Starting phenix.real_space_refine
on Wed Jun 11 00:33:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f35_28832/06_2025/8f35_28832.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f35_28832/06_2025/8f35_28832.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f35_28832/06_2025/8f35_28832.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f35_28832/06_2025/8f35_28832.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f35_28832/06_2025/8f35_28832.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f35_28832/06_2025/8f35_28832.cif"
  }
  resolution = 3.17
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    8165      2.51       5
     N    2080      2.21       5
     O    2250      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 12525
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2505
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 14, 'TRANS': 292}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 5.23, per 1000 atoms: 0.42
  Number of scatterers: 12525
  At special positions: 0
  Unit cell: (89.352, 90.009, 123.516, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O    2250      8.00
     N    2080      7.00
     C    8165      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.83
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2910

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 10 sheets defined
      38.1% alpha, 29.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'E' and resid 61 through 70
      removed outlier: 3.875A  pdb=" N   ARG E  65 " --> pdb=" O   THR E  61 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TRP E  66 " --> pdb=" O   GLN E  62 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 118 through 121
    Processing helix  chain 'E' and resid 177 through 182
      removed outlier: 4.276A  pdb=" N   VAL E 181 " --> pdb=" O   HIS E 177 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 201 through 208
    Processing helix  chain 'E' and resid 208 through 221
      removed outlier: 3.654A  pdb=" N   LEU E 212 " --> pdb=" O   PHE E 208 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 222 through 225
      removed outlier: 3.558A  pdb=" N   LEU E 225 " --> pdb=" O   VAL E 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 222 through 225'
    Processing helix  chain 'E' and resid 227 through 251
      removed outlier: 3.765A  pdb=" N   PHE E 247 " --> pdb=" O   VAL E 243 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 260 through 285
    Processing helix  chain 'E' and resid 296 through 300
      removed outlier: 3.502A  pdb=" N   CYS E 300 " --> pdb=" O   ILE E 297 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 303 through 317
      removed outlier: 3.556A  pdb=" N   ILE E 317 " --> pdb=" O   CYS E 313 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 70
      removed outlier: 3.876A  pdb=" N   ARG D  65 " --> pdb=" O   THR D  61 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TRP D  66 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 121
    Processing helix  chain 'D' and resid 177 through 182
      removed outlier: 4.276A  pdb=" N   VAL D 181 " --> pdb=" O   HIS D 177 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 201 through 208
    Processing helix  chain 'D' and resid 208 through 221
      removed outlier: 3.655A  pdb=" N   LEU D 212 " --> pdb=" O   PHE D 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 225
      removed outlier: 3.558A  pdb=" N   LEU D 225 " --> pdb=" O   VAL D 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 222 through 225'
    Processing helix  chain 'D' and resid 227 through 251
      removed outlier: 3.765A  pdb=" N   PHE D 247 " --> pdb=" O   VAL D 243 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 260 through 285
    Processing helix  chain 'D' and resid 296 through 300
      removed outlier: 3.503A  pdb=" N   CYS D 300 " --> pdb=" O   ILE D 297 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 303 through 317
      removed outlier: 3.555A  pdb=" N   ILE D 317 " --> pdb=" O   CYS D 313 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 70
      removed outlier: 3.874A  pdb=" N   ARG C  65 " --> pdb=" O   THR C  61 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 121
    Processing helix  chain 'C' and resid 177 through 182
      removed outlier: 4.276A  pdb=" N   VAL C 181 " --> pdb=" O   HIS C 177 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 208 through 221
      removed outlier: 3.655A  pdb=" N   LEU C 212 " --> pdb=" O   PHE C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 225
      removed outlier: 3.558A  pdb=" N   LEU C 225 " --> pdb=" O   VAL C 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 222 through 225'
    Processing helix  chain 'C' and resid 227 through 251
      removed outlier: 3.765A  pdb=" N   PHE C 247 " --> pdb=" O   VAL C 243 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 260 through 285
    Processing helix  chain 'C' and resid 296 through 300
      removed outlier: 3.501A  pdb=" N   CYS C 300 " --> pdb=" O   ILE C 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 303 through 317
      removed outlier: 3.556A  pdb=" N   ILE C 317 " --> pdb=" O   CYS C 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 70
      removed outlier: 3.875A  pdb=" N   ARG B  65 " --> pdb=" O   THR B  61 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   TRP B  66 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 121
    Processing helix  chain 'B' and resid 177 through 182
      removed outlier: 4.276A  pdb=" N   VAL B 181 " --> pdb=" O   HIS B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 208
    Processing helix  chain 'B' and resid 208 through 221
      removed outlier: 3.655A  pdb=" N   LEU B 212 " --> pdb=" O   PHE B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 225
      removed outlier: 3.558A  pdb=" N   LEU B 225 " --> pdb=" O   VAL B 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 222 through 225'
    Processing helix  chain 'B' and resid 227 through 251
      removed outlier: 3.765A  pdb=" N   PHE B 247 " --> pdb=" O   VAL B 243 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 285
    Processing helix  chain 'B' and resid 296 through 300
      removed outlier: 3.502A  pdb=" N   CYS B 300 " --> pdb=" O   ILE B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 317
      removed outlier: 3.555A  pdb=" N   ILE B 317 " --> pdb=" O   CYS B 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 70
      removed outlier: 3.876A  pdb=" N   ARG A  65 " --> pdb=" O   THR A  61 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   TRP A  66 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 121
    Processing helix  chain 'A' and resid 177 through 182
      removed outlier: 4.276A  pdb=" N   VAL A 181 " --> pdb=" O   HIS A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 208
    Processing helix  chain 'A' and resid 208 through 221
      removed outlier: 3.655A  pdb=" N   LEU A 212 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 225
      removed outlier: 3.558A  pdb=" N   LEU A 225 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 222 through 225'
    Processing helix  chain 'A' and resid 227 through 251
      removed outlier: 3.765A  pdb=" N   PHE A 247 " --> pdb=" O   VAL A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 285
    Processing helix  chain 'A' and resid 296 through 300
      removed outlier: 3.503A  pdb=" N   CYS A 300 " --> pdb=" O   ILE A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 317
      removed outlier: 3.555A  pdb=" N   ILE A 317 " --> pdb=" O   CYS A 313 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 56 through 58
      removed outlier: 6.687A  pdb=" N   THR E  32 " --> pdb=" O   VAL E  26 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   VAL E  26 " --> pdb=" O   THR E  32 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LYS E  22 " --> pdb=" O   ASP E  36 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   TYR E  38 " --> pdb=" O   ILE E  20 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   ILE E  20 " --> pdb=" O   TYR E  38 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   VAL E  40 " --> pdb=" O   ILE E  18 " (cutoff:3.500A)
      removed outlier: 5.402A  pdb=" N   ILE E  18 " --> pdb=" O   VAL E  40 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   GLN E  42 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 5.575A  pdb=" N   VAL E  16 " --> pdb=" O   GLN E  42 " (cutoff:3.500A)
      removed outlier: 8.495A  pdb=" N   THR E  44 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   VAL E  14 " --> pdb=" O   THR E  44 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   VAL E  12 " --> pdb=" O   ARG E 141 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   SER E 143 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   VAL E  14 " --> pdb=" O   SER E 143 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   ILE E 145 " --> pdb=" O   VAL E  14 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   VAL E  16 " --> pdb=" O   ILE E 145 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   VAL E 147 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   ILE E  18 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.672A  pdb=" N   SER E 189 " --> pdb=" O   PRO E 132 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   PHE E 188 " --> pdb=" O   SER E 171 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   SER E 171 " --> pdb=" O   PHE E 188 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   ARG E 190 " --> pdb=" O   HIS E 169 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   HIS E 169 " --> pdb=" O   ARG E 190 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   THR E 192 " --> pdb=" O   SER E 167 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   SER E 167 " --> pdb=" O   THR E 192 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   ARG E 194 " --> pdb=" O   LYS E 165 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   LYS E 165 " --> pdb=" O   ARG E 194 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   ASP E 196 " --> pdb=" O   ARG E 163 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 56 through 58
      removed outlier: 6.687A  pdb=" N   THR D  32 " --> pdb=" O   VAL D  26 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   VAL D  26 " --> pdb=" O   THR D  32 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LYS D  22 " --> pdb=" O   ASP D  36 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   TYR D  38 " --> pdb=" O   ILE D  20 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   ILE D  20 " --> pdb=" O   TYR D  38 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   VAL D  40 " --> pdb=" O   ILE D  18 " (cutoff:3.500A)
      removed outlier: 5.402A  pdb=" N   ILE D  18 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   GLN D  42 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 5.575A  pdb=" N   VAL D  16 " --> pdb=" O   GLN D  42 " (cutoff:3.500A)
      removed outlier: 8.494A  pdb=" N   THR D  44 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 7.662A  pdb=" N   VAL D  14 " --> pdb=" O   THR D  44 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   VAL D  12 " --> pdb=" O   ARG D 141 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   SER D 143 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 7.521A  pdb=" N   VAL D  14 " --> pdb=" O   SER D 143 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   ILE D 145 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   VAL D  16 " --> pdb=" O   ILE D 145 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   VAL D 147 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ILE D  18 " --> pdb=" O   VAL D 147 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.672A  pdb=" N   SER D 189 " --> pdb=" O   PRO D 132 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   PHE D 188 " --> pdb=" O   SER D 171 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   SER D 171 " --> pdb=" O   PHE D 188 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   ARG D 190 " --> pdb=" O   HIS D 169 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   HIS D 169 " --> pdb=" O   ARG D 190 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   THR D 192 " --> pdb=" O   SER D 167 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   SER D 167 " --> pdb=" O   THR D 192 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   ARG D 194 " --> pdb=" O   LYS D 165 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   LYS D 165 " --> pdb=" O   ARG D 194 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   ASP D 196 " --> pdb=" O   ARG D 163 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 58
      removed outlier: 6.688A  pdb=" N   THR C  32 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   VAL C  26 " --> pdb=" O   THR C  32 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LYS C  22 " --> pdb=" O   ASP C  36 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   TYR C  38 " --> pdb=" O   ILE C  20 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   ILE C  20 " --> pdb=" O   TYR C  38 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   VAL C  40 " --> pdb=" O   ILE C  18 " (cutoff:3.500A)
      removed outlier: 5.402A  pdb=" N   ILE C  18 " --> pdb=" O   VAL C  40 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   GLN C  42 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   VAL C  16 " --> pdb=" O   GLN C  42 " (cutoff:3.500A)
      removed outlier: 8.494A  pdb=" N   THR C  44 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   VAL C  14 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   VAL C  12 " --> pdb=" O   ARG C 141 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   SER C 143 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   VAL C  14 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   ILE C 145 " --> pdb=" O   VAL C  14 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   VAL C  16 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   VAL C 147 " --> pdb=" O   VAL C  16 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   ILE C  18 " --> pdb=" O   VAL C 147 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.672A  pdb=" N   SER C 189 " --> pdb=" O   PRO C 132 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   PHE C 188 " --> pdb=" O   SER C 171 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   SER C 171 " --> pdb=" O   PHE C 188 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   ARG C 190 " --> pdb=" O   HIS C 169 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   HIS C 169 " --> pdb=" O   ARG C 190 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   THR C 192 " --> pdb=" O   SER C 167 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   SER C 167 " --> pdb=" O   THR C 192 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   ARG C 194 " --> pdb=" O   LYS C 165 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   LYS C 165 " --> pdb=" O   ARG C 194 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   ASP C 196 " --> pdb=" O   ARG C 163 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 58
      removed outlier: 6.687A  pdb=" N   THR B  32 " --> pdb=" O   VAL B  26 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   VAL B  26 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LYS B  22 " --> pdb=" O   ASP B  36 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   TYR B  38 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   ILE B  20 " --> pdb=" O   TYR B  38 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   VAL B  40 " --> pdb=" O   ILE B  18 " (cutoff:3.500A)
      removed outlier: 5.402A  pdb=" N   ILE B  18 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   GLN B  42 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   VAL B  16 " --> pdb=" O   GLN B  42 " (cutoff:3.500A)
      removed outlier: 8.495A  pdb=" N   THR B  44 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   VAL B  14 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   VAL B  12 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   SER B 143 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   VAL B  14 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   ILE B 145 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   VAL B  16 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   VAL B 147 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ILE B  18 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.672A  pdb=" N   SER B 189 " --> pdb=" O   PRO B 132 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   PHE B 188 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   SER B 171 " --> pdb=" O   PHE B 188 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   ARG B 190 " --> pdb=" O   HIS B 169 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   HIS B 169 " --> pdb=" O   ARG B 190 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   THR B 192 " --> pdb=" O   SER B 167 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   SER B 167 " --> pdb=" O   THR B 192 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   ARG B 194 " --> pdb=" O   LYS B 165 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   LYS B 165 " --> pdb=" O   ARG B 194 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   ASP B 196 " --> pdb=" O   ARG B 163 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 56 through 58
      removed outlier: 6.687A  pdb=" N   THR A  32 " --> pdb=" O   VAL A  26 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   VAL A  26 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LYS A  22 " --> pdb=" O   ASP A  36 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   TYR A  38 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   ILE A  20 " --> pdb=" O   TYR A  38 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   VAL A  40 " --> pdb=" O   ILE A  18 " (cutoff:3.500A)
      removed outlier: 5.402A  pdb=" N   ILE A  18 " --> pdb=" O   VAL A  40 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   GLN A  42 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 5.575A  pdb=" N   VAL A  16 " --> pdb=" O   GLN A  42 " (cutoff:3.500A)
      removed outlier: 8.494A  pdb=" N   THR A  44 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   VAL A  14 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   VAL A  12 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   SER A 143 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
      removed outlier: 7.521A  pdb=" N   VAL A  14 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   ILE A 145 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   VAL A  16 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   VAL A 147 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   ILE A  18 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.672A  pdb=" N   SER A 189 " --> pdb=" O   PRO A 132 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   PHE A 188 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   SER A 171 " --> pdb=" O   PHE A 188 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   ARG A 190 " --> pdb=" O   HIS A 169 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   HIS A 169 " --> pdb=" O   ARG A 190 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   THR A 192 " --> pdb=" O   SER A 167 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   SER A 167 " --> pdb=" O   THR A 192 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   ARG A 194 " --> pdb=" O   LYS A 165 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   LYS A 165 " --> pdb=" O   ARG A 194 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   ASP A 196 " --> pdb=" O   ARG A 163 " (cutoff:3.500A)

    540 hydrogen bonds defined for protein.
    1575 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.30

  Time building geometry restraints manager: 3.37 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3131
        1.33 -     1.45: 2671
        1.45 -     1.57: 7013
        1.57 -     1.69: 0
        1.69 -     1.81: 50
  Bond restraints: 12865
  Sorted by residual:
  bond pdb=" CA  ILE C 157 "
       pdb=" C   ILE C 157 "
    ideal  model  delta    sigma   weight residual
    1.523  1.494  0.029 1.27e-02 6.20e+03 5.17e+00
  bond pdb=" CA  ILE A 157 "
       pdb=" C   ILE A 157 "
    ideal  model  delta    sigma   weight residual
    1.523  1.495  0.028 1.27e-02 6.20e+03 4.86e+00
  bond pdb=" CA  ILE D 157 "
       pdb=" C   ILE D 157 "
    ideal  model  delta    sigma   weight residual
    1.523  1.495  0.028 1.27e-02 6.20e+03 4.77e+00
  bond pdb=" CA  ILE E 157 "
       pdb=" C   ILE E 157 "
    ideal  model  delta    sigma   weight residual
    1.523  1.495  0.028 1.27e-02 6.20e+03 4.72e+00
  bond pdb=" CA  ILE B 157 "
       pdb=" C   ILE B 157 "
    ideal  model  delta    sigma   weight residual
    1.523  1.496  0.027 1.27e-02 6.20e+03 4.61e+00
  ... (remaining 12860 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 16493
        1.33 -     2.66: 812
        2.66 -     3.99: 135
        3.99 -     5.31: 60
        5.31 -     6.64: 35
  Bond angle restraints: 17535
  Sorted by residual:
  angle pdb=" N   VAL B 291 "
        pdb=" CA  VAL B 291 "
        pdb=" C   VAL B 291 "
      ideal   model   delta    sigma   weight residual
     113.53  109.61    3.92 9.80e-01 1.04e+00 1.60e+01
  angle pdb=" N   VAL D 291 "
        pdb=" CA  VAL D 291 "
        pdb=" C   VAL D 291 "
      ideal   model   delta    sigma   weight residual
     113.53  109.62    3.91 9.80e-01 1.04e+00 1.59e+01
  angle pdb=" N   VAL E 291 "
        pdb=" CA  VAL E 291 "
        pdb=" C   VAL E 291 "
      ideal   model   delta    sigma   weight residual
     113.53  109.62    3.91 9.80e-01 1.04e+00 1.59e+01
  angle pdb=" N   VAL A 291 "
        pdb=" CA  VAL A 291 "
        pdb=" C   VAL A 291 "
      ideal   model   delta    sigma   weight residual
     113.53  109.63    3.90 9.80e-01 1.04e+00 1.59e+01
  angle pdb=" N   VAL C 291 "
        pdb=" CA  VAL C 291 "
        pdb=" C   VAL C 291 "
      ideal   model   delta    sigma   weight residual
     113.53  109.66    3.87 9.80e-01 1.04e+00 1.56e+01
  ... (remaining 17530 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.75: 6727
       16.75 -    33.51: 618
       33.51 -    50.26: 130
       50.26 -    67.02: 25
       67.02 -    83.77: 25
  Dihedral angle restraints: 7525
    sinusoidal: 3020
      harmonic: 4505
  Sorted by residual:
  dihedral pdb=" CA  ARG A 117 "
           pdb=" C   ARG A 117 "
           pdb=" N   LEU A 118 "
           pdb=" CA  LEU A 118 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.49  -16.51     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  ARG D 117 "
           pdb=" C   ARG D 117 "
           pdb=" N   LEU D 118 "
           pdb=" CA  LEU D 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.51  -16.49     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  ARG B 117 "
           pdb=" C   ARG B 117 "
           pdb=" N   LEU B 118 "
           pdb=" CA  LEU B 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.51  -16.49     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 7522 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1003
       0.032 -    0.065: 578
       0.065 -    0.097: 200
       0.097 -    0.129: 143
       0.129 -    0.161: 26
  Chirality restraints: 1950
  Sorted by residual:
  chirality pdb=" CB  ILE D 145 "
            pdb=" CA  ILE D 145 "
            pdb=" CG1 ILE D 145 "
            pdb=" CG2 ILE D 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.51e-01
  chirality pdb=" CB  ILE A 145 "
            pdb=" CA  ILE A 145 "
            pdb=" CG1 ILE A 145 "
            pdb=" CG2 ILE A 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.41e-01
  chirality pdb=" CB  ILE E 145 "
            pdb=" CA  ILE E 145 "
            pdb=" CG1 ILE E 145 "
            pdb=" CG2 ILE E 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.32e-01
  ... (remaining 1947 not shown)

  Planarity restraints: 2235
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 255 "   -0.012 2.00e-02 2.50e+03   2.31e-02 5.34e+00
        pdb=" C   ARG B 255 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ARG B 255 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LEU B 256 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG D 255 "   -0.012 2.00e-02 2.50e+03   2.30e-02 5.31e+00
        pdb=" C   ARG D 255 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ARG D 255 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LEU D 256 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 255 "   -0.011 2.00e-02 2.50e+03   2.29e-02 5.23e+00
        pdb=" C   ARG E 255 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ARG E 255 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   LEU E 256 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 2232 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2156
        2.77 -     3.30: 11455
        3.30 -     3.83: 21643
        3.83 -     4.37: 25522
        4.37 -     4.90: 43725
  Nonbonded interactions: 104501
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG E 105 "
            pdb=" O   VAL D  81 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" N   PHE C 116 "
            pdb=" OH  TYR C 258 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" N   PHE E 116 "
            pdb=" OH  TYR E 258 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" N   PHE D 116 "
            pdb=" OH  TYR D 258 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" N   PHE B 116 "
            pdb=" OH  TYR B 258 "
     model   vdw
     2.243 3.120
  ... (remaining 104496 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'
}

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:             1.530
  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:          0.540
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     26.020
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12865  Z= 0.245
  Angle     :  0.746   6.643  17535  Z= 0.428
  Chirality :  0.051   0.161   1950
  Planarity :  0.005   0.037   2235
  Dihedral  : 14.231  83.771   4615
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.21), residues: 1525
  helix:  0.08 (0.22), residues: 510
  sheet:  0.45 (0.23), residues: 485
  loop : -2.55 (0.24), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  72 
 HIS   0.008   0.002   HIS A 285 
 PHE   0.017   0.002   PHE C 236 
 TYR   0.020   0.002   TYR C 270 
 ARG   0.003   0.000   ARG D  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12249 (  540)
  hydrogen bonds       : angle       5.86554 ( 1575)
  covalent geometry    : bond        0.00491 (12865)
  covalent geometry    : angle       0.74558 (17535)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 1.334 
Fit side-chains
REVERT: D   13 ASP cc_start: 0.6885 (m-30) cc_final: 0.6428 (m-30)
REVERT: C  122 ASP cc_start: 0.7345 (m-30) cc_final: 0.6954 (m-30)
REVERT: A  204 TYR cc_start: 0.8073 (m-80) cc_final: 0.7700 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 227
  average time/residue: 0.2638
  time to fit residues: 87.3038
Evaluate side-chains
  188 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 1.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    8.9990
   chunk 113 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 76 optimal weight:    0.0670
   chunk 60 optimal weight:    3.9990
   chunk 117 optimal weight:    6.9990
   chunk 45 optimal weight:   10.0000
   chunk 71 optimal weight:    0.9980
   chunk 87 optimal weight:    6.9990
   chunk 136 optimal weight:   20.0000
   overall best weight:    2.0124

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

Flipped N/Q/H residues before XYZ refinement:
E  60 ASN
D  60 ASN
D 169 HIS
C  60 ASN
C 169 HIS
B  60 ASN
B 169 HIS
A  60 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.154232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.125050 restraints weight = 13177.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 1.89
r_work: 0.3110 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.1885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  12865  Z= 0.157
  Angle     :  0.533   5.311  17535  Z= 0.285
  Chirality :  0.045   0.160   1950
  Planarity :  0.004   0.032   2235
  Dihedral  :  4.727  17.892   1685
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  7.27 %
    Favored  : 92.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.21), residues: 1525
  helix:  1.33 (0.24), residues: 500
  sheet:  0.27 (0.23), residues: 485
  loop : -2.26 (0.24), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 206 
 HIS   0.004   0.001   HIS E 285 
 PHE   0.015   0.002   PHE C 236 
 TYR   0.014   0.002   TYR A 270 
 ARG   0.004   0.000   ARG E 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03611 (  540)
  hydrogen bonds       : angle       4.57963 ( 1575)
  covalent geometry    : bond        0.00373 (12865)
  covalent geometry    : angle       0.53329 (17535)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 195
  time to evaluate  : 2.045 
Fit side-chains
REVERT: E  114 MET cc_start: 0.8543 (mtm) cc_final: 0.8341 (mtp)
REVERT: E  255 ARG cc_start: 0.7993 (mmp80) cc_final: 0.6941 (mmt90)
REVERT: E  258 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7592 (p90)
REVERT: D  216 ILE cc_start: 0.7610 (mt) cc_final: 0.7381 (mm)
REVERT: D  255 ARG cc_start: 0.7764 (mmp80) cc_final: 0.6930 (mmt90)
REVERT: C  114 MET cc_start: 0.8471 (mtm) cc_final: 0.8174 (mtp)
REVERT: B  115 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.6608 (p0)
REVERT: A  114 MET cc_start: 0.8492 (mtm) cc_final: 0.8213 (mtp)
REVERT: A  159 GLU cc_start: 0.7770 (tt0) cc_final: 0.7465 (tt0)
REVERT: A  174 ARG cc_start: 0.7147 (tmm160) cc_final: 0.6916 (tmm160)
  outliers start: 10
  outliers final: 6
  residues processed: 201
  average time/residue: 0.2976
  time to fit residues: 85.4714
Evaluate side-chains
  180 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 172
  time to evaluate  : 1.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain E residue  258 TYR
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain C residue  167 SER
Chi-restraints excluded: chain B residue  115 ASP
Chi-restraints excluded: chain B residue  167 SER
Chi-restraints excluded: chain A residue  167 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 66 optimal weight:    0.0570
   chunk 121 optimal weight:    6.9990
   chunk 123 optimal weight:    2.9990
   chunk 60 optimal weight:   10.0000
   chunk 142 optimal weight:    4.9990
   chunk 20 optimal weight:   10.0000
   chunk 58 optimal weight:    8.9990
   chunk 64 optimal weight:    6.9990
   chunk 5 optimal weight:    6.9990
   chunk 113 optimal weight:    0.9980
   chunk 120 optimal weight:    1.9990
   overall best weight:    2.2104

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

Flipped N/Q/H residues before XYZ refinement:
D 169 HIS
C 169 HIS
B 169 HIS
A 169 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.150610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.121367 restraints weight = 13373.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 1.80
r_work: 0.3102 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12865  Z= 0.162
  Angle     :  0.532   4.979  17535  Z= 0.281
  Chirality :  0.046   0.171   1950
  Planarity :  0.004   0.028   2235
  Dihedral  :  4.772  15.510   1685
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  8.44 %
    Favored  : 90.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.21), residues: 1525
  helix:  1.62 (0.23), residues: 505
  sheet:  0.23 (0.23), residues: 485
  loop : -2.17 (0.24), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 161 
 HIS   0.003   0.001   HIS E 285 
 PHE   0.016   0.002   PHE C 236 
 TYR   0.011   0.001   TYR C 270 
 ARG   0.002   0.000   ARG D 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03892 (  540)
  hydrogen bonds       : angle       4.49353 ( 1575)
  covalent geometry    : bond        0.00384 (12865)
  covalent geometry    : angle       0.53224 (17535)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 171
  time to evaluate  : 1.997 
Fit side-chains
REVERT: E  255 ARG cc_start: 0.7905 (mmp80) cc_final: 0.6873 (mmt90)
REVERT: E  258 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.7375 (p90)
REVERT: D  115 ASP cc_start: 0.7932 (t70) cc_final: 0.7695 (t70)
REVERT: D  255 ARG cc_start: 0.7786 (mmp80) cc_final: 0.6858 (mmt90)
REVERT: C  255 ARG cc_start: 0.7834 (mmp80) cc_final: 0.6836 (mmt90)
REVERT: B  255 ARG cc_start: 0.7719 (mmp80) cc_final: 0.6704 (mmt90)
REVERT: A  148 TYR cc_start: 0.8438 (m-80) cc_final: 0.8191 (m-80)
REVERT: A  150 GLU cc_start: 0.6990 (tt0) cc_final: 0.6396 (tp30)
REVERT: A  174 ARG cc_start: 0.7190 (tmm160) cc_final: 0.6671 (tmm-80)
REVERT: A  226 GLU cc_start: 0.7133 (mp0) cc_final: 0.6780 (mt-10)
REVERT: A  255 ARG cc_start: 0.7782 (mmp80) cc_final: 0.6826 (mmt90)
  outliers start: 16
  outliers final: 13
  residues processed: 178
  average time/residue: 0.3889
  time to fit residues: 96.3714
Evaluate side-chains
  178 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 164
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   97 ASP
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain E residue  258 TYR
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  115 ASP
Chi-restraints excluded: chain C residue  122 ASP
Chi-restraints excluded: chain C residue  167 SER
Chi-restraints excluded: chain B residue  167 SER
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue  167 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 129 optimal weight:   10.0000
   chunk 149 optimal weight:    7.9990
   chunk 28 optimal weight:    8.9990
   chunk 80 optimal weight:   10.0000
   chunk 81 optimal weight:    9.9990
   chunk 45 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   chunk 91 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 96 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
D 169 HIS
C 169 HIS
B 169 HIS
A 169 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.146226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.117552 restraints weight = 13418.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.49
r_work: 0.3033 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043  12865  Z= 0.300
  Angle     :  0.679   6.574  17535  Z= 0.356
  Chirality :  0.051   0.201   1950
  Planarity :  0.005   0.031   2235
  Dihedral  :  5.445  21.158   1685
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.78 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.21), residues: 1525
  helix:  1.30 (0.23), residues: 505
  sheet:  0.00 (0.22), residues: 485
  loop : -2.30 (0.23), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 206 
 HIS   0.004   0.001   HIS B 285 
 PHE   0.020   0.003   PHE C 236 
 TYR   0.015   0.002   TYR C 270 
 ARG   0.003   0.001   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04971 (  540)
  hydrogen bonds       : angle       4.80227 ( 1575)
  covalent geometry    : bond        0.00733 (12865)
  covalent geometry    : angle       0.67873 (17535)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 146
  time to evaluate  : 1.945 
Fit side-chains
REVERT: E  258 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7467 (p90)
REVERT: A  148 TYR cc_start: 0.8525 (m-80) cc_final: 0.8223 (m-80)
  outliers start: 26
  outliers final: 23
  residues processed: 162
  average time/residue: 0.2773
  time to fit residues: 63.8189
Evaluate side-chains
  150 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 1.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   60 ASN
Chi-restraints excluded: chain E residue   97 ASP
Chi-restraints excluded: chain E residue  115 ASP
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain E residue  258 TYR
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  115 ASP
Chi-restraints excluded: chain C residue  122 ASP
Chi-restraints excluded: chain C residue  167 SER
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  167 SER
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  167 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 112 optimal weight:    0.9980
   chunk 143 optimal weight:    0.7980
   chunk 141 optimal weight:    1.9990
   chunk 147 optimal weight:    4.9990
   chunk 0 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 98 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 134 optimal weight:   10.0000
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
D 169 HIS
C 169 HIS
B 169 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.154023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.126311 restraints weight = 13156.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 1.41
r_work: 0.3106 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  12865  Z= 0.106
  Angle     :  0.480   4.899  17535  Z= 0.254
  Chirality :  0.044   0.168   1950
  Planarity :  0.003   0.029   2235
  Dihedral  :  4.496  15.091   1685
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 12.80 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.21), residues: 1525
  helix:  1.94 (0.23), residues: 505
  sheet:  0.14 (0.23), residues: 490
  loop : -2.03 (0.25), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E 161 
 HIS   0.003   0.001   HIS C 285 
 PHE   0.010   0.001   PHE C 236 
 TYR   0.008   0.001   TYR A 245 
 ARG   0.002   0.000   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03252 (  540)
  hydrogen bonds       : angle       4.33480 ( 1575)
  covalent geometry    : bond        0.00241 (12865)
  covalent geometry    : angle       0.47985 (17535)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 169
  time to evaluate  : 1.566 
Fit side-chains
REVERT: E  258 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7387 (p90)
REVERT: D  255 ARG cc_start: 0.8073 (mmp80) cc_final: 0.6963 (mmt90)
REVERT: D  258 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7618 (p90)
REVERT: C  258 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7541 (p90)
REVERT: B   34 LYS cc_start: 0.8698 (mttp) cc_final: 0.8479 (mttt)
REVERT: B  247 PHE cc_start: 0.7188 (m-10) cc_final: 0.6973 (m-10)
REVERT: B  255 ARG cc_start: 0.7796 (mmp80) cc_final: 0.6788 (mmt90)
REVERT: A  174 ARG cc_start: 0.7100 (tmm160) cc_final: 0.6900 (tmm160)
  outliers start: 20
  outliers final: 14
  residues processed: 178
  average time/residue: 0.3815
  time to fit residues: 94.3000
Evaluate side-chains
  174 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 1.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   97 ASP
Chi-restraints excluded: chain E residue  150 GLU
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain E residue  258 TYR
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain D residue  258 TYR
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  115 ASP
Chi-restraints excluded: chain C residue  167 SER
Chi-restraints excluded: chain C residue  258 TYR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue  150 GLU
Chi-restraints excluded: chain B residue  167 SER
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  167 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 103 optimal weight:    0.8980
   chunk 99 optimal weight:   10.0000
   chunk 108 optimal weight:    5.9990
   chunk 105 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 48 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   chunk 136 optimal weight:    5.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
D 169 HIS
C  89 ASN
C 169 HIS
B 169 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.152044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.122940 restraints weight = 13460.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 1.51
r_work: 0.3104 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12865  Z= 0.140
  Angle     :  0.506   4.988  17535  Z= 0.266
  Chirality :  0.045   0.193   1950
  Planarity :  0.004   0.028   2235
  Dihedral  :  4.548  15.992   1685
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 12.65 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.22), residues: 1525
  helix:  1.96 (0.23), residues: 505
  sheet:  0.14 (0.23), residues: 485
  loop : -2.01 (0.25), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 161 
 HIS   0.004   0.001   HIS B 285 
 PHE   0.014   0.001   PHE D 282 
 TYR   0.011   0.001   TYR C 270 
 ARG   0.003   0.000   ARG B 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03590 (  540)
  hydrogen bonds       : angle       4.36470 ( 1575)
  covalent geometry    : bond        0.00329 (12865)
  covalent geometry    : angle       0.50631 (17535)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 152
  time to evaluate  : 1.397 
Fit side-chains
REVERT: E  258 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7447 (p90)
REVERT: E  297 ILE cc_start: 0.6475 (OUTLIER) cc_final: 0.6235 (tp)
REVERT: D  255 ARG cc_start: 0.8107 (mmp80) cc_final: 0.7044 (mmt90)
REVERT: D  258 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.7651 (p90)
REVERT: C  258 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.7695 (p90)
REVERT: B  122 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7929 (m-30)
REVERT: B  255 ARG cc_start: 0.7817 (mmp80) cc_final: 0.6716 (mmt90)
REVERT: B  258 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7680 (p90)
REVERT: A  174 ARG cc_start: 0.7169 (tmm160) cc_final: 0.6917 (tmm160)
  outliers start: 30
  outliers final: 20
  residues processed: 167
  average time/residue: 0.2758
  time to fit residues: 65.0854
Evaluate side-chains
  171 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 145
  time to evaluate  : 1.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain E residue  258 TYR
Chi-restraints excluded: chain E residue  297 ILE
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain D residue  258 TYR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  115 ASP
Chi-restraints excluded: chain C residue  167 SER
Chi-restraints excluded: chain C residue  258 TYR
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  167 SER
Chi-restraints excluded: chain B residue  258 TYR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  259 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 142 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 92 optimal weight:    2.9990
   chunk 120 optimal weight:    9.9990
   chunk 49 optimal weight:    5.9990
   chunk 144 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 110 optimal weight:    9.9990
   chunk 60 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
E 169 HIS
D 169 HIS
C 169 HIS
B 169 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.146281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.119047 restraints weight = 13566.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.39
r_work: 0.2943 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.3193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037  12865  Z= 0.256
  Angle     :  0.634   6.387  17535  Z= 0.333
  Chirality :  0.049   0.164   1950
  Planarity :  0.005   0.032   2235
  Dihedral  :  5.158  18.911   1685
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 12.80 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.21), residues: 1525
  helix:  1.49 (0.23), residues: 505
  sheet: -0.10 (0.22), residues: 485
  loop : -2.12 (0.24), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D 161 
 HIS   0.005   0.001   HIS B 285 
 PHE   0.015   0.002   PHE D 282 
 TYR   0.013   0.002   TYR C 270 
 ARG   0.004   0.000   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04683 (  540)
  hydrogen bonds       : angle       4.68269 ( 1575)
  covalent geometry    : bond        0.00619 (12865)
  covalent geometry    : angle       0.63443 (17535)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 136
  time to evaluate  : 1.344 
Fit side-chains
REVERT: E  258 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7466 (p90)
REVERT: D  255 ARG cc_start: 0.8171 (mmp80) cc_final: 0.7193 (mmt90)
REVERT: D  258 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.7889 (p90)
REVERT: B  258 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7841 (p90)
REVERT: A  148 TYR cc_start: 0.8532 (m-80) cc_final: 0.8245 (m-80)
REVERT: A  255 ARG cc_start: 0.8124 (mmp80) cc_final: 0.7161 (mmt90)
  outliers start: 40
  outliers final: 29
  residues processed: 163
  average time/residue: 0.2757
  time to fit residues: 63.3902
Evaluate side-chains
  161 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 129
  time to evaluate  : 1.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   60 ASN
Chi-restraints excluded: chain E residue   97 ASP
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain E residue  258 TYR
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain D residue  258 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  115 ASP
Chi-restraints excluded: chain C residue  167 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  167 SER
Chi-restraints excluded: chain B residue  258 TYR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  167 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 68 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 139 optimal weight:    0.8980
   chunk 136 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 127 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
D 169 HIS
C 169 HIS
B 169 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.150863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.124303 restraints weight = 13332.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 1.48
r_work: 0.3083 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  12865  Z= 0.123
  Angle     :  0.498   4.966  17535  Z= 0.264
  Chirality :  0.045   0.168   1950
  Planarity :  0.003   0.030   2235
  Dihedral  :  4.603  15.571   1685
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 13.53 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.22), residues: 1525
  helix:  1.91 (0.23), residues: 505
  sheet: -0.01 (0.23), residues: 485
  loop : -2.02 (0.25), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 161 
 HIS   0.003   0.001   HIS B 285 
 PHE   0.011   0.001   PHE D 282 
 TYR   0.010   0.001   TYR C 270 
 ARG   0.003   0.000   ARG B 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03504 (  540)
  hydrogen bonds       : angle       4.40920 ( 1575)
  covalent geometry    : bond        0.00283 (12865)
  covalent geometry    : angle       0.49790 (17535)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 157
  time to evaluate  : 2.615 
Fit side-chains
REVERT: E  149 THR cc_start: 0.8099 (t) cc_final: 0.7620 (p)
REVERT: E  258 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.7519 (p90)
REVERT: D  255 ARG cc_start: 0.8087 (mmp80) cc_final: 0.7076 (mmt90)
REVERT: D  258 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.7730 (p90)
REVERT: B  122 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7873 (m-30)
REVERT: B  258 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7721 (p90)
REVERT: A  174 ARG cc_start: 0.7112 (tmm160) cc_final: 0.6888 (tmm160)
REVERT: A  255 ARG cc_start: 0.7971 (mmp80) cc_final: 0.6903 (mmt90)
  outliers start: 27
  outliers final: 21
  residues processed: 172
  average time/residue: 0.4273
  time to fit residues: 107.2689
Evaluate side-chains
  168 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 1.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain E residue  258 TYR
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain D residue   13 ASP
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain D residue  258 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  115 ASP
Chi-restraints excluded: chain C residue  167 SER
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  167 SER
Chi-restraints excluded: chain B residue  258 TYR
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  167 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 86 optimal weight:   10.0000
   chunk 109 optimal weight:    6.9990
   chunk 143 optimal weight:    0.7980
   chunk 44 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9990
   chunk 62 optimal weight:    9.9990
   chunk 95 optimal weight:    5.9990
   chunk 100 optimal weight:    8.9990
   chunk 148 optimal weight:    8.9990
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
D 169 HIS
C 169 HIS
B 169 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.147354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.122217 restraints weight = 13476.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 1.17
r_work: 0.3022 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.3254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032  12865  Z= 0.214
  Angle     :  0.586   5.634  17535  Z= 0.308
  Chirality :  0.048   0.215   1950
  Planarity :  0.004   0.027   2235
  Dihedral  :  4.945  17.027   1685
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.53 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.21), residues: 1525
  helix:  1.66 (0.23), residues: 505
  sheet: -0.15 (0.23), residues: 485
  loop : -2.08 (0.25), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP E 161 
 HIS   0.004   0.001   HIS B 285 
 PHE   0.014   0.002   PHE C 282 
 TYR   0.012   0.001   TYR C 270 
 ARG   0.004   0.000   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04291 (  540)
  hydrogen bonds       : angle       4.58153 ( 1575)
  covalent geometry    : bond        0.00518 (12865)
  covalent geometry    : angle       0.58610 (17535)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 137
  time to evaluate  : 1.215 
Fit side-chains
REVERT: E  149 THR cc_start: 0.8171 (t) cc_final: 0.7686 (p)
REVERT: E  255 ARG cc_start: 0.8134 (mmp80) cc_final: 0.7174 (mmt90)
REVERT: E  258 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7540 (p90)
REVERT: D  255 ARG cc_start: 0.8101 (mmp80) cc_final: 0.7209 (mmt90)
REVERT: D  258 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7839 (p90)
REVERT: C  258 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7821 (p90)
REVERT: B  255 ARG cc_start: 0.8258 (mmp80) cc_final: 0.7081 (mmt90)
REVERT: B  258 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.7868 (p90)
REVERT: A  255 ARG cc_start: 0.8079 (mmp80) cc_final: 0.7115 (mmt90)
  outliers start: 33
  outliers final: 26
  residues processed: 158
  average time/residue: 0.2816
  time to fit residues: 62.4922
Evaluate side-chains
  166 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 136
  time to evaluate  : 1.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain E residue  258 TYR
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain D residue  258 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  115 ASP
Chi-restraints excluded: chain C residue  122 ASP
Chi-restraints excluded: chain C residue  167 SER
Chi-restraints excluded: chain C residue  258 TYR
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  167 SER
Chi-restraints excluded: chain B residue  258 TYR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  167 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 128 optimal weight:    4.9990
   chunk 80 optimal weight:    9.9990
   chunk 28 optimal weight:    3.9990
   chunk 136 optimal weight:   10.0000
   chunk 34 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 142 optimal weight:    3.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
D 169 HIS
C 169 HIS
B 169 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.150480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.122375 restraints weight = 13211.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 1.43
r_work: 0.3004 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  12865  Z= 0.148
  Angle     :  0.518   4.984  17535  Z= 0.273
  Chirality :  0.046   0.210   1950
  Planarity :  0.004   0.028   2235
  Dihedral  :  4.654  16.150   1685
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 14.04 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.22), residues: 1525
  helix:  1.86 (0.23), residues: 505
  sheet: -0.08 (0.23), residues: 485
  loop : -2.00 (0.25), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 161 
 HIS   0.004   0.001   HIS B 285 
 PHE   0.012   0.001   PHE C 282 
 TYR   0.011   0.001   TYR C 270 
 ARG   0.003   0.000   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03703 (  540)
  hydrogen bonds       : angle       4.45218 ( 1575)
  covalent geometry    : bond        0.00350 (12865)
  covalent geometry    : angle       0.51791 (17535)

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

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

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3050 Ramachandran restraints generated.
    1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 139
  time to evaluate  : 1.455 
Fit side-chains
REVERT: E  149 THR cc_start: 0.8086 (t) cc_final: 0.7631 (p)
REVERT: E  258 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7488 (p90)
REVERT: D  255 ARG cc_start: 0.8023 (mmp80) cc_final: 0.7032 (mmt90)
REVERT: D  258 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.7795 (p90)
REVERT: C  258 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7758 (p90)
REVERT: B  255 ARG cc_start: 0.8241 (mmp80) cc_final: 0.6975 (mmt90)
REVERT: B  258 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7778 (p90)
REVERT: A  174 ARG cc_start: 0.7120 (tmm160) cc_final: 0.6883 (tmm160)
REVERT: A  255 ARG cc_start: 0.8054 (mmp80) cc_final: 0.6985 (mmt90)
  outliers start: 28
  outliers final: 23
  residues processed: 158
  average time/residue: 0.2922
  time to fit residues: 63.9177
Evaluate side-chains
  165 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 1.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  167 SER
Chi-restraints excluded: chain E residue  258 TYR
Chi-restraints excluded: chain E residue  259 THR
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   60 ASN
Chi-restraints excluded: chain D residue   97 ASP
Chi-restraints excluded: chain D residue  118 LEU
Chi-restraints excluded: chain D residue  167 SER
Chi-restraints excluded: chain D residue  258 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   97 ASP
Chi-restraints excluded: chain C residue  115 ASP
Chi-restraints excluded: chain C residue  167 SER
Chi-restraints excluded: chain C residue  258 TYR
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  167 SER
Chi-restraints excluded: chain B residue  258 TYR
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain A residue   60 ASN
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  115 ASP
Chi-restraints excluded: chain A residue  167 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 37 optimal weight:    8.9990
   chunk 131 optimal weight:    4.9990
   chunk 120 optimal weight:    9.9990
   chunk 100 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   chunk 128 optimal weight:    0.5980
   chunk 3 optimal weight:    6.9990
   chunk 146 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   overall best weight:    3.9188

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

Flipped N/Q/H residues before XYZ refinement:
D 169 HIS
A 169 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.146887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.117923 restraints weight = 13471.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 1.81
r_work: 0.2972 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.3368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036  12865  Z= 0.241
  Angle     :  0.618   6.278  17535  Z= 0.325
  Chirality :  0.049   0.209   1950
  Planarity :  0.004   0.031   2235
  Dihedral  :  5.089  18.374   1685
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 13.75 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.46 (0.21), residues: 1525
  helix:  1.49 (0.23), residues: 505
  sheet: -0.24 (0.23), residues: 485
  loop : -2.13 (0.25), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP E 161 
 HIS   0.004   0.001   HIS B 285 
 PHE   0.014   0.002   PHE D 282 
 TYR   0.013   0.002   TYR C 270 
 ARG   0.004   0.000   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04557 (  540)
  hydrogen bonds       : angle       4.66512 ( 1575)
  covalent geometry    : bond        0.00585 (12865)
  covalent geometry    : angle       0.61843 (17535)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6673.41 seconds
wall clock time: 121 minutes 12.56 seconds (7272.56 seconds total)