335 (t)
REVERT: E   75 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.6584 (t80)
REVERT: E  126 ASP cc_start: 0.4838 (p0) cc_final: 0.4034 (t0)
REVERT: E  146 TRP cc_start: 0.7505 (OUTLIER) cc_final: 0.6490 (m-90)
REVERT: F   75 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.6305 (t80)
REVERT: F  126 ASP cc_start: 0.4574 (p0) cc_final: 0.3706 (t0)
REVERT: F  127 MET cc_start: 0.2557 (OUTLIER) cc_final: 0.1556 (ttm)
  outliers start: 32
  outliers final: 10
  residues processed: 118
  average time/residue: 0.8789
  time to fit residues: 113.2699
Evaluate side-chains
  121 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue  146 TRP
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  146 TRP
Chi-restraints excluded: chain C residue   23 LYS
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue  146 TRP
Chi-restraints excluded: chain D residue   22 THR
Chi-restraints excluded: chain D residue  146 TRP
Chi-restraints excluded: chain D residue  168 LYS
Chi-restraints excluded: chain E residue   48 ILE
Chi-restraints excluded: chain E residue   75 PHE
Chi-restraints excluded: chain E residue  146 TRP
Chi-restraints excluded: chain F residue   75 PHE
Chi-restraints excluded: chain F residue  127 MET
Chi-restraints excluded: chain F residue  146 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 97 optimal weight:    0.7980
   chunk 73 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 46 optimal weight:    7.9990
   chunk 65 optimal weight:    7.9990
   chunk 98 optimal weight:    4.9990
   chunk 104 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   overall best weight:    1.7184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9396  Z= 0.182
  Angle     :  0.513   6.657  12804  Z= 0.255
  Chirality :  0.039   0.135   1440
  Planarity :  0.003   0.027   1470
  Dihedral  : 10.813  59.635   1436
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 13.07 %
    Favored  : 83.66 %
  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:  0.29 (0.25), residues: 1068
  helix:  0.85 (0.18), residues: 816
  sheet:  None (None), residues: 0
  loop : -1.87 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 142 
 HIS   0.002   0.001   HIS E 123 
 PHE   0.016   0.001   PHE C 110 
 TYR   0.018   0.001   TYR F   8 
 ARG   0.002   0.001   ARG A 102 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 112
  time to evaluate  : 0.846 
Fit side-chains
REVERT: A  125 SER cc_start: 0.7617 (m) cc_final: 0.7389 (t)
REVERT: B   75 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.6626 (t80)
REVERT: B  125 SER cc_start: 0.7323 (m) cc_final: 0.6989 (t)
REVERT: B  126 ASP cc_start: 0.4686 (p0) cc_final: 0.4116 (t0)
REVERT: B  134 LEU cc_start: 0.4186 (OUTLIER) cc_final: 0.3927 (tt)
REVERT: B  146 TRP cc_start: 0.7578 (OUTLIER) cc_final: 0.6895 (m-10)
REVERT: C   75 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.6379 (t80)
REVERT: C  126 ASP cc_start: 0.4328 (p0) cc_final: 0.3576 (t0)
REVERT: D  125 SER cc_start: 0.7590 (m) cc_final: 0.7358 (t)
REVERT: E   75 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.6556 (t80)
REVERT: E  126 ASP cc_start: 0.4677 (p0) cc_final: 0.4012 (t0)
REVERT: E  146 TRP cc_start: 0.7482 (OUTLIER) cc_final: 0.6798 (m-10)
REVERT: F   75 PHE cc_start: 0.6962 (OUTLIER) cc_final: 0.6411 (t80)
REVERT: F  126 ASP cc_start: 0.4305 (p0) cc_final: 0.3549 (t0)
  outliers start: 30
  outliers final: 11
  residues processed: 125
  average time/residue: 0.9080
  time to fit residues: 123.7388
Evaluate side-chains
  124 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue  146 TRP
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  146 TRP
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue  137 THR
Chi-restraints excluded: chain C residue  146 TRP
Chi-restraints excluded: chain D residue   22 THR
Chi-restraints excluded: chain D residue  146 TRP
Chi-restraints excluded: chain D residue  168 LYS
Chi-restraints excluded: chain E residue   75 PHE
Chi-restraints excluded: chain E residue  137 THR
Chi-restraints excluded: chain E residue  146 TRP
Chi-restraints excluded: chain F residue   75 PHE
Chi-restraints excluded: chain F residue  137 THR
Chi-restraints excluded: chain F residue  146 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 59 optimal weight:    9.9990
   chunk 1 optimal weight:    7.9990
   chunk 77 optimal weight:   10.0000
   chunk 43 optimal weight:    6.9990
   chunk 89 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9990
   chunk 93 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  95 HIS
C  95 HIS
D  95 HIS
F  95 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   9396  Z= 0.305
  Angle     :  0.575   6.567  12804  Z= 0.288
  Chirality :  0.042   0.143   1440
  Planarity :  0.003   0.028   1470
  Dihedral  : 10.510  59.909   1436
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.71 %
    Favored  : 82.68 %
  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:  0.27 (0.25), residues: 1068
  helix:  0.78 (0.17), residues: 822
  sheet:  None (None), residues: 0
  loop : -1.72 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 172 
 HIS   0.003   0.001   HIS E 123 
 PHE   0.016   0.002   PHE C 110 
 TYR   0.022   0.002   TYR F  90 
 ARG   0.003   0.001   ARG A 102 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A   22 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8450 (p)
REVERT: A   75 PHE cc_start: 0.7122 (OUTLIER) cc_final: 0.6840 (t80)
REVERT: A  125 SER cc_start: 0.7597 (m) cc_final: 0.7348 (t)
REVERT: B   75 PHE cc_start: 0.7105 (OUTLIER) cc_final: 0.6727 (t80)
REVERT: B  125 SER cc_start: 0.7545 (m) cc_final: 0.7200 (t)
REVERT: B  126 ASP cc_start: 0.4474 (p0) cc_final: 0.3984 (t0)
REVERT: B  134 LEU cc_start: 0.4468 (OUTLIER) cc_final: 0.4243 (tt)
REVERT: B  146 TRP cc_start: 0.7797 (OUTLIER) cc_final: 0.7153 (m-10)
REVERT: C   75 PHE cc_start: 0.6991 (OUTLIER) cc_final: 0.6295 (t80)
REVERT: C  126 ASP cc_start: 0.4633 (p0) cc_final: 0.3846 (t0)
REVERT: D   22 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8438 (p)
REVERT: D  125 SER cc_start: 0.7603 (m) cc_final: 0.7359 (t)
REVERT: E   75 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.6658 (t80)
REVERT: E  126 ASP cc_start: 0.4670 (p0) cc_final: 0.4085 (t0)
REVERT: E  146 TRP cc_start: 0.7699 (OUTLIER) cc_final: 0.7028 (m-10)
REVERT: F   75 PHE cc_start: 0.7031 (OUTLIER) cc_final: 0.6293 (t80)
REVERT: F  126 ASP cc_start: 0.4416 (p0) cc_final: 0.3565 (t0)
  outliers start: 24
  outliers final: 9
  residues processed: 120
  average time/residue: 0.9284
  time to fit residues: 121.2084
Evaluate side-chains
  124 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   75 PHE
Chi-restraints excluded: chain A residue  146 TRP
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  146 TRP
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue  137 THR
Chi-restraints excluded: chain C residue  146 TRP
Chi-restraints excluded: chain D residue   22 THR
Chi-restraints excluded: chain D residue  146 TRP
Chi-restraints excluded: chain D residue  168 LYS
Chi-restraints excluded: chain E residue   75 PHE
Chi-restraints excluded: chain E residue  137 THR
Chi-restraints excluded: chain E residue  146 TRP
Chi-restraints excluded: chain F residue   75 PHE
Chi-restraints excluded: chain F residue  137 THR
Chi-restraints excluded: chain F residue  146 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 35 optimal weight:    0.4980
   chunk 94 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0170
   chunk 61 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 48 optimal weight:    8.9990
   chunk 8 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   overall best weight:    1.9024

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.2600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9396  Z= 0.195
  Angle     :  0.513   7.310  12804  Z= 0.255
  Chirality :  0.040   0.135   1440
  Planarity :  0.003   0.027   1470
  Dihedral  :  9.918  58.675   1436
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 13.94 %
    Favored  : 82.79 %
  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:  0.75 (0.25), residues: 1068
  helix:  1.12 (0.18), residues: 822
  sheet:  None (None), residues: 0
  loop : -1.50 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 153 
 HIS   0.002   0.001   HIS F 123 
 PHE   0.015   0.001   PHE C 110 
 TYR   0.019   0.001   TYR C   8 
 ARG   0.002   0.001   ARG E 102 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 0.894 
Fit side-chains
REVERT: A   22 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8468 (p)
REVERT: A   75 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6816 (t80)
REVERT: A  125 SER cc_start: 0.7530 (m) cc_final: 0.7300 (t)
REVERT: B   75 PHE cc_start: 0.6813 (OUTLIER) cc_final: 0.6499 (t80)
REVERT: B  125 SER cc_start: 0.7478 (m) cc_final: 0.7137 (t)
REVERT: B  126 ASP cc_start: 0.4745 (p0) cc_final: 0.4147 (t0)
REVERT: B  134 LEU cc_start: 0.4524 (OUTLIER) cc_final: 0.4319 (tt)
REVERT: B  146 TRP cc_start: 0.7692 (OUTLIER) cc_final: 0.7040 (m-10)
REVERT: C  126 ASP cc_start: 0.4605 (p0) cc_final: 0.3851 (t0)
REVERT: C  168 LYS cc_start: 0.8421 (tptt) cc_final: 0.8202 (mtpp)
REVERT: D   22 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8458 (p)
REVERT: D  125 SER cc_start: 0.7543 (m) cc_final: 0.7309 (t)
REVERT: E   75 PHE cc_start: 0.6724 (OUTLIER) cc_final: 0.6443 (t80)
REVERT: E  126 ASP cc_start: 0.4644 (p0) cc_final: 0.4003 (t0)
REVERT: E  146 TRP cc_start: 0.7595 (OUTLIER) cc_final: 0.6943 (m-10)
REVERT: F  126 ASP cc_start: 0.4584 (p0) cc_final: 0.3823 (t0)
REVERT: F  168 LYS cc_start: 0.8418 (tptt) cc_final: 0.8200 (mtpp)
  outliers start: 30
  outliers final: 13
  residues processed: 128
  average time/residue: 0.8712
  time to fit residues: 121.9265
Evaluate side-chains
  130 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   75 PHE
Chi-restraints excluded: chain A residue  146 TRP
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  146 TRP
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue  137 THR
Chi-restraints excluded: chain C residue  146 TRP
Chi-restraints excluded: chain D residue   22 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  146 TRP
Chi-restraints excluded: chain D residue  168 LYS
Chi-restraints excluded: chain E residue   75 PHE
Chi-restraints excluded: chain E residue  137 THR
Chi-restraints excluded: chain E residue  146 TRP
Chi-restraints excluded: chain F residue   75 PHE
Chi-restraints excluded: chain F residue  137 THR
Chi-restraints excluded: chain F residue  146 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 100 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0980
   chunk 59 optimal weight:    9.9990
   chunk 76 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0770
   chunk 104 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0370
   chunk 63 optimal weight:    0.7980
   chunk 48 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.3816

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   9396  Z= 0.114
  Angle     :  0.488   8.180  12804  Z= 0.239
  Chirality :  0.038   0.133   1440
  Planarity :  0.003   0.026   1470
  Dihedral  :  9.431  57.114   1436
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 15.03 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.26), residues: 1068
  helix:  1.49 (0.18), residues: 822
  sheet:  None (None), residues: 0
  loop : -1.37 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 142 
 HIS   0.001   0.000   HIS D  70 
 PHE   0.013   0.001   PHE C 110 
 TYR   0.018   0.001   TYR C   8 
 ARG   0.002   0.001   ARG E 102 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 0.968 
Fit side-chains
REVERT: A   22 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8458 (p)
REVERT: A   75 PHE cc_start: 0.6918 (OUTLIER) cc_final: 0.6677 (t80)
REVERT: A  125 SER cc_start: 0.7423 (m) cc_final: 0.7201 (t)
REVERT: B   75 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.6389 (t80)
REVERT: B  125 SER cc_start: 0.7393 (m) cc_final: 0.7021 (t)
REVERT: B  126 ASP cc_start: 0.4617 (p0) cc_final: 0.4152 (t0)
REVERT: B  146 TRP cc_start: 0.7643 (OUTLIER) cc_final: 0.7000 (m-10)
REVERT: C  126 ASP cc_start: 0.4527 (p0) cc_final: 0.3944 (t0)
REVERT: D   22 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8398 (p)
REVERT: D  125 SER cc_start: 0.7438 (m) cc_final: 0.7214 (t)
REVERT: E   75 PHE cc_start: 0.6535 (OUTLIER) cc_final: 0.6317 (t80)
REVERT: E  126 ASP cc_start: 0.4680 (p0) cc_final: 0.4107 (t0)
REVERT: E  146 TRP cc_start: 0.7563 (OUTLIER) cc_final: 0.6916 (m-10)
REVERT: F  126 ASP cc_start: 0.4517 (p0) cc_final: 0.3923 (t0)
  outliers start: 23
  outliers final: 8
  residues processed: 126
  average time/residue: 0.8861
  time to fit residues: 122.0661
Evaluate side-chains
  119 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   75 PHE
Chi-restraints excluded: chain A residue  146 TRP
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue  146 TRP
Chi-restraints excluded: chain C residue  146 TRP
Chi-restraints excluded: chain D residue   22 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  146 TRP
Chi-restraints excluded: chain D residue  168 LYS
Chi-restraints excluded: chain E residue   75 PHE
Chi-restraints excluded: chain E residue  137 THR
Chi-restraints excluded: chain E residue  146 TRP
Chi-restraints excluded: chain F residue  146 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0970
   chunk 66 optimal weight:    9.9990
   chunk 70 optimal weight:    0.0470
   chunk 51 optimal weight:    0.0040
   chunk 9 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9980
   chunk 94 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   overall best weight:    0.3688

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   9396  Z= 0.109
  Angle     :  0.477   8.699  12804  Z= 0.231
  Chirality :  0.037   0.134   1440
  Planarity :  0.003   0.024   1470
  Dihedral  :  8.833  54.048   1434
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 15.47 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.69 (0.26), residues: 1068
  helix:  1.79 (0.18), residues: 822
  sheet:  None (None), residues: 0
  loop : -1.21 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 153 
 HIS   0.001   0.000   HIS D  70 
 PHE   0.014   0.001   PHE F 110 
 TYR   0.018   0.001   TYR F   8 
 ARG   0.002   0.001   ARG A 102 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 114
  time to evaluate  : 0.875 
Fit side-chains
REVERT: A   22 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8339 (p)
REVERT: A   32 MET cc_start: 0.8581 (tpt) cc_final: 0.8295 (tpt)
REVERT: A   75 PHE cc_start: 0.6875 (OUTLIER) cc_final: 0.6616 (t80)
REVERT: B   75 PHE cc_start: 0.6595 (OUTLIER) cc_final: 0.6322 (t80)
REVERT: B  125 SER cc_start: 0.6931 (m) cc_final: 0.6525 (t)
REVERT: B  126 ASP cc_start: 0.4584 (p0) cc_final: 0.4324 (t0)
REVERT: B  146 TRP cc_start: 0.7675 (OUTLIER) cc_final: 0.6806 (m-90)
REVERT: C  126 ASP cc_start: 0.4641 (p0) cc_final: 0.4127 (t0)
REVERT: D   22 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8344 (p)
REVERT: D   32 MET cc_start: 0.8583 (tpt) cc_final: 0.8298 (tpt)
REVERT: E   75 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.6299 (t80)
REVERT: E  126 ASP cc_start: 0.4520 (p0) cc_final: 0.4078 (t0)
REVERT: E  146 TRP cc_start: 0.7581 (OUTLIER) cc_final: 0.6704 (m-90)
REVERT: F  126 ASP cc_start: 0.4646 (p0) cc_final: 0.4136 (t0)
  outliers start: 27
  outliers final: 11
  residues processed: 127
  average time/residue: 0.8160
  time to fit residues: 114.0777
Evaluate side-chains
  125 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   75 PHE
Chi-restraints excluded: chain A residue  146 TRP
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  146 TRP
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  146 TRP
Chi-restraints excluded: chain D residue   22 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  146 TRP
Chi-restraints excluded: chain D residue  168 LYS
Chi-restraints excluded: chain E residue   75 PHE
Chi-restraints excluded: chain E residue  137 THR
Chi-restraints excluded: chain E residue  146 TRP
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain F residue  146 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 99 optimal weight:    0.8980
   chunk 58 optimal weight:    0.3980
   chunk 42 optimal weight:    5.9990
   chunk 76 optimal weight:    3.9990
   chunk 29 optimal weight:   20.0000
   chunk 87 optimal weight:    4.9990
   chunk 91 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7215
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   9396  Z= 0.126
  Angle     :  0.483   8.744  12804  Z= 0.234
  Chirality :  0.038   0.133   1440
  Planarity :  0.003   0.024   1470
  Dihedral  :  8.644  51.910   1434
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 16.45 %
    Favored  : 80.94 %
  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:  1.88 (0.26), residues: 1068
  helix:  1.96 (0.18), residues: 816
  sheet:  None (None), residues: 0
  loop : -1.18 (0.40), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 153 
 HIS   0.001   0.000   HIS F 123 
 PHE   0.014   0.001   PHE F 110 
 TYR   0.018   0.001   TYR C   8 
 ARG   0.002   0.001   ARG A 102 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.996 
Fit side-chains
REVERT: A   22 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8375 (p)
REVERT: A   32 MET cc_start: 0.8545 (tpt) cc_final: 0.8266 (tpt)
REVERT: A   75 PHE cc_start: 0.6974 (OUTLIER) cc_final: 0.6617 (t80)
REVERT: A  134 LEU cc_start: 0.5757 (OUTLIER) cc_final: 0.5546 (tp)
REVERT: B   75 PHE cc_start: 0.6655 (OUTLIER) cc_final: 0.6361 (t80)
REVERT: B  125 SER cc_start: 0.6969 (m) cc_final: 0.6548 (t)
REVERT: B  126 ASP cc_start: 0.4756 (p0) cc_final: 0.4411 (t0)
REVERT: B  146 TRP cc_start: 0.7671 (OUTLIER) cc_final: 0.6755 (m-90)
REVERT: C  126 ASP cc_start: 0.4677 (p0) cc_final: 0.4159 (t0)
REVERT: D   22 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8351 (p)
REVERT: D   32 MET cc_start: 0.8546 (tpt) cc_final: 0.8267 (tpt)
REVERT: E   75 PHE cc_start: 0.6554 (OUTLIER) cc_final: 0.6293 (t80)
REVERT: E  126 ASP cc_start: 0.4859 (p0) cc_final: 0.4382 (t0)
REVERT: E  146 TRP cc_start: 0.7651 (OUTLIER) cc_final: 0.6748 (m-90)
REVERT: F  126 ASP cc_start: 0.4536 (p0) cc_final: 0.4096 (t0)
  outliers start: 24
  outliers final: 13
  residues processed: 118
  average time/residue: 0.8802
  time to fit residues: 113.9994
Evaluate side-chains
  129 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   75 PHE
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  146 TRP
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  146 TRP
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  137 THR
Chi-restraints excluded: chain C residue  146 TRP
Chi-restraints excluded: chain D residue   22 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  146 TRP
Chi-restraints excluded: chain D residue  168 LYS
Chi-restraints excluded: chain E residue   75 PHE
Chi-restraints excluded: chain E residue  137 THR
Chi-restraints excluded: chain E residue  146 TRP
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain F residue  137 THR
Chi-restraints excluded: chain F residue  146 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 102 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 48 optimal weight:    9.9990
   chunk 71 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 66 optimal weight:    8.9990
   chunk 52 optimal weight:    0.4980
   chunk 68 optimal weight:    5.9990
   overall best weight:    2.4988

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

Flipped N/Q/H residues before XYZ refinement:
D  71 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.2916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   9396  Z= 0.245
  Angle     :  0.545   8.298  12804  Z= 0.267
  Chirality :  0.040   0.141   1440
  Planarity :  0.003   0.024   1470
  Dihedral  :  8.851  49.971   1434
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 16.01 %
    Favored  : 80.94 %
  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:  1.58 (0.26), residues: 1068
  helix:  1.70 (0.18), residues: 822
  sheet:  None (None), residues: 0
  loop : -1.14 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 153 
 HIS   0.003   0.001   HIS B  95 
 PHE   0.016   0.001   PHE F 110 
 TYR   0.019   0.001   TYR C   8 
 ARG   0.003   0.001   ARG A 102 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.997 
Fit side-chains
REVERT: A   22 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8475 (p)
REVERT: A   75 PHE cc_start: 0.7135 (OUTLIER) cc_final: 0.6745 (t80)
REVERT: A  134 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5747 (tp)
REVERT: B   75 PHE cc_start: 0.6845 (OUTLIER) cc_final: 0.6528 (t80)
REVERT: B  125 SER cc_start: 0.7246 (m) cc_final: 0.6850 (t)
REVERT: B  126 ASP cc_start: 0.4617 (p0) cc_final: 0.4322 (t0)
REVERT: B  146 TRP cc_start: 0.7632 (OUTLIER) cc_final: 0.6973 (m-10)
REVERT: C  126 ASP cc_start: 0.4257 (p0) cc_final: 0.3793 (t0)
REVERT: D   22 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8478 (p)
REVERT: E   75 PHE cc_start: 0.6741 (OUTLIER) cc_final: 0.6461 (t80)
REVERT: E  126 ASP cc_start: 0.4936 (p0) cc_final: 0.4448 (t0)
REVERT: E  146 TRP cc_start: 0.7540 (OUTLIER) cc_final: 0.6845 (m-10)
REVERT: F  126 ASP cc_start: 0.4193 (p0) cc_final: 0.3785 (t0)
  outliers start: 28
  outliers final: 16
  residues processed: 117
  average time/residue: 0.8748
  time to fit residues: 111.9538
Evaluate side-chains
  127 residues out of total 918 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   75 PHE
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  146 TRP
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  146 TRP
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue  137 THR
Chi-restraints excluded: chain C residue  146 TRP
Chi-restraints excluded: chain D residue   22 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  146 TRP
Chi-restraints excluded: chain D residue  168 LYS
Chi-restraints excluded: chain E residue   75 PHE
Chi-restraints excluded: chain E residue  137 THR
Chi-restraints excluded: chain E residue  146 TRP
Chi-restraints excluded: chain F residue   15 SER
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain F residue   75 PHE
Chi-restraints excluded: chain F residue  137 THR
Chi-restraints excluded: chain F residue  146 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 79 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 23 optimal weight:    9.9990
   chunk 85 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3891 r_free = 0.3891 target = 0.126104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.087235 restraints weight = 12672.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 2.92
r_work: 0.3152 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.2994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9396  Z= 0.143
  Angle     :  0.506   8.785  12804  Z= 0.246
  Chirality :  0.038   0.137   1440
  Planarity :  0.003   0.024   1470
  Dihedral  :  8.667  50.223   1434
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.67 %
    Favored  : 80.83 %
  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:  1.73 (0.26), residues: 1068
  helix:  1.82 (0.18), residues: 822
  sheet:  None (None), residues: 0
  loop : -1.15 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 142 
 HIS   0.002   0.000   HIS D  71 
 PHE   0.015   0.001   PHE F 110 
 TYR   0.018   0.001   TYR F   8 
 ARG   0.002   0.001   ARG A 102 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2601.98 seconds
wall clock time: 46 minutes 57.40 seconds (2817.40 seconds total)