Starting phenix.real_space_refine
on Wed Mar  4 04:05:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ois_20080/03_2026/6ois_20080.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ois_20080/03_2026/6ois_20080.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ois_20080/03_2026/6ois_20080.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ois_20080/03_2026/6ois_20080.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ois_20080/03_2026/6ois_20080.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ois_20080/03_2026/6ois_20080.cif"
  }
  resolution = 3.6
  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=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    6785      2.51       5
     N    1875      2.21       5
     O    2010      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10732
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 1016
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 9, 'TRANS': 113}
    Chain: "B"
      Number of atoms: 1034
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 1034
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 9, 'TRANS': 115}
    Chain: "C"
      Number of atoms: 2591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2591
          Classifications: {'peptide': 330}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 321}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 1754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1754
          Classifications: {'peptide': 229}
          Link IDs: {'PTRANS': 8, 'TRANS': 220}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 2583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2583
          Classifications: {'peptide': 329}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 320}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "F"
      Number of atoms: 1754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1754
          Classifications: {'peptide': 229}
          Link IDs: {'PTRANS': 8, 'TRANS': 220}
          Chain breaks: 1
  Time building chain proxies: 2.16, per 1000 atoms: 0.20
  Number of scatterers: 10732
  At special positions: 0
  Unit cell: (84.53, 96.3, 143.38, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      62     16.00
     O    2010      8.00
     N    1875      7.00
     C    6785      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: 0.82
  Conformation dependent library (CDL) restraints added in 636.2 milliseconds
  

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2534

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 12 sheets defined
      53.1% alpha, 6.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 58
      removed outlier: 3.532A  pdb=" N   SER A  43 " --> pdb=" O   ALA A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 84
      removed outlier: 3.697A  pdb=" N   GLN A  82 " --> pdb=" O   ILE A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 102
    Processing helix  chain 'A' and resid 112 through 117
      removed outlier: 3.825A  pdb=" N   ILE A 116 " --> pdb=" O   ARG A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 136
    Processing helix  chain 'A' and resid 138 through 149
      removed outlier: 3.886A  pdb=" N   MET A 142 " --> pdb=" O   SER A 138 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ASP A 149 " --> pdb=" O   LEU A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 155
      removed outlier: 4.152A  pdb=" N   SER A 154 " --> pdb=" O   MET A 151 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   PHE A 155 " --> pdb=" O   TYR A 152 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 151 through 155'
    Processing helix  chain 'B' and resid 40 through 58
      removed outlier: 3.503A  pdb=" N   VAL B  58 " --> pdb=" O   TYR B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 84
    Processing helix  chain 'B' and resid 89 through 103
      removed outlier: 3.596A  pdb=" N   ARG B 103 " --> pdb=" O   TRP B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 117
      removed outlier: 3.527A  pdb=" N   ILE B 116 " --> pdb=" O   ARG B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 136
    Processing helix  chain 'B' and resid 138 through 149
      removed outlier: 3.671A  pdb=" N   MET B 142 " --> pdb=" O   SER B 138 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ASP B 149 " --> pdb=" O   LEU B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 155
      removed outlier: 3.771A  pdb=" N   SER B 154 " --> pdb=" O   MET B 151 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   PHE B 155 " --> pdb=" O   TYR B 152 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 151 through 155'
    Processing helix  chain 'C' and resid 53 through 99
    Processing helix  chain 'C' and resid 118 through 125
      removed outlier: 4.017A  pdb=" N   HIS C 125 " --> pdb=" O   GLN C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 139
      removed outlier: 3.563A  pdb=" N   VAL C 132 " --> pdb=" O   SER C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 148 through 152
    Processing helix  chain 'C' and resid 157 through 160
      No H-bonds generated for 'chain 'C' and resid 157 through 160'
    Processing helix  chain 'C' and resid 165 through 181
      removed outlier: 6.687A  pdb=" N   THR C 178 " --> pdb=" O   ASN C 174 " (cutoff:3.500A)
      removed outlier: 8.446A  pdb=" N   ARG C 179 " --> pdb=" O   TYR C 175 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   SER C 180 " --> pdb=" O   LEU C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 188 through 194
    Processing helix  chain 'C' and resid 208 through 218
    Processing helix  chain 'C' and resid 277 through 280
      removed outlier: 3.901A  pdb=" N   LEU C 280 " --> pdb=" O   PRO C 277 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 277 through 280'
    Processing helix  chain 'C' and resid 293 through 299
      removed outlier: 3.611A  pdb=" N   ASN C 297 " --> pdb=" O   THR C 293 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 307 through 314
    Processing helix  chain 'C' and resid 354 through 405
    Processing helix  chain 'D' and resid 118 through 125
      removed outlier: 4.293A  pdb=" N   HIS D 125 " --> pdb=" O   GLN D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 139
    Processing helix  chain 'D' and resid 148 through 152
    Processing helix  chain 'D' and resid 157 through 160
      No H-bonds generated for 'chain 'D' and resid 157 through 160'
    Processing helix  chain 'D' and resid 166 through 181
      removed outlier: 6.441A  pdb=" N   THR D 178 " --> pdb=" O   ASN D 174 " (cutoff:3.500A)
      removed outlier: 8.395A  pdb=" N   ARG D 179 " --> pdb=" O   TYR D 175 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   SER D 180 " --> pdb=" O   LEU D 176 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 196
      removed outlier: 3.605A  pdb=" N   VAL D 192 " --> pdb=" O   ASN D 188 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 218
    Processing helix  chain 'D' and resid 244 through 248
      removed outlier: 3.906A  pdb=" N   ARG D 247 " --> pdb=" O   ASP D 244 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ARG D 248 " --> pdb=" O   LEU D 245 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 244 through 248'
    Processing helix  chain 'D' and resid 277 through 280
      removed outlier: 3.889A  pdb=" N   LEU D 280 " --> pdb=" O   PRO D 277 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 277 through 280'
    Processing helix  chain 'D' and resid 293 through 299
    Processing helix  chain 'D' and resid 307 through 313
    Processing helix  chain 'E' and resid 53 through 98
    Processing helix  chain 'E' and resid 118 through 125
      removed outlier: 4.134A  pdb=" N   HIS E 125 " --> pdb=" O   GLN E 121 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 128 through 139
    Processing helix  chain 'E' and resid 148 through 152
    Processing helix  chain 'E' and resid 157 through 160
      No H-bonds generated for 'chain 'E' and resid 157 through 160'
    Processing helix  chain 'E' and resid 165 through 182
      removed outlier: 3.718A  pdb=" N   SER E 169 " --> pdb=" O   ASP E 165 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   THR E 178 " --> pdb=" O   ASN E 174 " (cutoff:3.500A)
      removed outlier: 8.509A  pdb=" N   ARG E 179 " --> pdb=" O   TYR E 175 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   SER E 180 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU E 182 " --> pdb=" O   THR E 178 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 188 through 196
      removed outlier: 3.598A  pdb=" N   VAL E 192 " --> pdb=" O   ASN E 188 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   GLU E 196 " --> pdb=" O   VAL E 192 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 208 through 218
    Processing helix  chain 'E' and resid 244 through 248
      removed outlier: 3.716A  pdb=" N   ARG E 247 " --> pdb=" O   ASP E 244 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ARG E 248 " --> pdb=" O   LEU E 245 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 244 through 248'
    Processing helix  chain 'E' and resid 277 through 280
      removed outlier: 3.721A  pdb=" N   LEU E 280 " --> pdb=" O   PRO E 277 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 277 through 280'
    Processing helix  chain 'E' and resid 289 through 299
      removed outlier: 3.943A  pdb=" N   THR E 293 " --> pdb=" O   GLY E 289 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   PHE E 295 " --> pdb=" O   ARG E 291 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   TYR E 296 " --> pdb=" O   GLU E 292 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 307 through 314
      removed outlier: 3.501A  pdb=" N   MET E 311 " --> pdb=" O   THR E 307 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 355 through 404
    Processing helix  chain 'F' and resid 118 through 125
      removed outlier: 4.294A  pdb=" N   HIS F 125 " --> pdb=" O   GLN F 121 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 129 through 139
    Processing helix  chain 'F' and resid 148 through 152
    Processing helix  chain 'F' and resid 157 through 160
      No H-bonds generated for 'chain 'F' and resid 157 through 160'
    Processing helix  chain 'F' and resid 166 through 181
      removed outlier: 6.441A  pdb=" N   THR F 178 " --> pdb=" O   ASN F 174 " (cutoff:3.500A)
      removed outlier: 8.395A  pdb=" N   ARG F 179 " --> pdb=" O   TYR F 175 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   SER F 180 " --> pdb=" O   LEU F 176 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 188 through 196
      removed outlier: 3.605A  pdb=" N   VAL F 192 " --> pdb=" O   ASN F 188 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 208 through 218
    Processing helix  chain 'F' and resid 244 through 248
      removed outlier: 3.906A  pdb=" N   ARG F 247 " --> pdb=" O   ASP F 244 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ARG F 248 " --> pdb=" O   LEU F 245 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 244 through 248'
    Processing helix  chain 'F' and resid 277 through 280
      removed outlier: 3.888A  pdb=" N   LEU F 280 " --> pdb=" O   PRO F 277 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 277 through 280'
    Processing helix  chain 'F' and resid 293 through 299
    Processing helix  chain 'F' and resid 307 through 313
    Processing sheet with id=AA1, first strand: chain 'C' and resid 153 through 156
    Processing sheet with id=AA2, first strand: chain 'C' and resid 161 through 162
    Processing sheet with id=AA3, first strand: chain 'C' and resid 265 through 268
      removed outlier: 6.400A  pdb=" N   VAL C 304 " --> pdb=" O   LEU C 266 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA C 322 " --> pdb=" O   ILE C 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 335 through 338
      removed outlier: 3.558A  pdb=" N   LEU C 338 " --> pdb=" O   PHE D 225 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   VAL D 185 " --> pdb=" O   VAL D 154 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 161 through 162
    Processing sheet with id=AA6, first strand: chain 'D' and resid 265 through 268
      removed outlier: 6.477A  pdb=" N   VAL D 304 " --> pdb=" O   LEU D 266 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   PHE D 268 " --> pdb=" O   LEU D 302 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   LEU D 302 " --> pdb=" O   PHE D 268 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 153 through 156
      removed outlier: 6.431A  pdb=" N   VAL E 184 " --> pdb=" O   ILE E 228 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 161 through 162
    Processing sheet with id=AA9, first strand: chain 'E' and resid 265 through 268
      removed outlier: 7.050A  pdb=" N   VAL E 304 " --> pdb=" O   LEU E 266 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   PHE E 268 " --> pdb=" O   LEU E 302 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   LEU E 302 " --> pdb=" O   PHE E 268 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 335 through 338
      removed outlier: 6.599A  pdb=" N   VAL F 185 " --> pdb=" O   VAL F 154 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 161 through 162
    Processing sheet with id=AB3, first strand: chain 'F' and resid 265 through 268
      removed outlier: 6.477A  pdb=" N   VAL F 304 " --> pdb=" O   LEU F 266 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   PHE F 268 " --> pdb=" O   LEU F 302 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   LEU F 302 " --> pdb=" O   PHE F 268 " (cutoff:3.500A)

    498 hydrogen bonds defined for protein.
    1461 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: 1.33

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2676
        1.33 -     1.45: 1999
        1.45 -     1.57: 6143
        1.57 -     1.69: 0
        1.69 -     1.81: 98
  Bond restraints: 10916
  Sorted by residual:
  bond pdb=" N   ILE E 318 "
       pdb=" CA  ILE E 318 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.22e-02 6.72e+03 1.11e+01
  bond pdb=" N   THR B 136 "
       pdb=" CA  THR B 136 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.042 1.41e-02 5.03e+03 8.86e+00
  bond pdb=" N   VAL F 237 "
       pdb=" CA  VAL F 237 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.52e+00
  bond pdb=" N   VAL E 237 "
       pdb=" CA  VAL E 237 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.24e+00
  bond pdb=" N   LEU B 135 "
       pdb=" CA  LEU B 135 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.20e-02 6.94e+03 7.64e+00
  ... (remaining 10911 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.61: 14260
        2.61 -     5.22: 409
        5.22 -     7.83: 50
        7.83 -    10.45: 20
       10.45 -    13.06: 1
  Bond angle restraints: 14740
  Sorted by residual:
  angle pdb=" N   PRO B 137 "
        pdb=" CA  PRO B 137 "
        pdb=" C   PRO B 137 "
      ideal   model   delta    sigma   weight residual
     111.38  124.44  -13.06 1.59e+00 3.96e-01 6.74e+01
  angle pdb=" N   THR A 136 "
        pdb=" CA  THR A 136 "
        pdb=" C   THR A 136 "
      ideal   model   delta    sigma   weight residual
     112.35  120.21   -7.86 1.34e+00 5.57e-01 3.44e+01
  angle pdb=" N   LEU B 135 "
        pdb=" CA  LEU B 135 "
        pdb=" C   LEU B 135 "
      ideal   model   delta    sigma   weight residual
     111.14  116.67   -5.53 1.08e+00 8.57e-01 2.62e+01
  angle pdb=" C   VAL F 237 "
        pdb=" N   GLY F 238 "
        pdb=" CA  GLY F 238 "
      ideal   model   delta    sigma   weight residual
     121.35  126.61   -5.26 1.03e+00 9.43e-01 2.61e+01
  angle pdb=" N   THR B 136 "
        pdb=" CA  THR B 136 "
        pdb=" C   THR B 136 "
      ideal   model   delta    sigma   weight residual
     109.81  119.87  -10.06 2.21e+00 2.05e-01 2.07e+01
  ... (remaining 14735 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.22: 6197
       15.22 -    30.44: 319
       30.44 -    45.66: 105
       45.66 -    60.88: 10
       60.88 -    76.10: 5
  Dihedral angle restraints: 6636
    sinusoidal: 2701
      harmonic: 3935
  Sorted by residual:
  dihedral pdb=" CA  ASN C 258 "
           pdb=" C   ASN C 258 "
           pdb=" N   GLY C 259 "
           pdb=" CA  GLY C 259 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.30  -26.70     0      5.00e+00 4.00e-02 2.85e+01
  dihedral pdb=" CA  THR A 136 "
           pdb=" C   THR A 136 "
           pdb=" N   PRO A 137 "
           pdb=" CA  PRO A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.09  -21.91     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  ASP C 244 "
           pdb=" C   ASP C 244 "
           pdb=" N   LEU C 245 "
           pdb=" CA  LEU C 245 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.36   19.64     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 6633 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1329
       0.068 -    0.136: 287
       0.136 -    0.204: 41
       0.204 -    0.272: 7
       0.272 -    0.340: 3
  Chirality restraints: 1667
  Sorted by residual:
  chirality pdb=" CA  THR B 136 "
            pdb=" N   THR B 136 "
            pdb=" C   THR B 136 "
            pdb=" CB  THR B 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.19    0.34 2.00e-01 2.50e+01 2.89e+00
  chirality pdb=" CB  ILE A  60 "
            pdb=" CA  ILE A  60 "
            pdb=" CG1 ILE A  60 "
            pdb=" CG2 ILE A  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CA  PRO B 137 "
            pdb=" N   PRO B 137 "
            pdb=" C   PRO B 137 "
            pdb=" CB  PRO B 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.43    0.29 2.00e-01 2.50e+01 2.05e+00
  ... (remaining 1664 not shown)

  Planarity restraints: 1905
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG F 234 "   -0.026 2.00e-02 2.50e+03   5.13e-02 2.64e+01
        pdb=" C   ARG F 234 "    0.089 2.00e-02 2.50e+03
        pdb=" O   ARG F 234 "   -0.034 2.00e-02 2.50e+03
        pdb=" N   PRO F 235 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG D 234 "    0.018 2.00e-02 2.50e+03   3.70e-02 1.37e+01
        pdb=" C   ARG D 234 "   -0.064 2.00e-02 2.50e+03
        pdb=" O   ARG D 234 "    0.024 2.00e-02 2.50e+03
        pdb=" N   PRO D 235 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG C 234 "    0.018 2.00e-02 2.50e+03   3.60e-02 1.30e+01
        pdb=" C   ARG C 234 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   ARG C 234 "    0.023 2.00e-02 2.50e+03
        pdb=" N   PRO C 235 "    0.021 2.00e-02 2.50e+03
  ... (remaining 1902 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 3271
        2.83 -     3.35: 10026
        3.35 -     3.87: 17028
        3.87 -     4.38: 19296
        4.38 -     4.90: 33141
  Nonbonded interactions: 82762
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A  93 "
            pdb=" O   PHE A 155 "
     model   vdw
     2.315 3.120
  nonbonded pdb=" O   LEU C 135 "
            pdb=" OG1 THR C 138 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" NH2 ARG A  47 "
            pdb=" OE1 GLN C  80 "
     model   vdw
     2.327 3.120
  nonbonded pdb=" O   ALA B 122 "
            pdb=" OG1 THR B 125 "
     model   vdw
     2.346 3.040
  nonbonded pdb=" NE2 HIS D 240 "
            pdb=" OE2 GLU D 292 "
     model   vdw
     2.350 3.120
  ... (remaining 82757 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 39 through 161)
}
ncs_group {
  reference = (chain 'C' and (resid 52 through 98 or resid 117 through 405))
  selection = chain 'E'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.770
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.310
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  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:1.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
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      :  0.009   0.078  10916  Z= 0.383
  Angle     :  1.051  13.058  14740  Z= 0.572
  Chirality :  0.060   0.340   1667
  Planarity :  0.007   0.065   1905
  Dihedral  : 10.801  76.103   4102
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  4.32 %
    Favored  : 95.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.46 (0.18), residues: 1341
  helix: -1.40 (0.17), residues: 649
  sheet: -1.78 (0.75), residues: 40
  loop : -1.80 (0.19), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG F 331 
 TYR   0.025   0.003   TYR E 288 
 PHE   0.029   0.004   PHE C 299 
 TRP   0.016   0.004   TRP A 127 
 HIS   0.019   0.004   HIS B 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00881 (10916)
  covalent geometry    : angle       1.05103 (14740)
  hydrogen bonds       : bond        0.15078 (  498)
  hydrogen bonds       : angle       6.76993 ( 1461)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 265
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
REVERT: B   49 GLU cc_start: 0.8073 (tt0) cc_final: 0.7807 (tt0)
REVERT: C  357 MET cc_start: 0.7518 (mpm) cc_final: 0.7210 (mpm)
REVERT: D  193 THR cc_start: 0.9013 (p) cc_final: 0.8807 (p)
REVERT: E  151 LYS cc_start: 0.8013 (tmtm) cc_final: 0.7097 (mptt)
REVERT: E  199 ASP cc_start: 0.5846 (t0) cc_final: 0.5142 (p0)
REVERT: E  311 MET cc_start: 0.9239 (ttp) cc_final: 0.8990 (ttm)
  outliers start: 8
  outliers final: 1
  residues processed: 273
  average time/residue: 0.1621
  time to fit residues: 55.8731
Evaluate side-chains
  135 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  237 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 118 HIS
A 133 HIS
C  92 GLN
C 297 ASN
C 340 ASN
** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 297 ASN
E  52 ASN
E 125 HIS
** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 246 GLN
E 297 ASN
E 340 ASN
** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 201 HIS
F 239 GLN
F 297 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.126940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.098348 restraints weight = 19323.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.099061 restraints weight = 12379.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.099674 restraints weight = 11105.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.099935 restraints weight = 9965.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.100253 restraints weight = 9267.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10916  Z= 0.137
  Angle     :  0.614   9.165  14740  Z= 0.316
  Chirality :  0.042   0.161   1667
  Planarity :  0.005   0.044   1905
  Dihedral  :  5.036  23.307   1478
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  :  8.81 %
    Favored  : 88.06 %
  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 are not related in a simple way.
  whole: -0.37 (0.22), residues: 1341
  helix:  0.76 (0.20), residues: 644
  sheet: -1.03 (0.84), residues: 40
  loop : -1.22 (0.21), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 331 
 TYR   0.014   0.002   TYR E 305 
 PHE   0.017   0.002   PHE C 225 
 TRP   0.007   0.001   TRP E 372 
 HIS   0.006   0.001   HIS B 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10916)
  covalent geometry    : angle       0.61397 (14740)
  hydrogen bonds       : bond        0.04930 (  498)
  hydrogen bonds       : angle       4.83017 ( 1461)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 154
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8147 (tptm) cc_final: 0.7899 (tptm)
REVERT: A  159 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8278 (pt)
REVERT: B   49 GLU cc_start: 0.7937 (tt0) cc_final: 0.7690 (tt0)
REVERT: B  113 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8677 (tp)
REVERT: C  237 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8221 (p)
REVERT: C  357 MET cc_start: 0.7467 (mpm) cc_final: 0.7177 (mpm)
REVERT: D  239 GLN cc_start: 0.7858 (tp40) cc_final: 0.7645 (tp-100)
REVERT: D  297 ASN cc_start: 0.8183 (m110) cc_final: 0.7913 (m-40)
REVERT: E  151 LYS cc_start: 0.8082 (tmtm) cc_final: 0.7085 (mmtt)
REVERT: E  199 ASP cc_start: 0.5682 (t0) cc_final: 0.5009 (p0)
  outliers start: 37
  outliers final: 19
  residues processed: 182
  average time/residue: 0.1037
  time to fit residues: 26.6868
Evaluate side-chains
  151 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain C residue  188 ASN
Chi-restraints excluded: chain C residue  200 ASN
Chi-restraints excluded: chain C residue  223 ASP
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  320 ASP
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain D residue  329 ILE
Chi-restraints excluded: chain E residue   74 LEU
Chi-restraints excluded: chain E residue  171 ILE
Chi-restraints excluded: chain E residue  185 VAL
Chi-restraints excluded: chain E residue  226 ASP
Chi-restraints excluded: chain E residue  245 LEU
Chi-restraints excluded: chain E residue  329 ILE
Chi-restraints excluded: chain F residue  135 LEU
Chi-restraints excluded: chain F residue  193 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 79 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   chunk 124 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 88 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0870
   overall best weight:    1.7762

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

Flipped N/Q/H residues before XYZ refinement:
C 240 HIS
** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 211 HIS
D 345 ASN
** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 239 GLN
F 345 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.123703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.094928 restraints weight = 19621.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.096834 restraints weight = 13209.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.097265 restraints weight = 10296.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.097383 restraints weight = 10057.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.097521 restraints weight = 9244.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10916  Z= 0.165
  Angle     :  0.583   7.148  14740  Z= 0.301
  Chirality :  0.043   0.188   1667
  Planarity :  0.004   0.038   1905
  Dihedral  :  4.747  24.886   1478
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 10.50 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.23), residues: 1341
  helix:  1.64 (0.21), residues: 645
  sheet: -0.94 (0.87), residues: 40
  loop : -0.94 (0.22), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 134 
 TYR   0.013   0.001   TYR D 296 
 PHE   0.018   0.002   PHE F 348 
 TRP   0.006   0.001   TRP E 372 
 HIS   0.005   0.001   HIS E 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (10916)
  covalent geometry    : angle       0.58278 (14740)
  hydrogen bonds       : bond        0.04481 (  498)
  hydrogen bonds       : angle       4.42272 ( 1461)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 127
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A  113 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8538 (tt)
REVERT: C  357 MET cc_start: 0.7172 (mpm) cc_final: 0.6509 (mpp)
REVERT: D  297 ASN cc_start: 0.8035 (m110) cc_final: 0.7776 (m-40)
REVERT: E  151 LYS cc_start: 0.8048 (tmtm) cc_final: 0.7087 (mmtt)
REVERT: E  199 ASP cc_start: 0.5740 (t0) cc_final: 0.5095 (p0)
REVERT: E  258 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.8033 (p0)
  outliers start: 36
  outliers final: 22
  residues processed: 157
  average time/residue: 0.0897
  time to fit residues: 20.7122
Evaluate side-chains
  142 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain C residue  200 ASN
Chi-restraints excluded: chain C residue  223 ASP
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  320 ASP
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain D residue  229 CYS
Chi-restraints excluded: chain D residue  275 ILE
Chi-restraints excluded: chain D residue  329 ILE
Chi-restraints excluded: chain E residue  171 ILE
Chi-restraints excluded: chain E residue  185 VAL
Chi-restraints excluded: chain E residue  226 ASP
Chi-restraints excluded: chain E residue  245 LEU
Chi-restraints excluded: chain E residue  258 ASN
Chi-restraints excluded: chain E residue  329 ILE
Chi-restraints excluded: chain F residue  135 LEU
Chi-restraints excluded: chain F residue  193 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 121 optimal weight:    6.9990
   chunk 99 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 76 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B  89 HIS
** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 239 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.124171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.096931 restraints weight = 19600.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.096920 restraints weight = 12747.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.096876 restraints weight = 11536.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.097469 restraints weight = 10901.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.097598 restraints weight = 9845.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.3115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10916  Z= 0.144
  Angle     :  0.552   8.935  14740  Z= 0.284
  Chirality :  0.042   0.175   1667
  Planarity :  0.004   0.038   1905
  Dihedral  :  4.580  26.519   1478
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 11.43 %
    Favored  : 85.18 %
  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 are not related in a simple way.
  whole:  0.96 (0.23), residues: 1341
  helix:  2.18 (0.21), residues: 631
  sheet: -1.18 (0.84), residues: 40
  loop : -0.80 (0.22), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 347 
 TYR   0.011   0.001   TYR D 296 
 PHE   0.014   0.002   PHE C 225 
 TRP   0.006   0.001   TRP E 372 
 HIS   0.005   0.001   HIS E 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (10916)
  covalent geometry    : angle       0.55250 (14740)
  hydrogen bonds       : bond        0.04117 (  498)
  hydrogen bonds       : angle       4.20342 ( 1461)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 126
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8502 (tt)
REVERT: C  357 MET cc_start: 0.7094 (mpm) cc_final: 0.6462 (mpp)
REVERT: D  297 ASN cc_start: 0.7964 (m110) cc_final: 0.7757 (m-40)
REVERT: E  151 LYS cc_start: 0.8068 (tmtm) cc_final: 0.7029 (mmtt)
REVERT: E  199 ASP cc_start: 0.5842 (t0) cc_final: 0.5142 (p0)
REVERT: E  204 ILE cc_start: 0.7008 (mp) cc_final: 0.6647 (pt)
  outliers start: 40
  outliers final: 25
  residues processed: 155
  average time/residue: 0.0897
  time to fit residues: 20.6349
Evaluate side-chains
  146 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 120
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain B residue  142 MET
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  159 ILE
Chi-restraints excluded: chain C residue  200 ASN
Chi-restraints excluded: chain C residue  223 ASP
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  320 ASP
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  229 CYS
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  275 ILE
Chi-restraints excluded: chain D residue  329 ILE
Chi-restraints excluded: chain E residue  185 VAL
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  226 ASP
Chi-restraints excluded: chain E residue  229 CYS
Chi-restraints excluded: chain E residue  237 VAL
Chi-restraints excluded: chain E residue  245 LEU
Chi-restraints excluded: chain E residue  258 ASN
Chi-restraints excluded: chain E residue  329 ILE
Chi-restraints excluded: chain F residue  135 LEU
Chi-restraints excluded: chain F residue  193 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 98 optimal weight:    0.4980
   chunk 56 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 103 optimal weight:    0.2980
   chunk 2 optimal weight:    1.9990
   chunk 97 optimal weight:   10.0000
   chunk 100 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 23 optimal weight:    0.3980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 239 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.126011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.098223 restraints weight = 19328.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.099311 restraints weight = 12822.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.099911 restraints weight = 10644.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.100211 restraints weight = 9714.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.100330 restraints weight = 8859.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.3298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  10916  Z= 0.101
  Angle     :  0.518   9.130  14740  Z= 0.263
  Chirality :  0.040   0.178   1667
  Planarity :  0.004   0.041   1905
  Dihedral  :  4.311  24.124   1477
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 12.45 %
    Favored  : 84.34 %
  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 are not related in a simple way.
  whole:  1.10 (0.23), residues: 1341
  helix:  2.19 (0.21), residues: 655
  sheet: -1.51 (1.02), residues: 20
  loop : -0.72 (0.23), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  64 
 TYR   0.017   0.001   TYR B  51 
 PHE   0.013   0.001   PHE C 225 
 TRP   0.005   0.001   TRP E 372 
 HIS   0.004   0.001   HIS E  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (10916)
  covalent geometry    : angle       0.51820 (14740)
  hydrogen bonds       : bond        0.03679 (  498)
  hydrogen bonds       : angle       3.99951 ( 1461)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 128
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.8002 (tptm) cc_final: 0.7759 (tptm)
REVERT: A  113 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8455 (tt)
REVERT: A  159 ILE cc_start: 0.8615 (pt) cc_final: 0.8275 (pt)
REVERT: D  195 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8271 (tt)
REVERT: D  297 ASN cc_start: 0.7900 (m110) cc_final: 0.7680 (m-40)
REVERT: E  151 LYS cc_start: 0.8050 (tmtm) cc_final: 0.7004 (mmtt)
REVERT: E  199 ASP cc_start: 0.5946 (t0) cc_final: 0.5279 (p0)
  outliers start: 38
  outliers final: 26
  residues processed: 156
  average time/residue: 0.0954
  time to fit residues: 21.5686
Evaluate side-chains
  146 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain C residue  200 ASN
Chi-restraints excluded: chain C residue  223 ASP
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  320 ASP
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  229 CYS
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  329 ILE
Chi-restraints excluded: chain E residue  185 VAL
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  226 ASP
Chi-restraints excluded: chain E residue  237 VAL
Chi-restraints excluded: chain E residue  245 LEU
Chi-restraints excluded: chain E residue  258 ASN
Chi-restraints excluded: chain E residue  329 ILE
Chi-restraints excluded: chain F residue  135 LEU
Chi-restraints excluded: chain F residue  193 THR
Chi-restraints excluded: chain F residue  256 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 83 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 90 optimal weight:    0.2980
   chunk 21 optimal weight:    2.9990
   chunk 124 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9980
   chunk 113 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
D 240 HIS
** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.124656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.097030 restraints weight = 19537.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.097723 restraints weight = 12892.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.098603 restraints weight = 10876.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.098912 restraints weight = 9798.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.098963 restraints weight = 8800.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.3423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10916  Z= 0.127
  Angle     :  0.534   8.930  14740  Z= 0.270
  Chirality :  0.041   0.181   1667
  Planarity :  0.004   0.038   1905
  Dihedral  :  4.254  24.513   1477
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 13.12 %
    Favored  : 83.49 %
  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 are not related in a simple way.
  whole:  1.28 (0.23), residues: 1341
  helix:  2.40 (0.21), residues: 645
  sheet: -1.51 (0.97), residues: 20
  loop : -0.65 (0.23), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 347 
 TYR   0.016   0.001   TYR B  51 
 PHE   0.014   0.001   PHE C 225 
 TRP   0.004   0.001   TRP A  99 
 HIS   0.004   0.001   HIS E  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (10916)
  covalent geometry    : angle       0.53418 (14740)
  hydrogen bonds       : bond        0.03729 (  498)
  hydrogen bonds       : angle       3.93210 ( 1461)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 125
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8473 (tt)
REVERT: D  195 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8315 (tt)
REVERT: E  151 LYS cc_start: 0.8054 (tmtm) cc_final: 0.7000 (mmtt)
REVERT: E  199 ASP cc_start: 0.6014 (t0) cc_final: 0.5310 (p0)
REVERT: F  196 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7455 (tp30)
  outliers start: 40
  outliers final: 26
  residues processed: 156
  average time/residue: 0.0910
  time to fit residues: 21.0422
Evaluate side-chains
  151 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 123
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain C residue  200 ASN
Chi-restraints excluded: chain C residue  223 ASP
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  320 ASP
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain D residue  193 THR
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  229 CYS
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  329 ILE
Chi-restraints excluded: chain E residue  185 VAL
Chi-restraints excluded: chain E residue  212 CYS
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  226 ASP
Chi-restraints excluded: chain E residue  237 VAL
Chi-restraints excluded: chain E residue  245 LEU
Chi-restraints excluded: chain E residue  258 ASN
Chi-restraints excluded: chain E residue  329 ILE
Chi-restraints excluded: chain F residue  135 LEU
Chi-restraints excluded: chain F residue  193 THR
Chi-restraints excluded: chain F residue  256 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 119 optimal weight:   10.0000
   chunk 80 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 117 optimal weight:    0.9980
   chunk 97 optimal weight:    8.9990
   chunk 3 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 78 optimal weight:    4.9990
   chunk 76 optimal weight:    6.9990
   chunk 7 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.127572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.100008 restraints weight = 19202.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.100366 restraints weight = 12680.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.101296 restraints weight = 10672.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.101437 restraints weight = 9591.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.101560 restraints weight = 9020.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.3562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10916  Z= 0.107
  Angle     :  0.523   9.550  14740  Z= 0.263
  Chirality :  0.040   0.188   1667
  Planarity :  0.003   0.039   1905
  Dihedral  :  4.149  23.447   1477
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 13.72 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.24), residues: 1341
  helix:  2.54 (0.21), residues: 639
  sheet: -1.66 (0.93), residues: 20
  loop : -0.53 (0.23), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 347 
 TYR   0.025   0.001   TYR B  51 
 PHE   0.013   0.001   PHE C 225 
 TRP   0.004   0.001   TRP A  99 
 HIS   0.004   0.001   HIS E  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (10916)
  covalent geometry    : angle       0.52333 (14740)
  hydrogen bonds       : bond        0.03502 (  498)
  hydrogen bonds       : angle       3.82430 ( 1461)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 129
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.8049 (tptm) cc_final: 0.7836 (tptm)
REVERT: A  113 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8446 (tt)
REVERT: D  195 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8311 (tt)
REVERT: D  272 MET cc_start: 0.7598 (mmp) cc_final: 0.7181 (mmp)
REVERT: E  151 LYS cc_start: 0.8057 (tmtm) cc_final: 0.7025 (mmtt)
REVERT: E  199 ASP cc_start: 0.6093 (t0) cc_final: 0.5381 (p0)
REVERT: F  260 GLU cc_start: 0.7632 (pm20) cc_final: 0.7296 (mp0)
  outliers start: 34
  outliers final: 25
  residues processed: 155
  average time/residue: 0.0955
  time to fit residues: 21.7210
Evaluate side-chains
  148 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 121
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  160 PHE
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain C residue  200 ASN
Chi-restraints excluded: chain C residue  223 ASP
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  229 CYS
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  329 ILE
Chi-restraints excluded: chain E residue  185 VAL
Chi-restraints excluded: chain E residue  212 CYS
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  226 ASP
Chi-restraints excluded: chain E residue  237 VAL
Chi-restraints excluded: chain E residue  258 ASN
Chi-restraints excluded: chain E residue  329 ILE
Chi-restraints excluded: chain F residue  135 LEU
Chi-restraints excluded: chain F residue  193 THR
Chi-restraints excluded: chain F residue  256 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 65 optimal weight:    8.9990
   chunk 70 optimal weight:    0.0470
   chunk 48 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 93 optimal weight:    0.2980
   chunk 79 optimal weight:    7.9990
   chunk 73 optimal weight:    9.9990
   chunk 38 optimal weight:    6.9990
   chunk 106 optimal weight:    7.9990
   chunk 110 optimal weight:    0.9980
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
A 101 GLN
** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.128609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.101358 restraints weight = 19186.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.101725 restraints weight = 12683.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.102290 restraints weight = 10659.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.102567 restraints weight = 10044.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.102779 restraints weight = 9354.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.3656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10916  Z= 0.102
  Angle     :  0.531  10.442  14740  Z= 0.265
  Chirality :  0.040   0.188   1667
  Planarity :  0.003   0.038   1905
  Dihedral  :  4.051  22.609   1477
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.56 %
    Favored  : 82.98 %
  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 are not related in a simple way.
  whole:  1.52 (0.24), residues: 1341
  helix:  2.57 (0.21), residues: 640
  sheet: -1.73 (0.90), residues: 20
  loop : -0.46 (0.23), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 347 
 TYR   0.025   0.001   TYR B  51 
 PHE   0.013   0.001   PHE C 225 
 TRP   0.012   0.001   TRP A 146 
 HIS   0.006   0.001   HIS D 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (10916)
  covalent geometry    : angle       0.53085 (14740)
  hydrogen bonds       : bond        0.03389 (  498)
  hydrogen bonds       : angle       3.77641 ( 1461)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 127
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: A  159 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8309 (pt)
REVERT: D  195 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8297 (tt)
REVERT: D  272 MET cc_start: 0.7497 (mmp) cc_final: 0.7159 (mmp)
REVERT: E  151 LYS cc_start: 0.8026 (tmtm) cc_final: 0.7031 (mmtt)
REVERT: E  199 ASP cc_start: 0.5996 (t0) cc_final: 0.5333 (p0)
REVERT: F  260 GLU cc_start: 0.7472 (pm20) cc_final: 0.7209 (mp0)
  outliers start: 29
  outliers final: 21
  residues processed: 149
  average time/residue: 0.0974
  time to fit residues: 21.1831
Evaluate side-chains
  143 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain C residue  200 ASN
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  229 CYS
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  329 ILE
Chi-restraints excluded: chain E residue  185 VAL
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  226 ASP
Chi-restraints excluded: chain E residue  237 VAL
Chi-restraints excluded: chain E residue  258 ASN
Chi-restraints excluded: chain E residue  329 ILE
Chi-restraints excluded: chain F residue  135 LEU
Chi-restraints excluded: chain F residue  193 THR
Chi-restraints excluded: chain F residue  256 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 124 optimal weight:    0.9990
   chunk 120 optimal weight:    9.9990
   chunk 126 optimal weight:    0.6980
   chunk 58 optimal weight:    6.9990
   chunk 7 optimal weight:    0.3980
   chunk 55 optimal weight:    2.9990
   chunk 79 optimal weight:    8.9990
   chunk 36 optimal weight:    2.9990
   chunk 64 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.125291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.098107 restraints weight = 19380.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.098567 restraints weight = 13965.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.099289 restraints weight = 11393.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.099475 restraints weight = 10471.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.099700 restraints weight = 9231.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.3743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10916  Z= 0.127
  Angle     :  0.550  11.157  14740  Z= 0.277
  Chirality :  0.041   0.187   1667
  Planarity :  0.004   0.036   1905
  Dihedral  :  4.110  23.054   1477
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 14.65 %
    Favored  : 82.81 %
  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 are not related in a simple way.
  whole:  1.51 (0.24), residues: 1341
  helix:  2.54 (0.21), residues: 642
  sheet: -1.77 (0.90), residues: 20
  loop : -0.43 (0.23), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 347 
 TYR   0.023   0.001   TYR B  51 
 PHE   0.014   0.001   PHE C 225 
 TRP   0.013   0.001   TRP A 146 
 HIS   0.004   0.001   HIS E  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10916)
  covalent geometry    : angle       0.55001 (14740)
  hydrogen bonds       : bond        0.03512 (  498)
  hydrogen bonds       : angle       3.78256 ( 1461)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 121
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
REVERT: C  367 MET cc_start: 0.8854 (tpp) cc_final: 0.8627 (tpp)
REVERT: D  272 MET cc_start: 0.7527 (mmp) cc_final: 0.7238 (mmp)
REVERT: E  151 LYS cc_start: 0.8041 (tmtm) cc_final: 0.7046 (mmtt)
REVERT: E  199 ASP cc_start: 0.6052 (t0) cc_final: 0.5379 (p0)
REVERT: F  196 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7476 (tp30)
REVERT: F  260 GLU cc_start: 0.7529 (pm20) cc_final: 0.7255 (mp0)
  outliers start: 30
  outliers final: 23
  residues processed: 143
  average time/residue: 0.0970
  time to fit residues: 20.2185
Evaluate side-chains
  137 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain C residue  200 ASN
Chi-restraints excluded: chain C residue  217 ILE
Chi-restraints excluded: chain C residue  223 ASP
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain D residue  229 CYS
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  329 ILE
Chi-restraints excluded: chain E residue  185 VAL
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  226 ASP
Chi-restraints excluded: chain E residue  237 VAL
Chi-restraints excluded: chain E residue  258 ASN
Chi-restraints excluded: chain E residue  329 ILE
Chi-restraints excluded: chain F residue  135 LEU
Chi-restraints excluded: chain F residue  193 THR
Chi-restraints excluded: chain F residue  256 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 115 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 52 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.126009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.098343 restraints weight = 19215.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.099207 restraints weight = 12664.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.099827 restraints weight = 10953.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.100113 restraints weight = 9892.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.100219 restraints weight = 8919.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.3804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10916  Z= 0.108
  Angle     :  0.536  10.742  14740  Z= 0.269
  Chirality :  0.041   0.189   1667
  Planarity :  0.003   0.037   1905
  Dihedral  :  4.037  22.171   1477
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 14.82 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.56 (0.24), residues: 1341
  helix:  2.55 (0.21), residues: 643
  sheet: -1.88 (0.87), residues: 20
  loop : -0.39 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  98 
 TYR   0.030   0.001   TYR B  51 
 PHE   0.012   0.001   PHE C 225 
 TRP   0.013   0.001   TRP A 146 
 HIS   0.004   0.001   HIS E  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (10916)
  covalent geometry    : angle       0.53648 (14740)
  hydrogen bonds       : bond        0.03372 (  498)
  hydrogen bonds       : angle       3.73863 ( 1461)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
REVERT: C  367 MET cc_start: 0.8811 (tpp) cc_final: 0.8557 (tpp)
REVERT: D  195 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8308 (tt)
REVERT: D  272 MET cc_start: 0.7501 (mmp) cc_final: 0.7198 (mmp)
REVERT: E  151 LYS cc_start: 0.8046 (tmtm) cc_final: 0.7039 (mmtt)
REVERT: E  199 ASP cc_start: 0.6093 (t0) cc_final: 0.5456 (p0)
REVERT: F  196 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7343 (tp30)
REVERT: F  260 GLU cc_start: 0.7472 (pm20) cc_final: 0.7239 (mp0)
  outliers start: 25
  outliers final: 23
  residues processed: 135
  average time/residue: 0.1007
  time to fit residues: 19.6266
Evaluate side-chains
  138 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain C residue  200 ASN
Chi-restraints excluded: chain C residue  217 ILE
Chi-restraints excluded: chain C residue  223 ASP
Chi-restraints excluded: chain C residue  338 LEU
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  229 CYS
Chi-restraints excluded: chain D residue  256 LEU
Chi-restraints excluded: chain D residue  329 ILE
Chi-restraints excluded: chain E residue  185 VAL
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  226 ASP
Chi-restraints excluded: chain E residue  237 VAL
Chi-restraints excluded: chain E residue  258 ASN
Chi-restraints excluded: chain E residue  329 ILE
Chi-restraints excluded: chain F residue  135 LEU
Chi-restraints excluded: chain F residue  193 THR
Chi-restraints excluded: chain F residue  256 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 97 optimal weight:    5.9990
   chunk 131 optimal weight:    0.8980
   chunk 95 optimal weight:    7.9990
   chunk 132 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 90 optimal weight:    0.0010
   chunk 82 optimal weight:    8.9990
   chunk 57 optimal weight:   10.0000
   chunk 114 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.9590

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

Flipped N/Q/H residues before XYZ refinement:
** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.125997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.098875 restraints weight = 19426.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.100411 restraints weight = 14040.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.100586 restraints weight = 12102.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.101010 restraints weight = 10831.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.100923 restraints weight = 9620.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.3873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10916  Z= 0.112
  Angle     :  0.539  10.377  14740  Z= 0.271
  Chirality :  0.041   0.190   1667
  Planarity :  0.003   0.037   1905
  Dihedral  :  4.025  22.036   1477
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 14.99 %
    Favored  : 82.90 %
  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 are not related in a simple way.
  whole:  1.59 (0.24), residues: 1341
  helix:  2.58 (0.21), residues: 643
  sheet: -1.89 (0.88), residues: 20
  loop : -0.36 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  98 
 TYR   0.029   0.001   TYR B  51 
 PHE   0.013   0.001   PHE C 225 
 TRP   0.011   0.001   TRP A 146 
 HIS   0.004   0.001   HIS E  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (10916)
  covalent geometry    : angle       0.53939 (14740)
  hydrogen bonds       : bond        0.03375 (  498)
  hydrogen bonds       : angle       3.71260 ( 1461)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1636.17 seconds
wall clock time: 29 minutes 1.88 seconds (1741.88 seconds total)