Starting phenix.real_space_refine
on Fri Jun 13 03:07:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9e4r_47518/06_2025/9e4r_47518.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9e4r_47518/06_2025/9e4r_47518.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9e4r_47518/06_2025/9e4r_47518.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9e4r_47518/06_2025/9e4r_47518.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9e4r_47518/06_2025/9e4r_47518.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9e4r_47518/06_2025/9e4r_47518.cif"
  }
  resolution = 3.31
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
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
     Fe      6      7.16       5
     S      60      5.16       5
     C    9384      2.51       5
     N    2502      2.21       5
     O    2832      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14784
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 311, 2421
          Classifications: {'peptide': 311}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 294}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 6.14, per 1000 atoms: 0.42
  Number of scatterers: 14784
  At special positions: 0
  Unit cell: (102.83, 99.19, 95.55, 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)
     Fe      6     26.01
     S      60     16.00
     O    2832      8.00
     N    2502      7.00
     C    9384      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=6, symmetry=0
  Number of additional bonds: simple=6, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.79
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3396

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 30 sheets defined
      39.2% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 16
    Processing helix  chain 'A' and resid 31 through 55
      removed outlier: 3.699A  pdb=" N   GLU A  35 " --> pdb=" O   GLY A  31 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   SER A  43 " --> pdb=" O   ARG A  39 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE A  44 " --> pdb=" O   ALA A  40 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   SER A  46 " --> pdb=" O   CYS A  42 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   SER A  47 " --> pdb=" O   SER A  43 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ARG A  55 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 76
    Processing helix  chain 'A' and resid 111 through 127
      removed outlier: 3.876A  pdb=" N   CYS A 115 " --> pdb=" O   ARG A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 167
    Processing helix  chain 'A' and resid 172 through 176
    Processing helix  chain 'A' and resid 189 through 196
    Processing helix  chain 'A' and resid 197 through 206
    Processing helix  chain 'A' and resid 224 through 229
    Processing helix  chain 'A' and resid 265 through 278
      removed outlier: 4.357A  pdb=" N   ILE A 269 " --> pdb=" O   LYS A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 290
    Processing helix  chain 'A' and resid 304 through 310
    Processing helix  chain 'B' and resid 10 through 16
    Processing helix  chain 'B' and resid 31 through 55
      removed outlier: 3.699A  pdb=" N   GLU B  35 " --> pdb=" O   GLY B  31 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   SER B  43 " --> pdb=" O   ARG B  39 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE B  44 " --> pdb=" O   ALA B  40 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   SER B  46 " --> pdb=" O   CYS B  42 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   SER B  47 " --> pdb=" O   SER B  43 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ARG B  55 " --> pdb=" O   GLY B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 76
    Processing helix  chain 'B' and resid 111 through 127
      removed outlier: 3.876A  pdb=" N   CYS B 115 " --> pdb=" O   ARG B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 167
    Processing helix  chain 'B' and resid 172 through 176
    Processing helix  chain 'B' and resid 189 through 196
    Processing helix  chain 'B' and resid 197 through 206
    Processing helix  chain 'B' and resid 224 through 229
    Processing helix  chain 'B' and resid 265 through 278
      removed outlier: 4.357A  pdb=" N   ILE B 269 " --> pdb=" O   LYS B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 290
    Processing helix  chain 'B' and resid 304 through 310
    Processing helix  chain 'C' and resid 10 through 16
    Processing helix  chain 'C' and resid 31 through 55
      removed outlier: 3.700A  pdb=" N   GLU C  35 " --> pdb=" O   GLY C  31 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   SER C  43 " --> pdb=" O   ARG C  39 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ILE C  44 " --> pdb=" O   ALA C  40 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   SER C  46 " --> pdb=" O   CYS C  42 " (cutoff:3.500A)
      removed outlier: 5.028A  pdb=" N   SER C  47 " --> pdb=" O   SER C  43 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ARG C  55 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 68 through 76
    Processing helix  chain 'C' and resid 111 through 127
      removed outlier: 3.876A  pdb=" N   CYS C 115 " --> pdb=" O   ARG C 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 167
    Processing helix  chain 'C' and resid 172 through 176
    Processing helix  chain 'C' and resid 189 through 196
    Processing helix  chain 'C' and resid 197 through 206
    Processing helix  chain 'C' and resid 224 through 229
    Processing helix  chain 'C' and resid 265 through 278
      removed outlier: 4.356A  pdb=" N   ILE C 269 " --> pdb=" O   LYS C 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 290
    Processing helix  chain 'C' and resid 304 through 310
    Processing helix  chain 'D' and resid 10 through 16
    Processing helix  chain 'D' and resid 31 through 55
      removed outlier: 3.699A  pdb=" N   GLU D  35 " --> pdb=" O   GLY D  31 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   SER D  43 " --> pdb=" O   ARG D  39 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE D  44 " --> pdb=" O   ALA D  40 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   SER D  46 " --> pdb=" O   CYS D  42 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   SER D  47 " --> pdb=" O   SER D  43 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ARG D  55 " --> pdb=" O   GLY D  51 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 76
    Processing helix  chain 'D' and resid 111 through 127
      removed outlier: 3.877A  pdb=" N   CYS D 115 " --> pdb=" O   ARG D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 167
    Processing helix  chain 'D' and resid 172 through 176
    Processing helix  chain 'D' and resid 189 through 196
    Processing helix  chain 'D' and resid 197 through 206
    Processing helix  chain 'D' and resid 224 through 229
    Processing helix  chain 'D' and resid 265 through 278
      removed outlier: 4.357A  pdb=" N   ILE D 269 " --> pdb=" O   LYS D 265 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 290
    Processing helix  chain 'D' and resid 304 through 310
    Processing helix  chain 'E' and resid 10 through 16
    Processing helix  chain 'E' and resid 31 through 55
      removed outlier: 3.699A  pdb=" N   GLU E  35 " --> pdb=" O   GLY E  31 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   SER E  43 " --> pdb=" O   ARG E  39 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ILE E  44 " --> pdb=" O   ALA E  40 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   SER E  46 " --> pdb=" O   CYS E  42 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   SER E  47 " --> pdb=" O   SER E  43 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   ARG E  55 " --> pdb=" O   GLY E  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 68 through 76
    Processing helix  chain 'E' and resid 111 through 127
      removed outlier: 3.876A  pdb=" N   CYS E 115 " --> pdb=" O   ARG E 111 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 159 through 167
    Processing helix  chain 'E' and resid 172 through 176
    Processing helix  chain 'E' and resid 189 through 196
    Processing helix  chain 'E' and resid 197 through 206
    Processing helix  chain 'E' and resid 224 through 229
    Processing helix  chain 'E' and resid 265 through 278
      removed outlier: 4.357A  pdb=" N   ILE E 269 " --> pdb=" O   LYS E 265 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 286 through 290
    Processing helix  chain 'E' and resid 304 through 310
    Processing helix  chain 'F' and resid 10 through 16
    Processing helix  chain 'F' and resid 31 through 55
      removed outlier: 3.699A  pdb=" N   GLU F  35 " --> pdb=" O   GLY F  31 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   SER F  43 " --> pdb=" O   ARG F  39 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE F  44 " --> pdb=" O   ALA F  40 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   SER F  46 " --> pdb=" O   CYS F  42 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   SER F  47 " --> pdb=" O   SER F  43 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ARG F  55 " --> pdb=" O   GLY F  51 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 68 through 76
    Processing helix  chain 'F' and resid 111 through 127
      removed outlier: 3.876A  pdb=" N   CYS F 115 " --> pdb=" O   ARG F 111 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 159 through 167
    Processing helix  chain 'F' and resid 172 through 176
    Processing helix  chain 'F' and resid 189 through 196
    Processing helix  chain 'F' and resid 197 through 206
    Processing helix  chain 'F' and resid 224 through 229
    Processing helix  chain 'F' and resid 265 through 278
      removed outlier: 4.356A  pdb=" N   ILE F 269 " --> pdb=" O   LYS F 265 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 286 through 290
    Processing helix  chain 'F' and resid 304 through 310
    Processing sheet with id=1, first strand: chain 'A' and resid 62 through 67
      removed outlier: 6.599A  pdb=" N   ALA A  21 " --> pdb=" O   GLN A 137 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   GLN A 137 " --> pdb=" O   ALA A  21 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   PHE A  23 " --> pdb=" O   SER A 135 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   SER A 135 " --> pdb=" O   PHE A  23 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   VAL A  25 " --> pdb=" O   VAL A 133 " (cutoff:3.500A)
    Processing sheet with id=2, first strand: chain 'A' and resid 90 through 91
      removed outlier: 3.625A  pdb=" N   ILE A  90 " --> pdb=" O   ALA A  96 " (cutoff:3.500A)
    Processing sheet with id=3, first strand: chain 'A' and resid 241 through 242
    Processing sheet with id=4, first strand: chain 'A' and resid 241 through 242
      removed outlier: 5.177A  pdb=" N   PHE A 255 " --> pdb=" O   HIS A 188 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   THR A 296 " --> pdb=" O   LYS A 185 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   LEU A 187 " --> pdb=" O   ALA A 294 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   ALA A 294 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
    Processing sheet with id=5, first strand: chain 'A' and resid 232 through 233
    Processing sheet with id=6, first strand: chain 'B' and resid 62 through 67
      removed outlier: 6.600A  pdb=" N   ALA B  21 " --> pdb=" O   GLN B 137 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   GLN B 137 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   PHE B  23 " --> pdb=" O   SER B 135 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   SER B 135 " --> pdb=" O   PHE B  23 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   VAL B  25 " --> pdb=" O   VAL B 133 " (cutoff:3.500A)
    Processing sheet with id=7, first strand: chain 'B' and resid 90 through 91
      removed outlier: 3.625A  pdb=" N   ILE B  90 " --> pdb=" O   ALA B  96 " (cutoff:3.500A)
    Processing sheet with id=8, first strand: chain 'B' and resid 241 through 242
    Processing sheet with id=9, first strand: chain 'B' and resid 241 through 242
      removed outlier: 5.176A  pdb=" N   PHE B 255 " --> pdb=" O   HIS B 188 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   THR B 296 " --> pdb=" O   LYS B 185 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   LEU B 187 " --> pdb=" O   ALA B 294 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   ALA B 294 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
    Processing sheet with id=10, first strand: chain 'B' and resid 232 through 233
    Processing sheet with id=11, first strand: chain 'C' and resid 62 through 67
      removed outlier: 6.599A  pdb=" N   ALA C  21 " --> pdb=" O   GLN C 137 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   GLN C 137 " --> pdb=" O   ALA C  21 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   PHE C  23 " --> pdb=" O   SER C 135 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   SER C 135 " --> pdb=" O   PHE C  23 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   VAL C  25 " --> pdb=" O   VAL C 133 " (cutoff:3.500A)
    Processing sheet with id=12, first strand: chain 'C' and resid 90 through 91
      removed outlier: 3.624A  pdb=" N   ILE C  90 " --> pdb=" O   ALA C  96 " (cutoff:3.500A)
    Processing sheet with id=13, first strand: chain 'C' and resid 241 through 242
    Processing sheet with id=14, first strand: chain 'C' and resid 241 through 242
      removed outlier: 5.176A  pdb=" N   PHE C 255 " --> pdb=" O   HIS C 188 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   THR C 296 " --> pdb=" O   LYS C 185 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   LEU C 187 " --> pdb=" O   ALA C 294 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   ALA C 294 " --> pdb=" O   LEU C 187 " (cutoff:3.500A)
    Processing sheet with id=15, first strand: chain 'C' and resid 232 through 233
    Processing sheet with id=16, first strand: chain 'D' and resid 62 through 67
      removed outlier: 6.600A  pdb=" N   ALA D  21 " --> pdb=" O   GLN D 137 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   GLN D 137 " --> pdb=" O   ALA D  21 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   PHE D  23 " --> pdb=" O   SER D 135 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   SER D 135 " --> pdb=" O   PHE D  23 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   VAL D  25 " --> pdb=" O   VAL D 133 " (cutoff:3.500A)
    Processing sheet with id=17, first strand: chain 'D' and resid 90 through 91
      removed outlier: 3.625A  pdb=" N   ILE D  90 " --> pdb=" O   ALA D  96 " (cutoff:3.500A)
    Processing sheet with id=18, first strand: chain 'D' and resid 241 through 242
    Processing sheet with id=19, first strand: chain 'D' and resid 241 through 242
      removed outlier: 5.177A  pdb=" N   PHE D 255 " --> pdb=" O   HIS D 188 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   THR D 296 " --> pdb=" O   LYS D 185 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   LEU D 187 " --> pdb=" O   ALA D 294 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   ALA D 294 " --> pdb=" O   LEU D 187 " (cutoff:3.500A)
    Processing sheet with id=20, first strand: chain 'D' and resid 232 through 233
    Processing sheet with id=21, first strand: chain 'E' and resid 62 through 67
      removed outlier: 6.599A  pdb=" N   ALA E  21 " --> pdb=" O   GLN E 137 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   GLN E 137 " --> pdb=" O   ALA E  21 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   PHE E  23 " --> pdb=" O   SER E 135 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   SER E 135 " --> pdb=" O   PHE E  23 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   VAL E  25 " --> pdb=" O   VAL E 133 " (cutoff:3.500A)
    Processing sheet with id=22, first strand: chain 'E' and resid 90 through 91
      removed outlier: 3.625A  pdb=" N   ILE E  90 " --> pdb=" O   ALA E  96 " (cutoff:3.500A)
    Processing sheet with id=23, first strand: chain 'E' and resid 241 through 242
    Processing sheet with id=24, first strand: chain 'E' and resid 241 through 242
      removed outlier: 5.177A  pdb=" N   PHE E 255 " --> pdb=" O   HIS E 188 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   THR E 296 " --> pdb=" O   LYS E 185 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   LEU E 187 " --> pdb=" O   ALA E 294 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   ALA E 294 " --> pdb=" O   LEU E 187 " (cutoff:3.500A)
    Processing sheet with id=25, first strand: chain 'E' and resid 232 through 233
    Processing sheet with id=26, first strand: chain 'F' and resid 62 through 67
      removed outlier: 6.599A  pdb=" N   ALA F  21 " --> pdb=" O   GLN F 137 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   GLN F 137 " --> pdb=" O   ALA F  21 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   PHE F  23 " --> pdb=" O   SER F 135 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   SER F 135 " --> pdb=" O   PHE F  23 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   VAL F  25 " --> pdb=" O   VAL F 133 " (cutoff:3.500A)
    Processing sheet with id=27, first strand: chain 'F' and resid 90 through 91
      removed outlier: 3.623A  pdb=" N   ILE F  90 " --> pdb=" O   ALA F  96 " (cutoff:3.500A)
    Processing sheet with id=28, first strand: chain 'F' and resid 241 through 242
    Processing sheet with id=29, first strand: chain 'F' and resid 241 through 242
      removed outlier: 5.176A  pdb=" N   PHE F 255 " --> pdb=" O   HIS F 188 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   THR F 296 " --> pdb=" O   LYS F 185 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   LEU F 187 " --> pdb=" O   ALA F 294 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   ALA F 294 " --> pdb=" O   LEU F 187 " (cutoff:3.500A)
    Processing sheet with id=30, first strand: chain 'F' and resid 232 through 233

    684 hydrogen bonds defined for protein.
    1818 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: 6.51

  Time building geometry restraints manager: 4.46 seconds

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

  Histogram of bond lengths:
        1.23 -     1.39: 6282
        1.39 -     1.55: 8736
        1.55 -     1.72: 0
        1.72 -     1.88: 96
        1.88 -     2.04: 24
  Bond restraints: 15138
  Sorted by residual:
  bond pdb=" CA  ASP A 212 "
       pdb=" C   ASP A 212 "
    ideal  model  delta    sigma   weight residual
    1.525  1.542 -0.017 1.63e-02 3.76e+03 1.15e+00
  bond pdb=" CA  ASP D 212 "
       pdb=" C   ASP D 212 "
    ideal  model  delta    sigma   weight residual
    1.525  1.542 -0.017 1.63e-02 3.76e+03 1.15e+00
  bond pdb=" CA  ASP C 212 "
       pdb=" C   ASP C 212 "
    ideal  model  delta    sigma   weight residual
    1.525  1.542 -0.017 1.63e-02 3.76e+03 1.12e+00
  bond pdb=" CA  ASP F 212 "
       pdb=" C   ASP F 212 "
    ideal  model  delta    sigma   weight residual
    1.525  1.542 -0.017 1.63e-02 3.76e+03 1.12e+00
  bond pdb=" CA  ASP B 212 "
       pdb=" C   ASP B 212 "
    ideal  model  delta    sigma   weight residual
    1.525  1.542 -0.017 1.63e-02 3.76e+03 1.11e+00
  ... (remaining 15133 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.08: 19652
        1.08 -     2.17: 675
        2.17 -     3.25: 173
        3.25 -     4.33: 68
        4.33 -     5.42: 42
  Bond angle restraints: 20610
  Sorted by residual:
  angle pdb=" C   ARG B  55 "
        pdb=" CA  ARG B  55 "
        pdb=" CB  ARG B  55 "
      ideal   model   delta    sigma   weight residual
     110.67  105.25    5.42 1.92e+00 2.71e-01 7.96e+00
  angle pdb=" C   ARG E  55 "
        pdb=" CA  ARG E  55 "
        pdb=" CB  ARG E  55 "
      ideal   model   delta    sigma   weight residual
     110.67  105.26    5.41 1.92e+00 2.71e-01 7.94e+00
  angle pdb=" C   ARG C  55 "
        pdb=" CA  ARG C  55 "
        pdb=" CB  ARG C  55 "
      ideal   model   delta    sigma   weight residual
     110.67  105.26    5.41 1.92e+00 2.71e-01 7.93e+00
  angle pdb=" C   ARG D  55 "
        pdb=" CA  ARG D  55 "
        pdb=" CB  ARG D  55 "
      ideal   model   delta    sigma   weight residual
     110.67  105.27    5.40 1.92e+00 2.71e-01 7.90e+00
  angle pdb=" C   ARG A  55 "
        pdb=" CA  ARG A  55 "
        pdb=" CB  ARG A  55 "
      ideal   model   delta    sigma   weight residual
     110.67  105.28    5.39 1.92e+00 2.71e-01 7.89e+00
  ... (remaining 20605 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 7945
       17.82 -    35.65: 737
       35.65 -    53.47: 168
       53.47 -    71.30: 24
       71.30 -    89.12: 30
  Dihedral angle restraints: 8904
    sinusoidal: 3594
      harmonic: 5310
  Sorted by residual:
  dihedral pdb=" C2A HEM F 401 "
           pdb=" CAA HEM F 401 "
           pdb=" CBA HEM F 401 "
           pdb=" CGA HEM F 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00  -90.88  -89.12     2      2.00e+01 2.50e-03 1.20e+01
  dihedral pdb=" C2A HEM C 401 "
           pdb=" CAA HEM C 401 "
           pdb=" CBA HEM C 401 "
           pdb=" CGA HEM C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  -90.89  -89.11     2      2.00e+01 2.50e-03 1.20e+01
  dihedral pdb=" C2A HEM B 401 "
           pdb=" CAA HEM B 401 "
           pdb=" CBA HEM B 401 "
           pdb=" CGA HEM B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00  -90.90  -89.10     2      2.00e+01 2.50e-03 1.20e+01
  ... (remaining 8901 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1385
       0.032 -    0.064: 540
       0.064 -    0.096: 169
       0.096 -    0.128: 108
       0.128 -    0.161: 12
  Chirality restraints: 2214
  Sorted by residual:
  chirality pdb=" CB  THR D 166 "
            pdb=" CA  THR D 166 "
            pdb=" OG1 THR D 166 "
            pdb=" CG2 THR D 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.45e-01
  chirality pdb=" CB  THR B 166 "
            pdb=" CA  THR B 166 "
            pdb=" OG1 THR B 166 "
            pdb=" CG2 THR B 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.32e-01
  chirality pdb=" CB  THR F 166 "
            pdb=" CA  THR F 166 "
            pdb=" OG1 THR F 166 "
            pdb=" CG2 THR F 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.29e-01
  ... (remaining 2211 not shown)

  Planarity restraints: 2712
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B 212 "    0.010 2.00e-02 2.50e+03   2.02e-02 4.07e+00
        pdb=" CG  ASP B 212 "   -0.035 2.00e-02 2.50e+03
        pdb=" OD1 ASP B 212 "    0.013 2.00e-02 2.50e+03
        pdb=" OD2 ASP B 212 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP E 212 "   -0.010 2.00e-02 2.50e+03   2.01e-02 4.03e+00
        pdb=" CG  ASP E 212 "    0.035 2.00e-02 2.50e+03
        pdb=" OD1 ASP E 212 "   -0.013 2.00e-02 2.50e+03
        pdb=" OD2 ASP E 212 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP F 212 "    0.010 2.00e-02 2.50e+03   2.01e-02 4.03e+00
        pdb=" CG  ASP F 212 "   -0.035 2.00e-02 2.50e+03
        pdb=" OD1 ASP F 212 "    0.013 2.00e-02 2.50e+03
        pdb=" OD2 ASP F 212 "    0.012 2.00e-02 2.50e+03
  ... (remaining 2709 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 5300
        2.86 -     3.37: 13370
        3.37 -     3.88: 24789
        3.88 -     4.39: 27576
        4.39 -     4.90: 49289
  Nonbonded interactions: 120324
  Sorted by model distance:
  nonbonded pdb=" O   ASP D 164 "
            pdb=" NH1 ARG D 264 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" O   ASP C 164 "
            pdb=" NH1 ARG C 264 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" O   ASP A 164 "
            pdb=" NH1 ARG A 264 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" O   ASP E 164 "
            pdb=" NH1 ARG E 264 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" O   ASP B 164 "
            pdb=" NH1 ARG B 264 "
     model   vdw
     2.353 3.120
  ... (remaining 120319 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.620
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     35.890
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
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      :  0.003   0.045  15144  Z= 0.114
  Angle     :  0.570   5.417  20610  Z= 0.293
  Chirality :  0.043   0.161   2214
  Planarity :  0.004   0.046   2712
  Dihedral  : 15.255  89.121   5508
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 13.76 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  0.28 (0.20), residues: 1854
  helix:  1.09 (0.22), residues: 630
  sheet:  0.63 (0.24), residues: 456
  loop : -0.81 (0.22), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP F 193 
 HIS   0.001   0.000   HIS E 106 
 PHE   0.006   0.001   PHE C 116 
 TYR   0.004   0.001   TYR F 223 
 ARG   0.003   0.000   ARG C  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11480 (  672)
  hydrogen bonds       : angle       5.46445 ( 1818)
  covalent geometry    : bond        0.00286 (15138)
  covalent geometry    : angle       0.57040 (20610)
  Misc. bond           : bond        0.02953 (    6)

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

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

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 196
  time to evaluate  : 1.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 ASP cc_start: 0.6404 (t0) cc_final: 0.5469 (p0)
REVERT: A  295 ILE cc_start: 0.8804 (pt) cc_final: 0.8546 (pt)
REVERT: B  144 ASP cc_start: 0.8087 (m-30) cc_final: 0.7858 (m-30)
REVERT: B  172 ASP cc_start: 0.6051 (t0) cc_final: 0.5149 (p0)
REVERT: C  172 ASP cc_start: 0.6214 (t0) cc_final: 0.5348 (p0)
REVERT: C  212 ASP cc_start: 0.8608 (t0) cc_final: 0.8247 (t0)
REVERT: D  172 ASP cc_start: 0.6460 (t0) cc_final: 0.5475 (p0)
REVERT: D  295 ILE cc_start: 0.8797 (pt) cc_final: 0.8544 (pt)
REVERT: E  144 ASP cc_start: 0.8112 (m-30) cc_final: 0.7881 (m-30)
REVERT: E  172 ASP cc_start: 0.6038 (t0) cc_final: 0.5142 (p0)
REVERT: F  172 ASP cc_start: 0.6162 (t0) cc_final: 0.5354 (p0)
REVERT: F  212 ASP cc_start: 0.8610 (t0) cc_final: 0.8250 (t0)
  outliers start: 4
  outliers final: 0
  residues processed: 200
  average time/residue: 0.3380
  time to fit residues: 97.4099
Evaluate side-chains
  175 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 1.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 157 optimal weight:    5.9990
   chunk 140 optimal weight:    0.0980
   chunk 78 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   chunk 95 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 145 optimal weight:    6.9990
   chunk 56 optimal weight:    7.9990
   chunk 88 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   chunk 168 optimal weight:    1.9990
   overall best weight:    2.2188

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.125143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.103450 restraints weight = 20510.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 2.52
r_work: 0.3093 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.1183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.148  15144  Z= 0.174
  Angle     :  0.547   4.961  20610  Z= 0.276
  Chirality :  0.043   0.128   2214
  Planarity :  0.004   0.034   2712
  Dihedral  :  8.726  85.565   2082
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 14.27 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  0.54 (0.20), residues: 1854
  helix:  1.38 (0.22), residues: 630
  sheet:  0.63 (0.24), residues: 462
  loop : -0.64 (0.22), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 193 
 HIS   0.004   0.001   HIS C 225 
 PHE   0.016   0.001   PHE B  54 
 TYR   0.010   0.001   TYR F 186 
 ARG   0.002   0.000   ARG B 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03327 (  672)
  hydrogen bonds       : angle       4.76390 ( 1818)
  covalent geometry    : bond        0.00461 (15138)
  covalent geometry    : angle       0.54709 (20610)
  Misc. bond           : bond        0.13837 (    6)

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

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

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 180
  time to evaluate  : 1.623 
Fit side-chains
REVERT: A  172 ASP cc_start: 0.6654 (t0) cc_final: 0.5532 (p0)
REVERT: A  173 MET cc_start: 0.7354 (tpt) cc_final: 0.7047 (tpt)
REVERT: A  200 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7917 (tp40)
REVERT: A  212 ASP cc_start: 0.8635 (t0) cc_final: 0.8145 (t0)
REVERT: B  212 ASP cc_start: 0.8713 (t0) cc_final: 0.8438 (t0)
REVERT: B  262 TYR cc_start: 0.9088 (m-80) cc_final: 0.8883 (m-80)
REVERT: C  212 ASP cc_start: 0.8796 (t0) cc_final: 0.8472 (t0)
REVERT: D  172 ASP cc_start: 0.6656 (t0) cc_final: 0.5523 (p0)
REVERT: D  173 MET cc_start: 0.7420 (tpt) cc_final: 0.7122 (tpt)
REVERT: D  200 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7951 (tp40)
REVERT: D  212 ASP cc_start: 0.8629 (t0) cc_final: 0.8136 (t0)
REVERT: E  212 ASP cc_start: 0.8721 (t0) cc_final: 0.8441 (t0)
REVERT: E  262 TYR cc_start: 0.9088 (m-80) cc_final: 0.8881 (m-80)
REVERT: F  212 ASP cc_start: 0.8806 (t0) cc_final: 0.8478 (t0)
  outliers start: 11
  outliers final: 8
  residues processed: 191
  average time/residue: 0.3319
  time to fit residues: 90.4130
Evaluate side-chains
  153 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 145
  time to evaluate  : 1.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain C residue  134 ASP
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue  134 ASP
Chi-restraints excluded: chain E residue  284 ASN
Chi-restraints excluded: chain F residue  134 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 132 optimal weight:    0.9990
   chunk 124 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 159 optimal weight:    7.9990
   chunk 141 optimal weight:    6.9990
   chunk 4 optimal weight:    4.9990
   chunk 160 optimal weight:    5.9990
   chunk 167 optimal weight:    9.9990
   chunk 84 optimal weight:   20.0000
   chunk 28 optimal weight:    5.9990
   overall best weight:    3.7988

-------------------------------------------------------------------------------
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 = 0.3444 r_free = 0.3444 target = 0.120105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.098306 restraints weight = 20850.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 2.52
r_work: 0.3021 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.232  15144  Z= 0.267
  Angle     :  0.608   4.901  20610  Z= 0.309
  Chirality :  0.045   0.148   2214
  Planarity :  0.004   0.029   2712
  Dihedral  :  8.862  82.608   2082
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 12.94 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.19), residues: 1854
  helix:  0.98 (0.22), residues: 630
  sheet:  0.59 (0.25), residues: 438
  loop : -0.75 (0.21), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  72 
 HIS   0.005   0.001   HIS C 225 
 PHE   0.021   0.002   PHE A  54 
 TYR   0.012   0.002   TYR C 180 
 ARG   0.003   0.000   ARG B 242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04164 (  672)
  hydrogen bonds       : angle       5.03073 ( 1818)
  covalent geometry    : bond        0.00691 (15138)
  covalent geometry    : angle       0.60755 (20610)
  Misc. bond           : bond        0.21875 (    6)

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

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

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 157
  time to evaluate  : 1.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7618 (mp)
REVERT: A  200 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8192 (tp40)
REVERT: A  212 ASP cc_start: 0.8837 (t0) cc_final: 0.8306 (t0)
REVERT: B   16 ARG cc_start: 0.7750 (mmm-85) cc_final: 0.7291 (mtp-110)
REVERT: B  212 ASP cc_start: 0.8866 (t0) cc_final: 0.8555 (t0)
REVERT: C  212 ASP cc_start: 0.8943 (t0) cc_final: 0.8584 (t0)
REVERT: D   48 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7659 (mp)
REVERT: D  200 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8209 (tp40)
REVERT: D  212 ASP cc_start: 0.8850 (t0) cc_final: 0.8328 (t0)
REVERT: E   16 ARG cc_start: 0.7746 (mmm-85) cc_final: 0.7279 (mtp-110)
REVERT: E  212 ASP cc_start: 0.8859 (t0) cc_final: 0.8548 (t0)
REVERT: F  212 ASP cc_start: 0.8939 (t0) cc_final: 0.8585 (t0)
  outliers start: 56
  outliers final: 34
  residues processed: 209
  average time/residue: 0.3027
  time to fit residues: 90.0596
Evaluate side-chains
  180 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 144
  time to evaluate  : 1.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   73 GLU
Chi-restraints excluded: chain C residue  134 ASP
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  284 ASN
Chi-restraints excluded: chain C residue  289 LEU
Chi-restraints excluded: chain C residue  298 THR
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   48 LEU
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  298 THR
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  134 ASP
Chi-restraints excluded: chain E residue  158 VAL
Chi-restraints excluded: chain E residue  284 ASN
Chi-restraints excluded: chain E residue  298 THR
Chi-restraints excluded: chain F residue   18 THR
Chi-restraints excluded: chain F residue   73 GLU
Chi-restraints excluded: chain F residue  134 ASP
Chi-restraints excluded: chain F residue  158 VAL
Chi-restraints excluded: chain F residue  284 ASN
Chi-restraints excluded: chain F residue  289 LEU
Chi-restraints excluded: chain F residue  298 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 123 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 106 optimal weight:    3.9990
   chunk 114 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 56 optimal weight:    4.9990
   chunk 111 optimal weight:    0.6980
   chunk 177 optimal weight:   50.0000
   chunk 46 optimal weight:    9.9990
   chunk 136 optimal weight:    2.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 137 GLN
D 137 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.121743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.100162 restraints weight = 20698.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 2.47
r_work: 0.3048 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.177  15144  Z= 0.178
  Angle     :  0.550   5.812  20610  Z= 0.277
  Chirality :  0.043   0.132   2214
  Planarity :  0.004   0.041   2712
  Dihedral  :  8.823  83.582   2082
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.65 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  0.26 (0.20), residues: 1854
  helix:  1.09 (0.22), residues: 630
  sheet:  0.47 (0.24), residues: 462
  loop : -0.74 (0.21), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C  72 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.016   0.001   PHE B  54 
 TYR   0.008   0.001   TYR A 186 
 ARG   0.006   0.000   ARG C  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03405 (  672)
  hydrogen bonds       : angle       4.76591 ( 1818)
  covalent geometry    : bond        0.00470 (15138)
  covalent geometry    : angle       0.54991 (20610)
  Misc. bond           : bond        0.16557 (    6)

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

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

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 165
  time to evaluate  : 1.748 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  212 ASP cc_start: 0.8829 (t0) cc_final: 0.8278 (t0)
REVERT: B  212 ASP cc_start: 0.8809 (t0) cc_final: 0.8473 (t0)
REVERT: C  134 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7677 (p0)
REVERT: C  212 ASP cc_start: 0.8860 (t0) cc_final: 0.8537 (t0)
REVERT: D  212 ASP cc_start: 0.8834 (t0) cc_final: 0.8287 (t0)
REVERT: D  216 ARG cc_start: 0.7950 (mtm-85) cc_final: 0.7540 (mtp-110)
REVERT: E  212 ASP cc_start: 0.8824 (t0) cc_final: 0.8488 (t0)
REVERT: F  134 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7682 (p0)
REVERT: F  212 ASP cc_start: 0.8885 (t0) cc_final: 0.8556 (t0)
  outliers start: 39
  outliers final: 28
  residues processed: 204
  average time/residue: 0.3200
  time to fit residues: 92.6173
Evaluate side-chains
  171 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 141
  time to evaluate  : 2.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue  134 ASP
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  298 THR
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   73 GLU
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  298 THR
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  134 ASP
Chi-restraints excluded: chain E residue  230 SER
Chi-restraints excluded: chain E residue  298 THR
Chi-restraints excluded: chain F residue   18 THR
Chi-restraints excluded: chain F residue  104 LEU
Chi-restraints excluded: chain F residue  134 ASP
Chi-restraints excluded: chain F residue  158 VAL
Chi-restraints excluded: chain F residue  298 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 20 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   chunk 135 optimal weight:    0.7980
   chunk 34 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 129 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 155 optimal weight:   10.0000
   chunk 181 optimal weight:    5.9990
   chunk 185 optimal weight:    6.9990
   overall best weight:    3.5588

-------------------------------------------------------------------------------
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 = 0.3424 r_free = 0.3424 target = 0.118307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.096777 restraints weight = 21049.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 2.50
r_work: 0.3012 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.215  15144  Z= 0.252
  Angle     :  0.589   4.906  20610  Z= 0.298
  Chirality :  0.044   0.147   2214
  Planarity :  0.004   0.035   2712
  Dihedral  :  8.840  82.441   2082
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 15.97 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  0.09 (0.19), residues: 1854
  helix:  0.92 (0.22), residues: 630
  sheet:  0.46 (0.25), residues: 438
  loop : -0.83 (0.20), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP F  72 
 HIS   0.004   0.001   HIS F 225 
 PHE   0.016   0.002   PHE A  54 
 TYR   0.012   0.002   TYR B 180 
 ARG   0.006   0.000   ARG C  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03862 (  672)
  hydrogen bonds       : angle       4.92071 ( 1818)
  covalent geometry    : bond        0.00657 (15138)
  covalent geometry    : angle       0.58865 (20610)
  Misc. bond           : bond        0.20693 (    6)

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

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

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 147
  time to evaluate  : 2.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8678 (tp)
REVERT: A  212 ASP cc_start: 0.8845 (t0) cc_final: 0.8291 (t0)
REVERT: A  216 ARG cc_start: 0.7937 (mtm-85) cc_final: 0.7662 (mtp85)
REVERT: A  284 ASN cc_start: 0.9155 (t0) cc_final: 0.8943 (t0)
REVERT: B  212 ASP cc_start: 0.8818 (t0) cc_final: 0.8434 (t0)
REVERT: C  134 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7679 (p0)
REVERT: C  212 ASP cc_start: 0.8908 (t0) cc_final: 0.8576 (t0)
REVERT: D   48 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7593 (mp)
REVERT: D  210 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8683 (tp)
REVERT: D  212 ASP cc_start: 0.8858 (t0) cc_final: 0.8312 (t0)
REVERT: D  216 ARG cc_start: 0.7947 (mtm-85) cc_final: 0.7671 (mtp85)
REVERT: E  212 ASP cc_start: 0.8828 (t0) cc_final: 0.8443 (t0)
REVERT: F  134 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7677 (p0)
REVERT: F  212 ASP cc_start: 0.8932 (t0) cc_final: 0.8586 (t0)
  outliers start: 57
  outliers final: 46
  residues processed: 204
  average time/residue: 0.3398
  time to fit residues: 98.5104
Evaluate side-chains
  188 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 137
  time to evaluate  : 1.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   73 GLU
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  298 THR
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   73 GLU
Chi-restraints excluded: chain C residue  134 ASP
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  227 VAL
Chi-restraints excluded: chain C residue  298 THR
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   48 LEU
Chi-restraints excluded: chain D residue   73 GLU
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  210 LEU
Chi-restraints excluded: chain D residue  227 VAL
Chi-restraints excluded: chain D residue  298 THR
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue  134 ASP
Chi-restraints excluded: chain E residue  227 VAL
Chi-restraints excluded: chain E residue  230 SER
Chi-restraints excluded: chain E residue  288 ILE
Chi-restraints excluded: chain E residue  298 THR
Chi-restraints excluded: chain F residue   17 LEU
Chi-restraints excluded: chain F residue   18 THR
Chi-restraints excluded: chain F residue   73 GLU
Chi-restraints excluded: chain F residue  104 LEU
Chi-restraints excluded: chain F residue  134 ASP
Chi-restraints excluded: chain F residue  158 VAL
Chi-restraints excluded: chain F residue  210 LEU
Chi-restraints excluded: chain F residue  227 VAL
Chi-restraints excluded: chain F residue  298 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 94 optimal weight:    6.9990
   chunk 89 optimal weight:    6.9990
   chunk 102 optimal weight:    5.9990
   chunk 156 optimal weight:    0.7980
   chunk 101 optimal weight:    0.6980
   chunk 83 optimal weight:    8.9990
   chunk 75 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 117 optimal weight:    0.8980
   chunk 179 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3513 r_free = 0.3513 target = 0.124879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.103217 restraints weight = 20544.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.48
r_work: 0.3088 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.103  15144  Z= 0.100
  Angle     :  0.501   5.050  20610  Z= 0.245
  Chirality :  0.041   0.127   2214
  Planarity :  0.003   0.027   2712
  Dihedral  :  8.771  86.299   2082
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 17.11 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  0.45 (0.20), residues: 1854
  helix:  1.35 (0.23), residues: 636
  sheet:  0.39 (0.24), residues: 462
  loop : -0.61 (0.21), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP A 193 
 HIS   0.001   0.000   HIS C 225 
 PHE   0.012   0.001   PHE E  54 
 TYR   0.009   0.001   TYR E 223 
 ARG   0.003   0.000   ARG B  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02520 (  672)
  hydrogen bonds       : angle       4.43678 ( 1818)
  covalent geometry    : bond        0.00271 (15138)
  covalent geometry    : angle       0.50127 (20610)
  Misc. bond           : bond        0.09297 (    6)

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

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

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 180
  time to evaluate  : 1.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8679 (tp)
REVERT: A  212 ASP cc_start: 0.8797 (t0) cc_final: 0.8200 (t0)
REVERT: B  212 ASP cc_start: 0.8751 (t0) cc_final: 0.8391 (t0)
REVERT: C   88 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7516 (mtm-85)
REVERT: C  134 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7763 (p0)
REVERT: C  212 ASP cc_start: 0.8834 (t0) cc_final: 0.8466 (t0)
REVERT: D  210 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8683 (tp)
REVERT: D  212 ASP cc_start: 0.8806 (t0) cc_final: 0.8212 (t0)
REVERT: E  212 ASP cc_start: 0.8748 (t0) cc_final: 0.8390 (t0)
REVERT: F   88 ARG cc_start: 0.8027 (mtp85) cc_final: 0.7524 (mtm-85)
REVERT: F  134 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7776 (p0)
REVERT: F  212 ASP cc_start: 0.8847 (t0) cc_final: 0.8471 (t0)
  outliers start: 43
  outliers final: 30
  residues processed: 223
  average time/residue: 0.3391
  time to fit residues: 105.4824
Evaluate side-chains
  202 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 168
  time to evaluate  : 2.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  134 ASP
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  298 THR
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  210 LEU
Chi-restraints excluded: chain D residue  298 THR
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  134 ASP
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  230 SER
Chi-restraints excluded: chain F residue   18 THR
Chi-restraints excluded: chain F residue  104 LEU
Chi-restraints excluded: chain F residue  134 ASP
Chi-restraints excluded: chain F residue  158 VAL
Chi-restraints excluded: chain F residue  210 LEU
Chi-restraints excluded: chain F residue  298 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 86 optimal weight:    4.9990
   chunk 119 optimal weight:    6.9990
   chunk 14 optimal weight:    0.6980
   chunk 78 optimal weight:    6.9990
   chunk 135 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 161 optimal weight:    8.9990
   chunk 40 optimal weight:    0.0980
   chunk 79 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0050
   overall best weight:    0.5396

-------------------------------------------------------------------------------
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 = 0.3535 r_free = 0.3535 target = 0.126733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.105329 restraints weight = 20580.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.47
r_work: 0.3124 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080  15144  Z= 0.091
  Angle     :  0.488   5.029  20610  Z= 0.238
  Chirality :  0.041   0.130   2214
  Planarity :  0.003   0.026   2712
  Dihedral  :  8.747  88.268   2082
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.49 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  0.65 (0.20), residues: 1854
  helix:  1.55 (0.22), residues: 636
  sheet:  0.41 (0.23), residues: 462
  loop : -0.44 (0.22), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 193 
 HIS   0.001   0.000   HIS B 106 
 PHE   0.011   0.001   PHE C  54 
 TYR   0.008   0.001   TYR E 223 
 ARG   0.003   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02191 (  672)
  hydrogen bonds       : angle       4.25174 ( 1818)
  covalent geometry    : bond        0.00249 (15138)
  covalent geometry    : angle       0.48761 (20610)
  Misc. bond           : bond        0.07208 (    6)

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

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

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 196
  time to evaluate  : 1.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 ARG cc_start: 0.7749 (mmm-85) cc_final: 0.7147 (mtp-110)
REVERT: A   88 ARG cc_start: 0.7788 (mtp85) cc_final: 0.7315 (mtm-85)
REVERT: A  134 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7745 (p0)
REVERT: A  212 ASP cc_start: 0.8741 (t0) cc_final: 0.8383 (t0)
REVERT: B   57 SER cc_start: 0.8324 (m) cc_final: 0.7814 (p)
REVERT: B  212 ASP cc_start: 0.8691 (t0) cc_final: 0.8289 (t0)
REVERT: C   57 SER cc_start: 0.8164 (m) cc_final: 0.7882 (p)
REVERT: C   88 ARG cc_start: 0.7994 (mtp85) cc_final: 0.7504 (mtm-85)
REVERT: C  134 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7827 (p0)
REVERT: C  212 ASP cc_start: 0.8763 (t0) cc_final: 0.8373 (t0)
REVERT: D   16 ARG cc_start: 0.7817 (mmm-85) cc_final: 0.7188 (mtp-110)
REVERT: D   88 ARG cc_start: 0.7808 (mtp85) cc_final: 0.7303 (mtm-85)
REVERT: D  134 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7742 (p0)
REVERT: D  212 ASP cc_start: 0.8732 (t0) cc_final: 0.8380 (t0)
REVERT: E   16 ARG cc_start: 0.7826 (mmm-85) cc_final: 0.7431 (mtp-110)
REVERT: E   44 ILE cc_start: 0.8589 (tp) cc_final: 0.8239 (pt)
REVERT: E   57 SER cc_start: 0.8299 (m) cc_final: 0.7798 (p)
REVERT: E  212 ASP cc_start: 0.8723 (t0) cc_final: 0.8312 (t0)
REVERT: F   57 SER cc_start: 0.8114 (m) cc_final: 0.7871 (p)
REVERT: F   88 ARG cc_start: 0.8021 (mtp85) cc_final: 0.7527 (mtm-85)
REVERT: F  134 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7833 (p0)
REVERT: F  212 ASP cc_start: 0.8796 (t0) cc_final: 0.8413 (t0)
  outliers start: 41
  outliers final: 26
  residues processed: 232
  average time/residue: 0.3259
  time to fit residues: 104.5142
Evaluate side-chains
  211 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 181
  time to evaluate  : 1.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  134 ASP
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  298 THR
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  298 THR
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  230 SER
Chi-restraints excluded: chain F residue   18 THR
Chi-restraints excluded: chain F residue  104 LEU
Chi-restraints excluded: chain F residue  134 ASP
Chi-restraints excluded: chain F residue  158 VAL
Chi-restraints excluded: chain F residue  210 LEU
Chi-restraints excluded: chain F residue  298 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 99 optimal weight:   10.0000
   chunk 171 optimal weight:   10.0000
   chunk 67 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0980
   chunk 105 optimal weight:    9.9990
   chunk 166 optimal weight:    6.9990
   chunk 142 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 164 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 159 optimal weight:    2.9990
   overall best weight:    3.4188

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

Flipped N/Q/H residues before XYZ refinement:
A  95 HIS
D 275 ASN
E  91 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.120873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.098656 restraints weight = 20998.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.55
r_work: 0.3026 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.194  15144  Z= 0.242
  Angle     :  0.588   4.872  20610  Z= 0.295
  Chirality :  0.044   0.151   2214
  Planarity :  0.004   0.028   2712
  Dihedral  :  8.798  85.936   2082
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.80 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  0.33 (0.19), residues: 1854
  helix:  1.18 (0.22), residues: 636
  sheet:  0.31 (0.24), residues: 438
  loop : -0.56 (0.21), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E 193 
 HIS   0.005   0.001   HIS C 225 
 PHE   0.013   0.002   PHE B  54 
 TYR   0.011   0.002   TYR A 186 
 ARG   0.006   0.000   ARG B  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03628 (  672)
  hydrogen bonds       : angle       4.72188 ( 1818)
  covalent geometry    : bond        0.00632 (15138)
  covalent geometry    : angle       0.58776 (20610)
  Misc. bond           : bond        0.18691 (    6)

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

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

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 169
  time to evaluate  : 1.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8630 (tp)
REVERT: A  212 ASP cc_start: 0.8667 (t0) cc_final: 0.8064 (t0)
REVERT: B   44 ILE cc_start: 0.8530 (tp) cc_final: 0.8213 (pt)
REVERT: B   57 SER cc_start: 0.8416 (m) cc_final: 0.7950 (p)
REVERT: B  212 ASP cc_start: 0.8666 (t0) cc_final: 0.8239 (t0)
REVERT: C   57 SER cc_start: 0.8301 (m) cc_final: 0.7929 (p)
REVERT: C  212 ASP cc_start: 0.8666 (t0) cc_final: 0.8240 (t0)
REVERT: D  210 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8623 (tp)
REVERT: D  212 ASP cc_start: 0.8674 (t0) cc_final: 0.8074 (t0)
REVERT: E   44 ILE cc_start: 0.8523 (tp) cc_final: 0.8208 (pt)
REVERT: E   57 SER cc_start: 0.8415 (m) cc_final: 0.7948 (p)
REVERT: E  212 ASP cc_start: 0.8671 (t0) cc_final: 0.8243 (t0)
REVERT: F   57 SER cc_start: 0.8268 (m) cc_final: 0.7898 (p)
REVERT: F  212 ASP cc_start: 0.8687 (t0) cc_final: 0.8242 (t0)
  outliers start: 44
  outliers final: 37
  residues processed: 211
  average time/residue: 0.3223
  time to fit residues: 95.8973
Evaluate side-chains
  200 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 161
  time to evaluate  : 1.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  200 GLN
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  210 LEU
Chi-restraints excluded: chain C residue  298 THR
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  200 GLN
Chi-restraints excluded: chain D residue  210 LEU
Chi-restraints excluded: chain D residue  298 THR
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain E residue  230 SER
Chi-restraints excluded: chain F residue   18 THR
Chi-restraints excluded: chain F residue   73 GLU
Chi-restraints excluded: chain F residue  104 LEU
Chi-restraints excluded: chain F residue  158 VAL
Chi-restraints excluded: chain F residue  210 LEU
Chi-restraints excluded: chain F residue  298 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 120 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9990
   chunk 123 optimal weight:    7.9990
   chunk 35 optimal weight:    0.7980
   chunk 146 optimal weight:    5.9990
   chunk 152 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 97 optimal weight:    0.8980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3520 r_free = 0.3520 target = 0.125331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.103650 restraints weight = 20640.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.48
r_work: 0.3101 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.097  15144  Z= 0.107
  Angle     :  0.523   5.083  20610  Z= 0.257
  Chirality :  0.042   0.136   2214
  Planarity :  0.003   0.045   2712
  Dihedral  :  8.773  86.649   2082
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 18.94 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.20), residues: 1854
  helix:  1.39 (0.22), residues: 636
  sheet:  0.23 (0.23), residues: 462
  loop : -0.39 (0.22), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 193 
 HIS   0.002   0.000   HIS C 225 
 PHE   0.012   0.001   PHE F   5 
 TYR   0.007   0.001   TYR A 223 
 ARG   0.003   0.000   ARG D  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02436 (  672)
  hydrogen bonds       : angle       4.37695 ( 1818)
  covalent geometry    : bond        0.00285 (15138)
  covalent geometry    : angle       0.52298 (20610)
  Misc. bond           : bond        0.08996 (    6)

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

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

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 181
  time to evaluate  : 1.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 ARG cc_start: 0.7697 (mtp85) cc_final: 0.7255 (mtm-85)
REVERT: A  134 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7611 (p0)
REVERT: A  212 ASP cc_start: 0.8606 (t0) cc_final: 0.8240 (t0)
REVERT: B   44 ILE cc_start: 0.8545 (tp) cc_final: 0.8248 (pt)
REVERT: B   57 SER cc_start: 0.8241 (m) cc_final: 0.7761 (p)
REVERT: B   88 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7502 (tpp80)
REVERT: B  212 ASP cc_start: 0.8595 (t0) cc_final: 0.8178 (t0)
REVERT: C   16 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7806 (mmm-85)
REVERT: C   57 SER cc_start: 0.8190 (m) cc_final: 0.7745 (p)
REVERT: C   88 ARG cc_start: 0.7888 (mtp85) cc_final: 0.7410 (mtm-85)
REVERT: C  212 ASP cc_start: 0.8585 (t0) cc_final: 0.8149 (t0)
REVERT: D   44 ILE cc_start: 0.8591 (tp) cc_final: 0.8298 (pt)
REVERT: D   88 ARG cc_start: 0.7728 (mtp85) cc_final: 0.7252 (mtm-85)
REVERT: D  212 ASP cc_start: 0.8595 (t0) cc_final: 0.8228 (t0)
REVERT: E   44 ILE cc_start: 0.8601 (tp) cc_final: 0.8311 (pt)
REVERT: E   57 SER cc_start: 0.8252 (m) cc_final: 0.7770 (p)
REVERT: E  212 ASP cc_start: 0.8596 (t0) cc_final: 0.8169 (t0)
REVERT: F   16 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7806 (mmm-85)
REVERT: F   57 SER cc_start: 0.8154 (m) cc_final: 0.7720 (p)
REVERT: F   88 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7426 (mtm-85)
REVERT: F  212 ASP cc_start: 0.8601 (t0) cc_final: 0.8169 (t0)
  outliers start: 31
  outliers final: 29
  residues processed: 212
  average time/residue: 0.3390
  time to fit residues: 100.2945
Evaluate side-chains
  210 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 180
  time to evaluate  : 1.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  134 ASP
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   73 GLU
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  298 THR
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   73 GLU
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  298 THR
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain F residue   18 THR
Chi-restraints excluded: chain F residue  104 LEU
Chi-restraints excluded: chain F residue  158 VAL
Chi-restraints excluded: chain F residue  210 LEU
Chi-restraints excluded: chain F residue  298 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 184 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   chunk 156 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 81 optimal weight:    0.0970
   chunk 15 optimal weight:    0.0070
   chunk 116 optimal weight:    0.0040
   chunk 51 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 166 optimal weight:    2.9990
   chunk 159 optimal weight:    3.9990
   overall best weight:    0.3608

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

Flipped N/Q/H residues before XYZ refinement:
A 275 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.129652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.107861 restraints weight = 20495.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.51
r_work: 0.3164 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  15144  Z= 0.093
  Angle     :  0.507   5.103  20610  Z= 0.249
  Chirality :  0.041   0.147   2214
  Planarity :  0.003   0.025   2712
  Dihedral  :  8.755  89.945   2082
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 19.26 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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 (0.20), residues: 1854
  helix:  1.58 (0.22), residues: 642
  sheet:  0.31 (0.23), residues: 462
  loop : -0.23 (0.22), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP D  72 
 HIS   0.002   0.000   HIS B 225 
 PHE   0.012   0.001   PHE F   5 
 TYR   0.007   0.001   TYR F 223 
 ARG   0.005   0.000   ARG B  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01935 (  672)
  hydrogen bonds       : angle       4.18326 ( 1818)
  covalent geometry    : bond        0.00242 (15138)
  covalent geometry    : angle       0.50714 (20610)
  Misc. bond           : bond        0.04380 (    6)

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

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

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 218
  time to evaluate  : 1.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ILE cc_start: 0.8422 (tp) cc_final: 0.8118 (pt)
REVERT: A   88 ARG cc_start: 0.7647 (mtp85) cc_final: 0.7250 (mtm-85)
REVERT: A  212 ASP cc_start: 0.8498 (t0) cc_final: 0.8115 (t0)
REVERT: A  295 ILE cc_start: 0.8938 (pt) cc_final: 0.8648 (pt)
REVERT: B   44 ILE cc_start: 0.8468 (tp) cc_final: 0.8172 (pt)
REVERT: B   57 SER cc_start: 0.8135 (m) cc_final: 0.7579 (p)
REVERT: B   88 ARG cc_start: 0.7728 (mtp85) cc_final: 0.7434 (mtm-85)
REVERT: B  212 ASP cc_start: 0.8536 (t0) cc_final: 0.8083 (t0)
REVERT: B  280 ASN cc_start: 0.9039 (t0) cc_final: 0.8765 (p0)
REVERT: C   15 GLU cc_start: 0.7691 (tp30) cc_final: 0.7304 (mt-10)
REVERT: C   57 SER cc_start: 0.8012 (m) cc_final: 0.7511 (p)
REVERT: C   88 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7457 (mtm-85)
REVERT: C  212 ASP cc_start: 0.8467 (t0) cc_final: 0.7988 (t0)
REVERT: D   44 ILE cc_start: 0.8479 (tp) cc_final: 0.8175 (pt)
REVERT: D   88 ARG cc_start: 0.7708 (mtp85) cc_final: 0.7275 (mtm-85)
REVERT: D  212 ASP cc_start: 0.8482 (t0) cc_final: 0.8105 (t0)
REVERT: D  295 ILE cc_start: 0.8934 (pt) cc_final: 0.8638 (pt)
REVERT: E   44 ILE cc_start: 0.8520 (tp) cc_final: 0.8196 (pt)
REVERT: E   57 SER cc_start: 0.8081 (m) cc_final: 0.7529 (p)
REVERT: E   88 ARG cc_start: 0.7729 (mtp85) cc_final: 0.7444 (mtm-85)
REVERT: E  212 ASP cc_start: 0.8533 (t0) cc_final: 0.8093 (t0)
REVERT: E  280 ASN cc_start: 0.9009 (t0) cc_final: 0.8803 (p0)
REVERT: F   15 GLU cc_start: 0.7681 (tp30) cc_final: 0.7304 (mt-10)
REVERT: F   57 SER cc_start: 0.8006 (m) cc_final: 0.7504 (p)
REVERT: F   88 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7438 (mtm-85)
REVERT: F  212 ASP cc_start: 0.8506 (t0) cc_final: 0.8026 (t0)
REVERT: F  223 TYR cc_start: 0.8615 (p90) cc_final: 0.8193 (p90)
  outliers start: 29
  outliers final: 21
  residues processed: 247
  average time/residue: 0.3482
  time to fit residues: 121.2525
Evaluate side-chains
  219 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 198
  time to evaluate  : 1.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   93 VAL
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  298 THR
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   73 GLU
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  298 THR
Chi-restraints excluded: chain E residue   18 THR
Chi-restraints excluded: chain E residue   93 VAL
Chi-restraints excluded: chain E residue  210 LEU
Chi-restraints excluded: chain F residue   18 THR
Chi-restraints excluded: chain F residue  158 VAL
Chi-restraints excluded: chain F residue  298 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 186
   random chunks:
   chunk 111 optimal weight:    5.9990
   chunk 82 optimal weight:    0.0030
   chunk 130 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 169 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 184 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.7394

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

Flipped N/Q/H residues before XYZ refinement:
A 275 ASN
C  95 HIS
D  95 HIS
D 275 ASN
F  95 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.128559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.106500 restraints weight = 20473.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 2.54
r_work: 0.3129 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083  15144  Z= 0.102
  Angle     :  0.518   5.060  20610  Z= 0.256
  Chirality :  0.041   0.131   2214
  Planarity :  0.003   0.027   2712
  Dihedral  :  8.748  89.987   2082
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 20.01 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  0.82 (0.20), residues: 1854
  helix:  1.60 (0.22), residues: 642
  sheet:  0.37 (0.23), residues: 462
  loop : -0.18 (0.23), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP A 193 
 HIS   0.002   0.000   HIS B 225 
 PHE   0.018   0.001   PHE A  54 
 TYR   0.015   0.001   TYR F 262 
 ARG   0.005   0.000   ARG E  16 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02216 (  672)
  hydrogen bonds       : angle       4.20022 ( 1818)
  covalent geometry    : bond        0.00269 (15138)
  covalent geometry    : angle       0.51780 (20610)
  Misc. bond           : bond        0.06459 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6404.59 seconds
wall clock time: 111 minutes 47.97 seconds (6707.97 seconds total)