Starting phenix.real_space_refine
on Thu Sep 18 06:51:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kc9_62246/09_2025/9kc9_62246.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kc9_62246/09_2025/9kc9_62246.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kc9_62246/09_2025/9kc9_62246.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kc9_62246/09_2025/9kc9_62246.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kc9_62246/09_2025/9kc9_62246.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kc9_62246/09_2025/9kc9_62246.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.246
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: 6
    Type Number    sf(0)   Gaussians
     Ca      5      9.91       5
     S      80      5.16       5
     Cl     10      4.86       5
     C    9840      2.51       5
     N    2480      2.21       5
     O    2590      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15005
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2998
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 365, 2998
          Classifications: {'peptide': 365}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 16, 'TRANS': 348}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 1, ' CL': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    E, B, C, D
  Time building chain proxies: 2.68, per 1000 atoms: 0.18
  Number of scatterers: 15005
  At special positions: 0
  Unit cell: (97.44, 95.7, 113.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      5     19.99
     Cl     10     17.00
     S      80     16.00
     O    2590      8.00
     N    2480      7.00
     C    9840      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: 1.14
  Conformation dependent library (CDL) restraints added in 658.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3450

  Finding SS restraints...
    Secondary structure from input PDB file:
      90 helices and 0 sheets defined
      67.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 9
    Processing helix  chain 'A' and resid 18 through 23
      removed outlier: 3.681A  pdb=" N   LEU A  21 " --> pdb=" O   SER A  18 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU A  22 " --> pdb=" O   SER A  19 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   CYS A  23 " --> pdb=" O   LEU A  20 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 18 through 23'
    Processing helix  chain 'A' and resid 27 through 53
      removed outlier: 5.135A  pdb=" N   GLY A  34 " --> pdb=" O   LYS A  30 " (cutoff:3.500A)
      removed outlier: 5.417A  pdb=" N   GLU A  35 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   LEU A  37 " --> pdb=" O   TYR A  33 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   VAL A  38 " --> pdb=" O   GLY A  34 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE A  39 " --> pdb=" O   GLU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 71
    Processing helix  chain 'A' and resid 77 through 85
      removed outlier: 5.037A  pdb=" N   GLY A  83 " --> pdb=" O   SER A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 99
      removed outlier: 3.590A  pdb=" N   ASN A  99 " --> pdb=" O   SER A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 114
      removed outlier: 3.624A  pdb=" N   ILE A 108 " --> pdb=" O   ASP A 104 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   GLN A 109 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 144
      removed outlier: 3.742A  pdb=" N   ALA A 132 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ILE A 133 " --> pdb=" O   ILE A 129 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLY A 135 " --> pdb=" O   TYR A 131 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLN A 136 " --> pdb=" O   ALA A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 151
    Processing helix  chain 'A' and resid 153 through 160
      removed outlier: 3.837A  pdb=" N   LEU A 157 " --> pdb=" O   THR A 153 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL A 158 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 173
    Processing helix  chain 'A' and resid 182 through 197
      removed outlier: 3.684A  pdb=" N   VAL A 186 " --> pdb=" O   TRP A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 230
      removed outlier: 3.963A  pdb=" N   GLU A 213 " --> pdb=" O   SER A 209 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   VAL A 214 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   CYS A 215 " --> pdb=" O   MET A 211 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR A 216 " --> pdb=" O   ASN A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 253
      removed outlier: 3.746A  pdb=" N   PHE A 247 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   PHE A 248 " --> pdb=" O   VAL A 244 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ILE A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 263
      removed outlier: 4.045A  pdb=" N   LYS A 262 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ASP A 263 " --> pdb=" O   PRO A 260 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 259 through 263'
    Processing helix  chain 'A' and resid 274 through 295
      removed outlier: 3.781A  pdb=" N   ILE A 278 " --> pdb=" O   PRO A 274 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU A 279 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLN A 280 " --> pdb=" O   PHE A 276 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LEU A 288 " --> pdb=" O   TYR A 284 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   ALA A 291 " --> pdb=" O   TRP A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 324
    Processing helix  chain 'A' and resid 351 through 355
      removed outlier: 3.562A  pdb=" N   SER A 354 " --> pdb=" O   SER A 351 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ARG A 355 " --> pdb=" O   ALA A 352 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 351 through 355'
    Processing helix  chain 'E' and resid 5 through 9
    Processing helix  chain 'E' and resid 18 through 23
      removed outlier: 3.680A  pdb=" N   LEU E  21 " --> pdb=" O   SER E  18 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU E  22 " --> pdb=" O   SER E  19 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   CYS E  23 " --> pdb=" O   LEU E  20 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 18 through 23'
    Processing helix  chain 'E' and resid 27 through 53
      removed outlier: 5.135A  pdb=" N   GLY E  34 " --> pdb=" O   LYS E  30 " (cutoff:3.500A)
      removed outlier: 5.416A  pdb=" N   GLU E  35 " --> pdb=" O   LEU E  31 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   LEU E  37 " --> pdb=" O   TYR E  33 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   VAL E  38 " --> pdb=" O   GLY E  34 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE E  39 " --> pdb=" O   GLU E  35 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 71
    Processing helix  chain 'E' and resid 77 through 85
      removed outlier: 5.038A  pdb=" N   GLY E  83 " --> pdb=" O   SER E  79 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 99
      removed outlier: 3.590A  pdb=" N   ASN E  99 " --> pdb=" O   SER E  95 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 103 through 114
      removed outlier: 3.623A  pdb=" N   ILE E 108 " --> pdb=" O   ASP E 104 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   GLN E 109 " --> pdb=" O   ARG E 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 121 through 144
      removed outlier: 3.742A  pdb=" N   ALA E 132 " --> pdb=" O   LEU E 128 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ILE E 133 " --> pdb=" O   ILE E 129 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLY E 135 " --> pdb=" O   TYR E 131 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLN E 136 " --> pdb=" O   ALA E 132 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 144 through 151
    Processing helix  chain 'E' and resid 153 through 160
      removed outlier: 3.837A  pdb=" N   LEU E 157 " --> pdb=" O   THR E 153 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   VAL E 158 " --> pdb=" O   LEU E 154 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 164 through 173
    Processing helix  chain 'E' and resid 182 through 197
      removed outlier: 3.684A  pdb=" N   VAL E 186 " --> pdb=" O   TRP E 182 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 209 through 230
      removed outlier: 3.963A  pdb=" N   GLU E 213 " --> pdb=" O   SER E 209 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   VAL E 214 " --> pdb=" O   LEU E 210 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   CYS E 215 " --> pdb=" O   MET E 211 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR E 216 " --> pdb=" O   ASN E 212 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 233 through 253
      removed outlier: 3.746A  pdb=" N   PHE E 247 " --> pdb=" O   ALA E 243 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   PHE E 248 " --> pdb=" O   VAL E 244 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ILE E 253 " --> pdb=" O   LEU E 249 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 259 through 263
      removed outlier: 4.045A  pdb=" N   LYS E 262 " --> pdb=" O   ASN E 259 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ASP E 263 " --> pdb=" O   PRO E 260 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 259 through 263'
    Processing helix  chain 'E' and resid 274 through 295
      removed outlier: 3.782A  pdb=" N   ILE E 278 " --> pdb=" O   PRO E 274 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU E 279 " --> pdb=" O   VAL E 275 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLN E 280 " --> pdb=" O   PHE E 276 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LEU E 288 " --> pdb=" O   TYR E 284 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   ALA E 291 " --> pdb=" O   TRP E 287 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 312 through 324
    Processing helix  chain 'E' and resid 351 through 355
      removed outlier: 3.563A  pdb=" N   SER E 354 " --> pdb=" O   SER E 351 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ARG E 355 " --> pdb=" O   ALA E 352 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 351 through 355'
    Processing helix  chain 'B' and resid 5 through 9
    Processing helix  chain 'B' and resid 18 through 23
      removed outlier: 3.681A  pdb=" N   LEU B  21 " --> pdb=" O   SER B  18 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU B  22 " --> pdb=" O   SER B  19 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   CYS B  23 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 18 through 23'
    Processing helix  chain 'B' and resid 27 through 53
      removed outlier: 5.136A  pdb=" N   GLY B  34 " --> pdb=" O   LYS B  30 " (cutoff:3.500A)
      removed outlier: 5.417A  pdb=" N   GLU B  35 " --> pdb=" O   LEU B  31 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   LEU B  37 " --> pdb=" O   TYR B  33 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   VAL B  38 " --> pdb=" O   GLY B  34 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE B  39 " --> pdb=" O   GLU B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 71
    Processing helix  chain 'B' and resid 77 through 85
      removed outlier: 5.037A  pdb=" N   GLY B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 99
      removed outlier: 3.591A  pdb=" N   ASN B  99 " --> pdb=" O   SER B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 114
      removed outlier: 3.624A  pdb=" N   ILE B 108 " --> pdb=" O   ASP B 104 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   GLN B 109 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 144
      removed outlier: 3.742A  pdb=" N   ALA B 132 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ILE B 133 " --> pdb=" O   ILE B 129 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLY B 135 " --> pdb=" O   TYR B 131 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLN B 136 " --> pdb=" O   ALA B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 151
    Processing helix  chain 'B' and resid 153 through 160
      removed outlier: 3.837A  pdb=" N   LEU B 157 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL B 158 " --> pdb=" O   LEU B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 173
    Processing helix  chain 'B' and resid 182 through 197
      removed outlier: 3.684A  pdb=" N   VAL B 186 " --> pdb=" O   TRP B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 230
      removed outlier: 3.963A  pdb=" N   GLU B 213 " --> pdb=" O   SER B 209 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   VAL B 214 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   CYS B 215 " --> pdb=" O   MET B 211 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR B 216 " --> pdb=" O   ASN B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 253
      removed outlier: 3.747A  pdb=" N   PHE B 247 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   PHE B 248 " --> pdb=" O   VAL B 244 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ILE B 253 " --> pdb=" O   LEU B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 263
      removed outlier: 4.045A  pdb=" N   LYS B 262 " --> pdb=" O   ASN B 259 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ASP B 263 " --> pdb=" O   PRO B 260 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 259 through 263'
    Processing helix  chain 'B' and resid 274 through 295
      removed outlier: 3.781A  pdb=" N   ILE B 278 " --> pdb=" O   PRO B 274 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU B 279 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLN B 280 " --> pdb=" O   PHE B 276 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LEU B 288 " --> pdb=" O   TYR B 284 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   ALA B 291 " --> pdb=" O   TRP B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 324
    Processing helix  chain 'B' and resid 351 through 355
      removed outlier: 3.563A  pdb=" N   SER B 354 " --> pdb=" O   SER B 351 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ARG B 355 " --> pdb=" O   ALA B 352 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 351 through 355'
    Processing helix  chain 'C' and resid 5 through 9
    Processing helix  chain 'C' and resid 18 through 23
      removed outlier: 3.681A  pdb=" N   LEU C  21 " --> pdb=" O   SER C  18 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU C  22 " --> pdb=" O   SER C  19 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   CYS C  23 " --> pdb=" O   LEU C  20 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 18 through 23'
    Processing helix  chain 'C' and resid 27 through 53
      removed outlier: 5.135A  pdb=" N   GLY C  34 " --> pdb=" O   LYS C  30 " (cutoff:3.500A)
      removed outlier: 5.417A  pdb=" N   GLU C  35 " --> pdb=" O   LEU C  31 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   LEU C  37 " --> pdb=" O   TYR C  33 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   VAL C  38 " --> pdb=" O   GLY C  34 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE C  39 " --> pdb=" O   GLU C  35 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 71
    Processing helix  chain 'C' and resid 77 through 85
      removed outlier: 5.037A  pdb=" N   GLY C  83 " --> pdb=" O   SER C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 99
      removed outlier: 3.591A  pdb=" N   ASN C  99 " --> pdb=" O   SER C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 114
      removed outlier: 3.624A  pdb=" N   ILE C 108 " --> pdb=" O   ASP C 104 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   GLN C 109 " --> pdb=" O   ARG C 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 144
      removed outlier: 3.742A  pdb=" N   ALA C 132 " --> pdb=" O   LEU C 128 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ILE C 133 " --> pdb=" O   ILE C 129 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLY C 135 " --> pdb=" O   TYR C 131 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLN C 136 " --> pdb=" O   ALA C 132 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 151
    Processing helix  chain 'C' and resid 153 through 160
      removed outlier: 3.837A  pdb=" N   LEU C 157 " --> pdb=" O   THR C 153 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   VAL C 158 " --> pdb=" O   LEU C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 164 through 173
    Processing helix  chain 'C' and resid 182 through 197
      removed outlier: 3.684A  pdb=" N   VAL C 186 " --> pdb=" O   TRP C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 230
      removed outlier: 3.963A  pdb=" N   GLU C 213 " --> pdb=" O   SER C 209 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   VAL C 214 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   CYS C 215 " --> pdb=" O   MET C 211 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR C 216 " --> pdb=" O   ASN C 212 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 253
      removed outlier: 3.746A  pdb=" N   PHE C 247 " --> pdb=" O   ALA C 243 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   PHE C 248 " --> pdb=" O   VAL C 244 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ILE C 253 " --> pdb=" O   LEU C 249 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 263
      removed outlier: 4.045A  pdb=" N   LYS C 262 " --> pdb=" O   ASN C 259 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ASP C 263 " --> pdb=" O   PRO C 260 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 259 through 263'
    Processing helix  chain 'C' and resid 274 through 295
      removed outlier: 3.782A  pdb=" N   ILE C 278 " --> pdb=" O   PRO C 274 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU C 279 " --> pdb=" O   VAL C 275 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLN C 280 " --> pdb=" O   PHE C 276 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LEU C 288 " --> pdb=" O   TYR C 284 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   ALA C 291 " --> pdb=" O   TRP C 287 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 312 through 324
    Processing helix  chain 'C' and resid 351 through 355
      removed outlier: 3.563A  pdb=" N   SER C 354 " --> pdb=" O   SER C 351 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ARG C 355 " --> pdb=" O   ALA C 352 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 351 through 355'
    Processing helix  chain 'D' and resid 5 through 9
    Processing helix  chain 'D' and resid 18 through 23
      removed outlier: 3.681A  pdb=" N   LEU D  21 " --> pdb=" O   SER D  18 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   LEU D  22 " --> pdb=" O   SER D  19 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   CYS D  23 " --> pdb=" O   LEU D  20 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 18 through 23'
    Processing helix  chain 'D' and resid 27 through 53
      removed outlier: 5.135A  pdb=" N   GLY D  34 " --> pdb=" O   LYS D  30 " (cutoff:3.500A)
      removed outlier: 5.417A  pdb=" N   GLU D  35 " --> pdb=" O   LEU D  31 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   LEU D  37 " --> pdb=" O   TYR D  33 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   VAL D  38 " --> pdb=" O   GLY D  34 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   PHE D  39 " --> pdb=" O   GLU D  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 71
    Processing helix  chain 'D' and resid 77 through 85
      removed outlier: 5.037A  pdb=" N   GLY D  83 " --> pdb=" O   SER D  79 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 85 through 99
      removed outlier: 3.590A  pdb=" N   ASN D  99 " --> pdb=" O   SER D  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 114
      removed outlier: 3.624A  pdb=" N   ILE D 108 " --> pdb=" O   ASP D 104 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   GLN D 109 " --> pdb=" O   ARG D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 121 through 144
      removed outlier: 3.742A  pdb=" N   ALA D 132 " --> pdb=" O   LEU D 128 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ILE D 133 " --> pdb=" O   ILE D 129 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLY D 135 " --> pdb=" O   TYR D 131 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLN D 136 " --> pdb=" O   ALA D 132 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 144 through 151
    Processing helix  chain 'D' and resid 153 through 160
      removed outlier: 3.837A  pdb=" N   LEU D 157 " --> pdb=" O   THR D 153 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   VAL D 158 " --> pdb=" O   LEU D 154 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 164 through 173
    Processing helix  chain 'D' and resid 182 through 197
      removed outlier: 3.685A  pdb=" N   VAL D 186 " --> pdb=" O   TRP D 182 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 230
      removed outlier: 3.964A  pdb=" N   GLU D 213 " --> pdb=" O   SER D 209 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   VAL D 214 " --> pdb=" O   LEU D 210 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   CYS D 215 " --> pdb=" O   MET D 211 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR D 216 " --> pdb=" O   ASN D 212 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 233 through 253
      removed outlier: 3.746A  pdb=" N   PHE D 247 " --> pdb=" O   ALA D 243 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   PHE D 248 " --> pdb=" O   VAL D 244 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ILE D 253 " --> pdb=" O   LEU D 249 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 259 through 263
      removed outlier: 4.045A  pdb=" N   LYS D 262 " --> pdb=" O   ASN D 259 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ASP D 263 " --> pdb=" O   PRO D 260 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 259 through 263'
    Processing helix  chain 'D' and resid 274 through 295
      removed outlier: 3.781A  pdb=" N   ILE D 278 " --> pdb=" O   PRO D 274 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU D 279 " --> pdb=" O   VAL D 275 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLN D 280 " --> pdb=" O   PHE D 276 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LEU D 288 " --> pdb=" O   TYR D 284 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   ALA D 291 " --> pdb=" O   TRP D 287 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 312 through 324
    Processing helix  chain 'D' and resid 351 through 355
      removed outlier: 3.562A  pdb=" N   SER D 354 " --> pdb=" O   SER D 351 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ARG D 355 " --> pdb=" O   ALA D 352 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 351 through 355'

    710 hydrogen bonds defined for protein.
    2100 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.07

  Time building geometry restraints manager: 1.57 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 2270
        1.29 -     1.42: 4510
        1.42 -     1.56: 8515
        1.56 -     1.69: 0
        1.69 -     1.82: 135
  Bond restraints: 15430
  Sorted by residual:
  bond pdb=" C   GLN B 208 "
       pdb=" O   GLN B 208 "
    ideal  model  delta    sigma   weight residual
    1.236  1.161  0.075 1.32e-02 5.74e+03 3.27e+01
  bond pdb=" C   GLN A 208 "
       pdb=" O   GLN A 208 "
    ideal  model  delta    sigma   weight residual
    1.236  1.161  0.075 1.32e-02 5.74e+03 3.26e+01
  bond pdb=" C   GLN D 208 "
       pdb=" O   GLN D 208 "
    ideal  model  delta    sigma   weight residual
    1.236  1.161  0.075 1.32e-02 5.74e+03 3.24e+01
  bond pdb=" C   GLN C 208 "
       pdb=" O   GLN C 208 "
    ideal  model  delta    sigma   weight residual
    1.236  1.161  0.075 1.32e-02 5.74e+03 3.22e+01
  bond pdb=" C   GLN E 208 "
       pdb=" O   GLN E 208 "
    ideal  model  delta    sigma   weight residual
    1.236  1.161  0.075 1.32e-02 5.74e+03 3.22e+01
  ... (remaining 15425 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 20676
        1.99 -     3.98: 289
        3.98 -     5.97: 30
        5.97 -     7.97: 5
        7.97 -     9.96: 10
  Bond angle restraints: 21010
  Sorted by residual:
  angle pdb=" N   ILE B 311 "
        pdb=" CA  ILE B 311 "
        pdb=" C   ILE B 311 "
      ideal   model   delta    sigma   weight residual
     113.39  103.43    9.96 1.47e+00 4.63e-01 4.59e+01
  angle pdb=" N   ILE A 311 "
        pdb=" CA  ILE A 311 "
        pdb=" C   ILE A 311 "
      ideal   model   delta    sigma   weight residual
     113.39  103.43    9.96 1.47e+00 4.63e-01 4.59e+01
  angle pdb=" N   ILE D 311 "
        pdb=" CA  ILE D 311 "
        pdb=" C   ILE D 311 "
      ideal   model   delta    sigma   weight residual
     113.39  103.43    9.96 1.47e+00 4.63e-01 4.59e+01
  angle pdb=" N   ILE C 311 "
        pdb=" CA  ILE C 311 "
        pdb=" C   ILE C 311 "
      ideal   model   delta    sigma   weight residual
     113.39  103.45    9.94 1.47e+00 4.63e-01 4.57e+01
  angle pdb=" N   ILE E 311 "
        pdb=" CA  ILE E 311 "
        pdb=" C   ILE E 311 "
      ideal   model   delta    sigma   weight residual
     113.39  103.48    9.91 1.47e+00 4.63e-01 4.54e+01
  ... (remaining 21005 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.23: 7490
       17.23 -    34.47: 1085
       34.47 -    51.70: 285
       51.70 -    68.94: 70
       68.94 -    86.17: 30
  Dihedral angle restraints: 8960
    sinusoidal: 3585
      harmonic: 5375
  Sorted by residual:
  dihedral pdb=" C   GLN E 208 "
           pdb=" N   GLN E 208 "
           pdb=" CA  GLN E 208 "
           pdb=" CB  GLN E 208 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.14  -10.46     0      2.50e+00 1.60e-01 1.75e+01
  dihedral pdb=" C   GLN B 208 "
           pdb=" N   GLN B 208 "
           pdb=" CA  GLN B 208 "
           pdb=" CB  GLN B 208 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.20  -10.40     0      2.50e+00 1.60e-01 1.73e+01
  dihedral pdb=" C   GLN C 208 "
           pdb=" N   GLN C 208 "
           pdb=" CA  GLN C 208 "
           pdb=" CB  GLN C 208 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.21  -10.39     0      2.50e+00 1.60e-01 1.73e+01
  ... (remaining 8957 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1702
       0.039 -    0.079: 489
       0.079 -    0.118: 89
       0.118 -    0.157: 25
       0.157 -    0.197: 5
  Chirality restraints: 2310
  Sorted by residual:
  chirality pdb=" CA  GLN E 208 "
            pdb=" N   GLN E 208 "
            pdb=" C   GLN E 208 "
            pdb=" CB  GLN E 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.67e-01
  chirality pdb=" CA  GLN C 208 "
            pdb=" N   GLN C 208 "
            pdb=" C   GLN C 208 "
            pdb=" CB  GLN C 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.19 2.00e-01 2.50e+01 9.48e-01
  chirality pdb=" CA  GLN B 208 "
            pdb=" N   GLN B 208 "
            pdb=" C   GLN B 208 "
            pdb=" CB  GLN B 208 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.29e-01
  ... (remaining 2307 not shown)

  Planarity restraints: 2615
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 208 "    0.017 2.00e-02 2.50e+03   3.51e-02 1.23e+01
        pdb=" C   GLN A 208 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   GLN A 208 "    0.023 2.00e-02 2.50e+03
        pdb=" N   SER A 209 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN C 208 "   -0.017 2.00e-02 2.50e+03   3.50e-02 1.23e+01
        pdb=" C   GLN C 208 "    0.061 2.00e-02 2.50e+03
        pdb=" O   GLN C 208 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   SER C 209 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN E 208 "   -0.017 2.00e-02 2.50e+03   3.50e-02 1.22e+01
        pdb=" C   GLN E 208 "    0.060 2.00e-02 2.50e+03
        pdb=" O   GLN E 208 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   SER E 209 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 2612 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2799
        2.77 -     3.30: 13058
        3.30 -     3.84: 23694
        3.84 -     4.37: 26957
        4.37 -     4.90: 50387
  Nonbonded interactions: 116895
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  76 "
            pdb=" N   ILE B  78 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" O   ILE A  76 "
            pdb=" N   ILE A  78 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" O   ILE D  76 "
            pdb=" N   ILE D  78 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" O   ILE E  76 "
            pdb=" N   ILE E  78 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" O   ILE C  76 "
            pdb=" N   ILE C  78 "
     model   vdw
     2.239 3.120
  ... (remaining 116890 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
  selection = chain 'B'
  selection = chain 'C'
  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:             2.650
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.740
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  15430  Z= 0.194
  Angle     :  0.587   9.957  21010  Z= 0.353
  Chirality :  0.039   0.197   2310
  Planarity :  0.005   0.050   2615
  Dihedral  : 18.099  86.174   5510
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 28.44 %
    Favored  : 70.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.20), residues: 1815
  helix:  1.17 (0.16), residues: 1085
  sheet:  None (None), residues: 0
  loop : -1.37 (0.22), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  13 
 TYR   0.019   0.001   TYR B 236 
 PHE   0.009   0.001   PHE D 276 
 TRP   0.011   0.001   TRP B  93 
 HIS   0.002   0.000   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (15430)
  covalent geometry    : angle       0.58695 (21010)
  hydrogen bonds       : bond        0.08382 (  710)
  hydrogen bonds       : angle       3.95743 ( 2100)

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

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

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 226
  time to evaluate  : 0.576 
Fit side-chains
REVERT: A  208 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8270 (tm-30)
REVERT: E   13 ARG cc_start: 0.7713 (mmt90) cc_final: 0.7511 (mmt90)
REVERT: E  208 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7960 (tm-30)
REVERT: B   25 ARG cc_start: 0.7707 (mtp85) cc_final: 0.7392 (mtp85)
REVERT: B  208 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8006 (tm-30)
REVERT: C  208 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8212 (tm-30)
REVERT: C  328 ASN cc_start: 0.7874 (t0) cc_final: 0.7414 (t0)
REVERT: C  363 THR cc_start: 0.9308 (t) cc_final: 0.9036 (t)
REVERT: D   25 ARG cc_start: 0.7765 (mtp85) cc_final: 0.7359 (mtp85)
REVERT: D  208 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8243 (tm-30)
REVERT: D  310 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7659 (pt)
  outliers start: 10
  outliers final: 0
  residues processed: 235
  average time/residue: 0.1485
  time to fit residues: 48.7371
Evaluate side-chains
  229 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 223
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain E residue  208 GLN
Chi-restraints excluded: chain B residue  208 GLN
Chi-restraints excluded: chain C residue  208 GLN
Chi-restraints excluded: chain D residue  208 GLN
Chi-restraints excluded: chain D residue  310 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    9.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
E 328 ASN
C 296 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.127532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.089996 restraints weight = 16558.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.2847 rms_B_bonded: 2.22
r_work: 0.2685 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2525 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.0894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.036  15430  Z= 0.264
  Angle     :  0.622   6.841  21010  Z= 0.334
  Chirality :  0.043   0.178   2310
  Planarity :  0.005   0.059   2615
  Dihedral  :  6.389  80.849   2047
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 2.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 26.24 %
    Favored  : 70.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.20), residues: 1815
  helix:  0.73 (0.16), residues: 1090
  sheet:  None (None), residues: 0
  loop : -1.64 (0.22), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  13 
 TYR   0.029   0.002   TYR A 236 
 PHE   0.015   0.002   PHE E 283 
 TRP   0.016   0.002   TRP A  93 
 HIS   0.003   0.001   HIS C 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00656 (15430)
  covalent geometry    : angle       0.62172 (21010)
  hydrogen bonds       : bond        0.08025 (  710)
  hydrogen bonds       : angle       3.93869 ( 2100)

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

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

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 210
  time to evaluate  : 0.494 
Fit side-chains
REVERT: A   51 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6585 (mtt90)
REVERT: A  173 LYS cc_start: 0.7238 (mtpt) cc_final: 0.6984 (pttt)
REVERT: A  208 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8039 (tm-30)
REVERT: A  310 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7974 (pt)
REVERT: E   51 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6719 (mtt180)
REVERT: E  208 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8260 (tm-30)
REVERT: E  236 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.8416 (t80)
REVERT: B   25 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7507 (mtp85)
REVERT: B   51 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6768 (mtt180)
REVERT: B  159 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7744 (mp)
REVERT: B  173 LYS cc_start: 0.7227 (mtpt) cc_final: 0.6935 (pttt)
REVERT: B  208 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8113 (tm-30)
REVERT: B  310 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7937 (pt)
REVERT: B  328 ASN cc_start: 0.8098 (t0) cc_final: 0.7633 (t0)
REVERT: C   44 TYR cc_start: 0.7855 (m-80) cc_final: 0.7628 (m-80)
REVERT: C   51 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6740 (mtt180)
REVERT: C  120 GLU cc_start: 0.7857 (tp30) cc_final: 0.7211 (tp30)
REVERT: C  208 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8305 (tm-30)
REVERT: C  328 ASN cc_start: 0.8124 (t0) cc_final: 0.7834 (t0)
REVERT: D   25 ARG cc_start: 0.7905 (mtp85) cc_final: 0.7340 (mtp85)
REVERT: D   51 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6498 (mtt180)
REVERT: D  159 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7554 (mp)
REVERT: D  208 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8272 (tm-30)
REVERT: D  310 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7795 (pt)
  outliers start: 58
  outliers final: 26
  residues processed: 256
  average time/residue: 0.1492
  time to fit residues: 52.6934
Evaluate side-chains
  250 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 208
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain E residue   51 ARG
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue   90 VAL
Chi-restraints excluded: chain E residue  208 GLN
Chi-restraints excluded: chain E residue  236 TYR
Chi-restraints excluded: chain E residue  273 VAL
Chi-restraints excluded: chain E residue  354 SER
Chi-restraints excluded: chain B residue   16 SER
Chi-restraints excluded: chain B residue   51 ARG
Chi-restraints excluded: chain B residue   54 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  136 GLN
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  208 GLN
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue   16 SER
Chi-restraints excluded: chain C residue   51 ARG
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  159 LEU
Chi-restraints excluded: chain C residue  208 GLN
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain D residue   16 SER
Chi-restraints excluded: chain D residue   51 ARG
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  159 LEU
Chi-restraints excluded: chain D residue  208 GLN
Chi-restraints excluded: chain D residue  273 VAL
Chi-restraints excluded: chain D residue  310 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 171 optimal weight:    2.9990
   chunk 161 optimal weight:    0.0470
   chunk 167 optimal weight:    1.9990
   chunk 166 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0970
   chunk 21 optimal weight:    0.8980
   chunk 144 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 96 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.5476

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

Flipped N/Q/H residues before XYZ refinement:
C 296 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.134565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.097656 restraints weight = 16428.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 2.23
r_work: 0.2832 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2673 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.0713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  15430  Z= 0.103
  Angle     :  0.455   6.713  21010  Z= 0.247
  Chirality :  0.036   0.158   2310
  Planarity :  0.004   0.053   2615
  Dihedral  :  5.938  74.341   2047
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 26.36 %
    Favored  : 70.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (0.20), residues: 1815
  helix:  0.93 (0.16), residues: 1095
  sheet:  None (None), residues: 0
  loop : -1.46 (0.22), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  13 
 TYR   0.012   0.001   TYR E  97 
 PHE   0.009   0.001   PHE E 181 
 TRP   0.012   0.001   TRP D  93 
 HIS   0.001   0.000   HIS C 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (15430)
  covalent geometry    : angle       0.45486 (21010)
  hydrogen bonds       : bond        0.04621 (  710)
  hydrogen bonds       : angle       3.84500 ( 2100)

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

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

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 227
  time to evaluate  : 0.557 
Fit side-chains
REVERT: A   25 ARG cc_start: 0.7799 (mtp85) cc_final: 0.7446 (mtp85)
REVERT: A   51 ARG cc_start: 0.6896 (OUTLIER) cc_final: 0.6564 (mtt180)
REVERT: A  208 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8000 (tm-30)
REVERT: A  310 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7854 (pt)
REVERT: E   51 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6551 (mtt180)
REVERT: E  208 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8148 (tm-30)
REVERT: E  236 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.8225 (t80)
REVERT: E  310 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7864 (pt)
REVERT: B   25 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7413 (mtp85)
REVERT: B   51 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6673 (mtt180)
REVERT: B  159 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7723 (mp)
REVERT: B  173 LYS cc_start: 0.7009 (mtpt) cc_final: 0.6762 (pttt)
REVERT: B  208 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8039 (tm-30)
REVERT: B  310 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7814 (pt)
REVERT: C   25 ARG cc_start: 0.7883 (mtp85) cc_final: 0.7396 (mtp85)
REVERT: C   30 LYS cc_start: 0.8851 (tttt) cc_final: 0.8617 (ttpt)
REVERT: C  208 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8398 (tm-30)
REVERT: C  310 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7805 (pt)
REVERT: C  328 ASN cc_start: 0.7897 (t0) cc_final: 0.7248 (t0)
REVERT: D   25 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7316 (mtp85)
REVERT: D   51 ARG cc_start: 0.6757 (OUTLIER) cc_final: 0.6448 (mtt180)
REVERT: D  208 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8205 (tm-30)
REVERT: D  310 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7799 (pt)
  outliers start: 45
  outliers final: 21
  residues processed: 268
  average time/residue: 0.1550
  time to fit residues: 57.3369
Evaluate side-chains
  253 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 216
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain E residue   28 ILE
Chi-restraints excluded: chain E residue   51 ARG
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue  208 GLN
Chi-restraints excluded: chain E residue  236 TYR
Chi-restraints excluded: chain E residue  310 ILE
Chi-restraints excluded: chain E residue  322 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   51 ARG
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  208 GLN
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue  159 LEU
Chi-restraints excluded: chain C residue  208 GLN
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  310 ILE
Chi-restraints excluded: chain C residue  322 VAL
Chi-restraints excluded: chain D residue   28 ILE
Chi-restraints excluded: chain D residue   51 ARG
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  208 GLN
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  322 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 175 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 106 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 161 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 144 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
D  11 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.131721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.094614 restraints weight = 16492.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.2920 rms_B_bonded: 2.22
r_work: 0.2761 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2600 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.0790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15430  Z= 0.138
  Angle     :  0.480   7.087  21010  Z= 0.259
  Chirality :  0.037   0.166   2310
  Planarity :  0.005   0.056   2615
  Dihedral  :  5.826  73.381   2047
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 26.54 %
    Favored  : 70.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.20), residues: 1815
  helix:  0.94 (0.16), residues: 1095
  sheet:  None (None), residues: 0
  loop : -1.50 (0.22), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  13 
 TYR   0.018   0.001   TYR A 236 
 PHE   0.010   0.001   PHE C 283 
 TRP   0.012   0.001   TRP E  93 
 HIS   0.001   0.000   HIS C 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (15430)
  covalent geometry    : angle       0.47984 (21010)
  hydrogen bonds       : bond        0.05550 (  710)
  hydrogen bonds       : angle       3.78521 ( 2100)

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

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

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 219
  time to evaluate  : 0.523 
Fit side-chains
REVERT: A   25 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7478 (mtp85)
REVERT: A   51 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6589 (mtt180)
REVERT: A  208 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8021 (tm-30)
REVERT: A  282 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7703 (mp)
REVERT: A  310 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7933 (pt)
REVERT: E   25 ARG cc_start: 0.7767 (mtm110) cc_final: 0.7271 (mtp85)
REVERT: E  208 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8235 (tm-30)
REVERT: E  236 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.8298 (t80)
REVERT: E  282 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7634 (mp)
REVERT: E  310 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7894 (pt)
REVERT: B   25 ARG cc_start: 0.7941 (mtp85) cc_final: 0.7445 (mtp85)
REVERT: B   51 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6722 (mtt180)
REVERT: B  208 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8068 (tm-30)
REVERT: B  310 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7871 (pt)
REVERT: C   25 ARG cc_start: 0.7918 (mtp85) cc_final: 0.7418 (mtp85)
REVERT: C   30 LYS cc_start: 0.8905 (tttt) cc_final: 0.8623 (ttpt)
REVERT: C  208 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8403 (tm-30)
REVERT: C  310 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7887 (pt)
REVERT: C  328 ASN cc_start: 0.7919 (t0) cc_final: 0.7269 (t0)
REVERT: C  363 THR cc_start: 0.9314 (t) cc_final: 0.8998 (t)
REVERT: D   25 ARG cc_start: 0.7867 (mtp85) cc_final: 0.7344 (mtp85)
REVERT: D  208 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8258 (tm-30)
REVERT: D  310 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7818 (pt)
  outliers start: 52
  outliers final: 29
  residues processed: 269
  average time/residue: 0.1392
  time to fit residues: 52.3648
Evaluate side-chains
  257 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 213
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain E residue   28 ILE
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue  136 GLN
Chi-restraints excluded: chain E residue  208 GLN
Chi-restraints excluded: chain E residue  231 SER
Chi-restraints excluded: chain E residue  236 TYR
Chi-restraints excluded: chain E residue  282 LEU
Chi-restraints excluded: chain E residue  310 ILE
Chi-restraints excluded: chain E residue  322 VAL
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   51 ARG
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue  136 GLN
Chi-restraints excluded: chain B residue  208 GLN
Chi-restraints excluded: chain B residue  231 SER
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue  136 GLN
Chi-restraints excluded: chain C residue  208 GLN
Chi-restraints excluded: chain C residue  231 SER
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  310 ILE
Chi-restraints excluded: chain C residue  322 VAL
Chi-restraints excluded: chain C residue  329 LEU
Chi-restraints excluded: chain D residue   28 ILE
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  208 GLN
Chi-restraints excluded: chain D residue  231 SER
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  322 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 139 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 159 optimal weight:    0.0050
   chunk 40 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 16 optimal weight:    7.9990
   chunk 60 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.4000

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.135087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.098453 restraints weight = 16292.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 2.18
r_work: 0.2761 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2603 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.0881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15430  Z= 0.136
  Angle     :  0.478   6.947  21010  Z= 0.258
  Chirality :  0.037   0.156   2310
  Planarity :  0.005   0.056   2615
  Dihedral  :  5.687  71.501   2047
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 25.75 %
    Favored  : 70.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.20), residues: 1815
  helix:  0.93 (0.16), residues: 1100
  sheet:  None (None), residues: 0
  loop : -1.52 (0.22), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  13 
 TYR   0.018   0.001   TYR E 236 
 PHE   0.009   0.001   PHE E 283 
 TRP   0.013   0.001   TRP C  93 
 HIS   0.002   0.000   HIS D 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (15430)
  covalent geometry    : angle       0.47818 (21010)
  hydrogen bonds       : bond        0.05542 (  710)
  hydrogen bonds       : angle       3.79903 ( 2100)

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

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

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 225
  time to evaluate  : 0.562 
Fit side-chains
REVERT: A   25 ARG cc_start: 0.7843 (mtp85) cc_final: 0.7485 (mtp85)
REVERT: A   51 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6601 (mtt180)
REVERT: A  208 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8064 (tm-30)
REVERT: A  310 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7989 (pt)
REVERT: E   25 ARG cc_start: 0.7746 (mtm110) cc_final: 0.7280 (mtp85)
REVERT: E  236 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8310 (t80)
REVERT: E  310 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7918 (pt)
REVERT: B   25 ARG cc_start: 0.7988 (mtp85) cc_final: 0.7459 (mtp85)
REVERT: B   51 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6720 (mtt180)
REVERT: B   75 LEU cc_start: 0.2156 (OUTLIER) cc_final: 0.1782 (tt)
REVERT: B  159 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7716 (mp)
REVERT: B  310 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7878 (pt)
REVERT: C   25 ARG cc_start: 0.7954 (mtp85) cc_final: 0.7433 (mtp85)
REVERT: C  310 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7943 (pt)
REVERT: C  328 ASN cc_start: 0.7927 (t0) cc_final: 0.7289 (t0)
REVERT: C  363 THR cc_start: 0.9308 (t) cc_final: 0.8998 (t)
REVERT: D   25 ARG cc_start: 0.7843 (mtp85) cc_final: 0.7316 (mtp85)
REVERT: D  269 MET cc_start: 0.8397 (ttt) cc_final: 0.7973 (ttt)
REVERT: D  282 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7741 (mp)
  outliers start: 64
  outliers final: 46
  residues processed: 283
  average time/residue: 0.1453
  time to fit residues: 57.9955
Evaluate side-chains
  278 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 221
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain E residue   28 ILE
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue   90 VAL
Chi-restraints excluded: chain E residue  136 GLN
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  231 SER
Chi-restraints excluded: chain E residue  236 TYR
Chi-restraints excluded: chain E residue  310 ILE
Chi-restraints excluded: chain E residue  322 VAL
Chi-restraints excluded: chain E residue  354 SER
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   51 ARG
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   75 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  136 GLN
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  231 SER
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  136 GLN
Chi-restraints excluded: chain C residue  159 LEU
Chi-restraints excluded: chain C residue  231 SER
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  310 ILE
Chi-restraints excluded: chain C residue  322 VAL
Chi-restraints excluded: chain C residue  329 LEU
Chi-restraints excluded: chain D residue   16 SER
Chi-restraints excluded: chain D residue   28 ILE
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  231 SER
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  282 LEU
Chi-restraints excluded: chain D residue  322 VAL
Chi-restraints excluded: chain D residue  329 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 130 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0370
   chunk 141 optimal weight:    0.6980
   chunk 170 optimal weight:    6.9990
   chunk 16 optimal weight:    7.9990
   chunk 167 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 171 optimal weight:    0.9990
   overall best weight:    0.7464

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.134490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.097144 restraints weight = 16300.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 2.27
r_work: 0.2802 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.0906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  15430  Z= 0.101
  Angle     :  0.442   7.610  21010  Z= 0.237
  Chirality :  0.036   0.142   2310
  Planarity :  0.004   0.054   2615
  Dihedral  :  4.230  66.426   2033
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 26.79 %
    Favored  : 70.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.20), residues: 1815
  helix:  0.97 (0.16), residues: 1130
  sheet:  None (None), residues: 0
  loop : -1.45 (0.23), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  13 
 TYR   0.013   0.001   TYR E 236 
 PHE   0.008   0.001   PHE E 276 
 TRP   0.011   0.001   TRP C  93 
 HIS   0.001   0.000   HIS C 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (15430)
  covalent geometry    : angle       0.44201 (21010)
  hydrogen bonds       : bond        0.04500 (  710)
  hydrogen bonds       : angle       3.74645 ( 2100)

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

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

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 218
  time to evaluate  : 0.579 
Fit side-chains
REVERT: A   25 ARG cc_start: 0.7702 (mtp85) cc_final: 0.7444 (mtp85)
REVERT: A   51 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6556 (mtt180)
REVERT: A  208 GLN cc_start: 0.8655 (tm130) cc_final: 0.8227 (tm-30)
REVERT: A  310 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7869 (pt)
REVERT: E   25 ARG cc_start: 0.7599 (mtm110) cc_final: 0.7220 (mtp85)
REVERT: E  236 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.8086 (t80)
REVERT: E  310 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7810 (pt)
REVERT: E  351 SER cc_start: 0.8739 (t) cc_final: 0.8532 (t)
REVERT: B   25 ARG cc_start: 0.7827 (mtp85) cc_final: 0.7415 (mtp85)
REVERT: B   51 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6674 (mtt180)
REVERT: B  310 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7759 (pt)
REVERT: C   25 ARG cc_start: 0.7820 (mtp85) cc_final: 0.7415 (mtp85)
REVERT: C   30 LYS cc_start: 0.8821 (tttt) cc_final: 0.8581 (ttpt)
REVERT: C  282 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7244 (mp)
REVERT: C  310 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7780 (pt)
REVERT: C  328 ASN cc_start: 0.7869 (t0) cc_final: 0.7256 (t0)
REVERT: D   25 ARG cc_start: 0.7712 (mtp85) cc_final: 0.7300 (mtp85)
REVERT: D  269 MET cc_start: 0.8153 (ttt) cc_final: 0.7700 (ttt)
  outliers start: 52
  outliers final: 36
  residues processed: 269
  average time/residue: 0.1466
  time to fit residues: 55.0512
Evaluate side-chains
  262 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 218
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain E residue   28 ILE
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue  136 GLN
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  231 SER
Chi-restraints excluded: chain E residue  236 TYR
Chi-restraints excluded: chain E residue  310 ILE
Chi-restraints excluded: chain E residue  322 VAL
Chi-restraints excluded: chain E residue  354 SER
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   51 ARG
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue  136 GLN
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  231 SER
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain C residue  136 GLN
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  310 ILE
Chi-restraints excluded: chain C residue  322 VAL
Chi-restraints excluded: chain D residue   28 ILE
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  136 GLN
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  322 VAL
Chi-restraints excluded: chain D residue  329 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 129 optimal weight:    2.9990
   chunk 99 optimal weight:    0.6980
   chunk 67 optimal weight:    5.9990
   chunk 171 optimal weight:    0.2980
   chunk 76 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 153 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 107 optimal weight:    6.9990
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.134670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.098344 restraints weight = 16244.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 2.16
r_work: 0.2795 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2637 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.0964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15430  Z= 0.112
  Angle     :  0.458   9.108  21010  Z= 0.243
  Chirality :  0.036   0.148   2310
  Planarity :  0.004   0.055   2615
  Dihedral  :  3.814  15.816   2030
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 26.48 %
    Favored  : 69.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.20), residues: 1815
  helix:  1.03 (0.16), residues: 1130
  sheet:  None (None), residues: 0
  loop : -1.45 (0.23), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  13 
 TYR   0.015   0.001   TYR E 236 
 PHE   0.008   0.001   PHE A 276 
 TRP   0.012   0.001   TRP C  93 
 HIS   0.001   0.000   HIS A 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (15430)
  covalent geometry    : angle       0.45790 (21010)
  hydrogen bonds       : bond        0.04813 (  710)
  hydrogen bonds       : angle       3.72524 ( 2100)

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

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

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 216
  time to evaluate  : 0.559 
Fit side-chains
REVERT: A   25 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7442 (mtp85)
REVERT: A   51 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6642 (mtt180)
REVERT: A  208 GLN cc_start: 0.8738 (tm130) cc_final: 0.8318 (tm-30)
REVERT: E   25 ARG cc_start: 0.7740 (mtm110) cc_final: 0.7297 (mtp85)
REVERT: E  208 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8225 (tm-30)
REVERT: E  236 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8241 (t80)
REVERT: B   14 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8584 (tt)
REVERT: B   25 ARG cc_start: 0.8001 (mtp85) cc_final: 0.7542 (mtp85)
REVERT: B   51 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6757 (mtt180)
REVERT: C   25 ARG cc_start: 0.7918 (mtp85) cc_final: 0.7427 (mtp85)
REVERT: C   30 LYS cc_start: 0.8909 (tttt) cc_final: 0.8633 (ttpt)
REVERT: C  282 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7496 (mp)
REVERT: C  328 ASN cc_start: 0.7942 (t0) cc_final: 0.7320 (t0)
REVERT: D   25 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7363 (mtp85)
REVERT: D  269 MET cc_start: 0.8232 (ttt) cc_final: 0.7770 (ttt)
REVERT: D  282 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7603 (mp)
  outliers start: 59
  outliers final: 45
  residues processed: 271
  average time/residue: 0.1437
  time to fit residues: 55.1997
Evaluate side-chains
  265 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 213
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain E residue   28 ILE
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue   78 ILE
Chi-restraints excluded: chain E residue  129 ILE
Chi-restraints excluded: chain E residue  136 GLN
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  208 GLN
Chi-restraints excluded: chain E residue  231 SER
Chi-restraints excluded: chain E residue  236 TYR
Chi-restraints excluded: chain E residue  322 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   51 ARG
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue  136 GLN
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  231 SER
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain C residue  136 GLN
Chi-restraints excluded: chain C residue  159 LEU
Chi-restraints excluded: chain C residue  211 MET
Chi-restraints excluded: chain C residue  231 SER
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  322 VAL
Chi-restraints excluded: chain D residue   28 ILE
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue  136 GLN
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  231 SER
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  282 LEU
Chi-restraints excluded: chain D residue  322 VAL
Chi-restraints excluded: chain D residue  329 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 161 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 162 optimal weight:    0.9980
   chunk 70 optimal weight:    0.2980
   chunk 171 optimal weight:    0.5980
   chunk 1 optimal weight:   10.0000
   chunk 99 optimal weight:    0.2980
   chunk 35 optimal weight:    2.9990
   chunk 150 optimal weight:    0.8980
   chunk 114 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  11 ASN
B  11 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.136516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.100325 restraints weight = 16296.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 2.17
r_work: 0.2833 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2676 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  15430  Z= 0.093
  Angle     :  0.434   9.874  21010  Z= 0.230
  Chirality :  0.035   0.140   2310
  Planarity :  0.004   0.053   2615
  Dihedral  :  3.693  14.183   2030
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 26.79 %
    Favored  : 69.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.20), residues: 1815
  helix:  1.13 (0.16), residues: 1130
  sheet:  None (None), residues: 0
  loop : -1.39 (0.23), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E  13 
 TYR   0.011   0.001   TYR E 236 
 PHE   0.008   0.001   PHE A 276 
 TRP   0.012   0.001   TRP C  93 
 HIS   0.001   0.000   HIS C 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 (15430)
  covalent geometry    : angle       0.43449 (21010)
  hydrogen bonds       : bond        0.04062 (  710)
  hydrogen bonds       : angle       3.68871 ( 2100)

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

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

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 213
  time to evaluate  : 0.546 
Fit side-chains
REVERT: A   25 ARG cc_start: 0.7734 (mtp85) cc_final: 0.7432 (mtp85)
REVERT: A   49 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6274 (tt)
REVERT: A   51 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.6618 (mtt180)
REVERT: A  208 GLN cc_start: 0.8701 (tm130) cc_final: 0.8271 (tm-30)
REVERT: E   25 ARG cc_start: 0.7686 (mtm110) cc_final: 0.7274 (mtp85)
REVERT: E  208 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8185 (tm-30)
REVERT: E  211 MET cc_start: 0.8525 (mtp) cc_final: 0.8203 (mmm)
REVERT: E  236 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.8174 (t80)
REVERT: B   14 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8567 (tt)
REVERT: B   25 ARG cc_start: 0.7935 (mtp85) cc_final: 0.7502 (mtp85)
REVERT: B   51 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6673 (mtt180)
REVERT: C   13 ARG cc_start: 0.7669 (mmt90) cc_final: 0.7407 (mmt90)
REVERT: C   25 ARG cc_start: 0.7877 (mtp85) cc_final: 0.7405 (mtp85)
REVERT: C   30 LYS cc_start: 0.8885 (tttt) cc_final: 0.8620 (ttpt)
REVERT: C   49 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6332 (tt)
REVERT: C  328 ASN cc_start: 0.7848 (t0) cc_final: 0.7250 (t0)
REVERT: D   25 ARG cc_start: 0.7757 (mtp85) cc_final: 0.7305 (mtp85)
REVERT: D   49 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6321 (tt)
REVERT: D  269 MET cc_start: 0.8216 (ttt) cc_final: 0.7719 (ttt)
REVERT: D  282 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7505 (mp)
  outliers start: 57
  outliers final: 43
  residues processed: 268
  average time/residue: 0.1487
  time to fit residues: 55.8680
Evaluate side-chains
  267 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 215
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain E residue   28 ILE
Chi-restraints excluded: chain E residue   49 LEU
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue   78 ILE
Chi-restraints excluded: chain E residue  136 GLN
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  208 GLN
Chi-restraints excluded: chain E residue  231 SER
Chi-restraints excluded: chain E residue  236 TYR
Chi-restraints excluded: chain E residue  322 VAL
Chi-restraints excluded: chain E residue  354 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   51 ARG
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  231 SER
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   71 SER
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain C residue  129 ILE
Chi-restraints excluded: chain C residue  136 GLN
Chi-restraints excluded: chain C residue  231 SER
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  322 VAL
Chi-restraints excluded: chain D residue   28 ILE
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  136 GLN
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  231 SER
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  282 LEU
Chi-restraints excluded: chain D residue  322 VAL
Chi-restraints excluded: chain D residue  329 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 115 optimal weight:    0.1980
   chunk 172 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   chunk 136 optimal weight:    0.6980
   chunk 160 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0170
   chunk 79 optimal weight:    0.0060
   chunk 106 optimal weight:    0.0020
   chunk 35 optimal weight:    0.9980
   chunk 179 optimal weight:    6.9990
   overall best weight:    0.1842

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.142276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.106747 restraints weight = 16179.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 2.15
r_work: 0.2908 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2754 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  15430  Z= 0.083
  Angle     :  0.420  11.659  21010  Z= 0.218
  Chirality :  0.034   0.143   2310
  Planarity :  0.004   0.052   2615
  Dihedral  :  3.464  14.230   2030
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 27.22 %
    Favored  : 70.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.20), residues: 1815
  helix:  1.30 (0.16), residues: 1135
  sheet:  None (None), residues: 0
  loop : -1.29 (0.24), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 356 
 TYR   0.009   0.001   TYR C  33 
 PHE   0.008   0.001   PHE E 276 
 TRP   0.010   0.001   TRP A  93 
 HIS   0.003   0.000   HIS B 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00190 (15430)
  covalent geometry    : angle       0.42039 (21010)
  hydrogen bonds       : bond        0.03208 (  710)
  hydrogen bonds       : angle       3.59289 ( 2100)

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

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

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 216
  time to evaluate  : 0.598 
Fit side-chains
REVERT: A   25 ARG cc_start: 0.7646 (mtp85) cc_final: 0.7392 (mtp85)
REVERT: A   51 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6608 (mtt180)
REVERT: A  208 GLN cc_start: 0.8698 (tm130) cc_final: 0.8271 (tm-30)
REVERT: E   25 ARG cc_start: 0.7603 (mtm110) cc_final: 0.7234 (mtp85)
REVERT: E  211 MET cc_start: 0.8352 (mtp) cc_final: 0.8100 (mmm)
REVERT: E  236 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7987 (t80)
REVERT: E  246 SER cc_start: 0.7977 (p) cc_final: 0.7755 (m)
REVERT: B   14 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8571 (tt)
REVERT: B   25 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7477 (mtp85)
REVERT: B   51 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6657 (mtt180)
REVERT: C   13 ARG cc_start: 0.7750 (mmt90) cc_final: 0.7387 (mmt90)
REVERT: C   25 ARG cc_start: 0.7772 (mtp85) cc_final: 0.7308 (mtp85)
REVERT: C   30 LYS cc_start: 0.8848 (tttt) cc_final: 0.8596 (ttpt)
REVERT: C   49 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6350 (tt)
REVERT: C  328 ASN cc_start: 0.7818 (t0) cc_final: 0.7214 (t0)
REVERT: D   25 ARG cc_start: 0.7703 (mtp85) cc_final: 0.7320 (mtp85)
REVERT: D   49 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6316 (tt)
REVERT: D  269 MET cc_start: 0.8102 (ttt) cc_final: 0.7580 (ttt)
REVERT: D  282 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7284 (mp)
  outliers start: 45
  outliers final: 37
  residues processed: 259
  average time/residue: 0.1487
  time to fit residues: 53.9379
Evaluate side-chains
  254 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 210
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain E residue   28 ILE
Chi-restraints excluded: chain E residue   49 LEU
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue   78 ILE
Chi-restraints excluded: chain E residue  129 ILE
Chi-restraints excluded: chain E residue  136 GLN
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  231 SER
Chi-restraints excluded: chain E residue  236 TYR
Chi-restraints excluded: chain E residue  322 VAL
Chi-restraints excluded: chain E residue  354 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   51 ARG
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain C residue  129 ILE
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  322 VAL
Chi-restraints excluded: chain D residue   28 ILE
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  136 GLN
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  282 LEU
Chi-restraints excluded: chain D residue  322 VAL
Chi-restraints excluded: chain D residue  329 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 154 optimal weight:    0.9980
   chunk 160 optimal weight:    1.9990
   chunk 116 optimal weight:    2.9990
   chunk 136 optimal weight:    1.9990
   chunk 133 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 178 optimal weight:   10.0000
   chunk 147 optimal weight:    0.4980
   chunk 71 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A  11 ASN
E  11 ASN

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 = 0.138212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.102240 restraints weight = 16276.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 2.13
r_work: 0.2817 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2660 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.1204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15430  Z= 0.114
  Angle     :  0.464  11.618  21010  Z= 0.242
  Chirality :  0.036   0.139   2310
  Planarity :  0.004   0.056   2615
  Dihedral  :  3.566  13.614   2030
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 27.65 %
    Favored  : 69.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.20), residues: 1815
  helix:  1.32 (0.16), residues: 1130
  sheet:  None (None), residues: 0
  loop : -1.25 (0.24), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E  13 
 TYR   0.017   0.001   TYR E 236 
 PHE   0.010   0.001   PHE B 283 
 TRP   0.010   0.001   TRP A  93 
 HIS   0.002   0.000   HIS C 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (15430)
  covalent geometry    : angle       0.46395 (21010)
  hydrogen bonds       : bond        0.04787 (  710)
  hydrogen bonds       : angle       3.60482 ( 2100)

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

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

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3630 Ramachandran restraints generated.
    1815 Oldfield, 0 Emsley, 1815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 217
  time to evaluate  : 0.488 
Fit side-chains
REVERT: A   25 ARG cc_start: 0.7752 (mtp85) cc_final: 0.7462 (mtp85)
REVERT: A   51 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6665 (mtt180)
REVERT: A  208 GLN cc_start: 0.8742 (tm130) cc_final: 0.8310 (tm-30)
REVERT: E   25 ARG cc_start: 0.7694 (mtm110) cc_final: 0.7292 (mtp85)
REVERT: E  211 MET cc_start: 0.8471 (mtp) cc_final: 0.8173 (mmm)
REVERT: E  236 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.8133 (t80)
REVERT: B   14 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8581 (tt)
REVERT: B   25 ARG cc_start: 0.7926 (mtp85) cc_final: 0.7513 (mtp85)
REVERT: B   51 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6707 (mtt180)
REVERT: C   13 ARG cc_start: 0.7693 (mmt90) cc_final: 0.7332 (mmt90)
REVERT: C   25 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7406 (mtp85)
REVERT: C   30 LYS cc_start: 0.8895 (tttt) cc_final: 0.8618 (tttt)
REVERT: C   49 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6397 (tt)
REVERT: C  328 ASN cc_start: 0.7929 (t0) cc_final: 0.7684 (t0)
REVERT: D   25 ARG cc_start: 0.7761 (mtp85) cc_final: 0.7332 (mtp85)
REVERT: D   49 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6389 (tt)
REVERT: D  269 MET cc_start: 0.8203 (ttt) cc_final: 0.7703 (ttt)
REVERT: D  282 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7512 (mp)
  outliers start: 45
  outliers final: 37
  residues processed: 260
  average time/residue: 0.1495
  time to fit residues: 54.5224
Evaluate side-chains
  261 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 217
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue   51 ARG
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain E residue   28 ILE
Chi-restraints excluded: chain E residue   49 LEU
Chi-restraints excluded: chain E residue   67 LEU
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue   78 ILE
Chi-restraints excluded: chain E residue  129 ILE
Chi-restraints excluded: chain E residue  136 GLN
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  231 SER
Chi-restraints excluded: chain E residue  236 TYR
Chi-restraints excluded: chain E residue  322 VAL
Chi-restraints excluded: chain E residue  354 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue   51 ARG
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  231 SER
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  322 VAL
Chi-restraints excluded: chain D residue   28 ILE
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  136 GLN
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  282 LEU
Chi-restraints excluded: chain D residue  322 VAL
Chi-restraints excluded: chain D residue  329 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 102 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 99 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 55 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 112 optimal weight:    4.9990
   chunk 117 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 89 optimal weight:    0.1980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
E 328 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.135390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.098884 restraints weight = 16317.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 2.17
r_work: 0.2816 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2658 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.1193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  15430  Z= 0.106
  Angle     :  0.456  11.913  21010  Z= 0.237
  Chirality :  0.036   0.138   2310
  Planarity :  0.004   0.055   2615
  Dihedral  :  3.603  13.828   2030
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 27.52 %
    Favored  : 69.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.20), residues: 1815
  helix:  1.29 (0.16), residues: 1130
  sheet:  None (None), residues: 0
  loop : -1.26 (0.24), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  13 
 TYR   0.014   0.001   TYR E 236 
 PHE   0.008   0.001   PHE A 276 
 TRP   0.012   0.001   TRP A  93 
 HIS   0.001   0.000   HIS C 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (15430)
  covalent geometry    : angle       0.45569 (21010)
  hydrogen bonds       : bond        0.04548 (  710)
  hydrogen bonds       : angle       3.62419 ( 2100)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3534.97 seconds
wall clock time: 61 minutes 18.69 seconds (3678.69 seconds total)