Starting phenix.real_space_refine
on Wed Mar  4 15:28:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ni3_9376/03_2026/6ni3_9376.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ni3_9376/03_2026/6ni3_9376.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ni3_9376/03_2026/6ni3_9376.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ni3_9376/03_2026/6ni3_9376.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ni3_9376/03_2026/6ni3_9376.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ni3_9376/03_2026/6ni3_9376.map"
  }
  resolution = 3.8
  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=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 8114 atoms to isotropic.
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      55      5.16       5
     C    5164      2.51       5
     N    1399      2.21       5
     O    1518      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 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: 8136
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1912
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1912
          Classifications: {'peptide': 234}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 2587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2587
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 18
    Chain: "G"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 438
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          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: "R"
      Number of atoms: 2202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2202
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 7, 'TRANS': 276}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 86
          Unresolved non-hydrogen angles: 106
          Unresolved non-hydrogen dihedrals: 77
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 4, 'TRP:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 54
    Chain: "N"
      Number of atoms: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 970
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "R"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'P0G': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.06, per 1000 atoms: 0.25
  Number of scatterers: 8136
  At special positions: 0
  Unit cell: (101.92, 122.72, 101.92, 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      55     16.00
     O    1518      8.00
     N    1399      7.00
     C    5164      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.02

  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: 0.56
  Conformation dependent library (CDL) restraints added in 283.3 milliseconds
  

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1962

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 10 sheets defined
      44.3% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 40
      removed outlier: 3.578A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 57
      removed outlier: 4.078A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 52 through 57'
    Processing helix  chain 'A' and resid 234 through 238
    Processing helix  chain 'A' and resid 264 through 279
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.337A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 4.000A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 391
    Processing helix  chain 'B' and resid 3 through 25
      removed outlier: 3.581A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 6 through 23
      removed outlier: 3.977A  pdb=" N   ALA G  10 " --> pdb=" O   THR G   6 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLN G  11 " --> pdb=" O   ALA G   7 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'R' and resid 31 through 60
      removed outlier: 3.928A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 61 through 65
      removed outlier: 3.656A  pdb=" N   LEU R  64 " --> pdb=" O   PHE R  61 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLN R  65 " --> pdb=" O   GLU R  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 61 through 65'
    Processing helix  chain 'R' and resid 66 through 85
      removed outlier: 3.502A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA R  85 " --> pdb=" O   VAL R  81 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 85 through 97
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.030A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 172
      removed outlier: 4.971A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 180 through 187
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.592A  pdb=" N   ALA R 202 " --> pdb=" O   ALA R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 266 through 299
      removed outlier: 4.119A  pdb=" N   THR R 274 " --> pdb=" O   LYS R 270 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   LEU R 275 " --> pdb=" O   ALA R 271 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   CYS R 285 " --> pdb=" O   THR R 281 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   TRP R 286 " --> pdb=" O   PHE R 282 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.711A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 3.713A  pdb=" N   TYR R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ILE R 309 " --> pdb=" O   LYS R 305 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340
      removed outlier: 3.563A  pdb=" N   LEU R 339 " --> pdb=" O   ALA R 335 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
      removed outlier: 3.632A  pdb=" N   LYS N  65 " --> pdb=" O   GLY N  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 62 through 65'
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.977A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 6.186A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.696A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.949A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.326A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.564A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.600A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL B 158 " --> pdb=" O   ARG B 150 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.823A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.835A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.600A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.913A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 4.058A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  25 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   SER N  25 " --> pdb=" O   GLN N   3 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   SER N  21 " --> pdb=" O   SER N   7 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 3.501A  pdb=" N   THR N 122 " --> pdb=" O   TYR N  94 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.126A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    421 hydrogen bonds defined for protein.
    1215 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: 1.10

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1883
        1.33 -     1.45: 2038
        1.45 -     1.58: 4300
        1.58 -     1.70: 2
        1.70 -     1.83: 76
  Bond restraints: 8299
  Sorted by residual:
  bond pdb=" CAO P0G R1601 "
       pdb=" CAV P0G R1601 "
    ideal  model  delta    sigma   weight residual
    1.506  1.600 -0.094 2.00e-02 2.50e+03 2.21e+01
  bond pdb=" CAY P0G R1601 "
       pdb=" OAR P0G R1601 "
    ideal  model  delta    sigma   weight residual
    1.357  1.446 -0.089 2.00e-02 2.50e+03 1.97e+01
  bond pdb=" CAA P0G R1601 "
       pdb=" CAT P0G R1601 "
    ideal  model  delta    sigma   weight residual
    1.504  1.584 -0.080 2.00e-02 2.50e+03 1.59e+01
  bond pdb=" CAX P0G R1601 "
       pdb=" NAQ P0G R1601 "
    ideal  model  delta    sigma   weight residual
    1.398  1.476 -0.078 2.00e-02 2.50e+03 1.54e+01
  bond pdb=" CB  TRP R 313 "
       pdb=" CG  TRP R 313 "
    ideal  model  delta    sigma   weight residual
    1.498  1.408  0.090 3.10e-02 1.04e+03 8.46e+00
  ... (remaining 8294 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.79: 11173
        4.79 -     9.57: 78
        9.57 -    14.36: 7
       14.36 -    19.15: 0
       19.15 -    23.93: 2
  Bond angle restraints: 11260
  Sorted by residual:
  angle pdb=" CAA P0G R1601 "
        pdb=" CAT P0G R1601 "
        pdb=" CAI P0G R1601 "
      ideal   model   delta    sigma   weight residual
     117.83   93.90   23.93 3.00e+00 1.11e-01 6.36e+01
  angle pdb=" CAA P0G R1601 "
        pdb=" CAT P0G R1601 "
        pdb=" CAV P0G R1601 "
      ideal   model   delta    sigma   weight residual
     123.39  145.42  -22.03 3.00e+00 1.11e-01 5.39e+01
  angle pdb=" CB  ARG R 221 "
        pdb=" CG  ARG R 221 "
        pdb=" CD  ARG R 221 "
      ideal   model   delta    sigma   weight residual
     111.30  101.01   10.29 2.30e+00 1.89e-01 2.00e+01
  angle pdb=" C   THR N 113 "
        pdb=" N   THR N 114 "
        pdb=" CA  THR N 114 "
      ideal   model   delta    sigma   weight residual
     121.54  129.65   -8.11 1.91e+00 2.74e-01 1.80e+01
  angle pdb=" CA  THR N 114 "
        pdb=" CB  THR N 114 "
        pdb=" CG2 THR N 114 "
      ideal   model   delta    sigma   weight residual
     110.50  117.56   -7.06 1.70e+00 3.46e-01 1.72e+01
  ... (remaining 11255 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.41: 4654
       16.41 -    32.82: 218
       32.82 -    49.23: 44
       49.23 -    65.64: 9
       65.64 -    82.05: 5
  Dihedral angle restraints: 4930
    sinusoidal: 1899
      harmonic: 3031
  Sorted by residual:
  dihedral pdb=" CA  THR A 364 "
           pdb=" C   THR A 364 "
           pdb=" N   CYS A 365 "
           pdb=" CA  CYS A 365 "
      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  PHE A 363 "
           pdb=" C   PHE A 363 "
           pdb=" N   THR A 364 "
           pdb=" CA  THR A 364 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.57  -25.43     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  THR N 113 "
           pdb=" C   THR N 113 "
           pdb=" N   THR N 114 "
           pdb=" CA  THR N 114 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.98  -24.02     0      5.00e+00 4.00e-02 2.31e+01
  ... (remaining 4927 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 1098
       0.095 -    0.191: 166
       0.191 -    0.286: 14
       0.286 -    0.381: 0
       0.381 -    0.477: 2
  Chirality restraints: 1280
  Sorted by residual:
  chirality pdb=" CB  ILE N  70 "
            pdb=" CA  ILE N  70 "
            pdb=" CG1 ILE N  70 "
            pdb=" CG2 ILE N  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.17    0.48 2.00e-01 2.50e+01 5.68e+00
  chirality pdb=" CB  ILE B 232 "
            pdb=" CA  ILE B 232 "
            pdb=" CG1 ILE B 232 "
            pdb=" CG2 ILE B 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.25    0.39 2.00e-01 2.50e+01 3.88e+00
  chirality pdb=" CB  ILE B  58 "
            pdb=" CA  ILE B  58 "
            pdb=" CG1 ILE B  58 "
            pdb=" CG2 ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.66e+00
  ... (remaining 1277 not shown)

  Planarity restraints: 1436
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 294 "   -0.018 2.00e-02 2.50e+03   3.68e-02 1.35e+01
        pdb=" C   ILE R 294 "    0.064 2.00e-02 2.50e+03
        pdb=" O   ILE R 294 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   VAL R 295 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 325 "   -0.016 2.00e-02 2.50e+03   3.24e-02 1.05e+01
        pdb=" C   ILE R 325 "    0.056 2.00e-02 2.50e+03
        pdb=" O   ILE R 325 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   TYR R 326 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R  44 "    0.014 2.00e-02 2.50e+03   2.83e-02 8.02e+00
        pdb=" C   VAL R  44 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   VAL R  44 "    0.018 2.00e-02 2.50e+03
        pdb=" N   LEU R  45 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1433 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1808
        2.79 -     3.31: 7612
        3.31 -     3.84: 13364
        3.84 -     4.37: 14832
        4.37 -     4.90: 26033
  Nonbonded interactions: 63649
  Sorted by model distance:
  nonbonded pdb=" O   VAL A  36 "
            pdb=" OG1 THR A  40 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OG1 THR N 104 "
            pdb=" OD1 ASP N 106 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   GLU B 226 "
            pdb=" NH2 ARG N  98 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" OG1 THR B 128 "
            pdb=" O   GLY B 131 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" NE2 HIS A 362 "
            pdb=" OD2 ASP A 378 "
     model   vdw
     2.338 3.120
  ... (remaining 63644 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.210
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
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      :  0.010   0.126   8302  Z= 0.455
  Angle     :  1.263  23.932  11266  Z= 0.695
  Chirality :  0.069   0.477   1280
  Planarity :  0.008   0.063   1436
  Dihedral  : 10.755  82.046   2959
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  5.09 %
    Favored  : 94.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.86 (0.22), residues: 1025
  helix: -2.10 (0.19), residues: 413
  sheet: -1.40 (0.30), residues: 230
  loop : -1.68 (0.28), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  68 
 TYR   0.042   0.005   TYR R 316 
 PHE   0.045   0.005   PHE B 234 
 TRP   0.041   0.006   TRP B 211 
 HIS   0.010   0.003   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.01020 ( 8299)
  covalent geometry    : angle       1.26226 (11260)
  SS BOND              : bond        0.00576 (    3)
  SS BOND              : angle       2.40558 (    6)
  hydrogen bonds       : bond        0.16252 (  421)
  hydrogen bonds       : angle       7.43174 ( 1215)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 249
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7363 (tm-30)
REVERT: A  222 PHE cc_start: 0.5346 (t80) cc_final: 0.4601 (t80)
REVERT: B   18 ILE cc_start: 0.8840 (mt) cc_final: 0.8517 (tp)
REVERT: R   36 MET cc_start: 0.7182 (mmm) cc_final: 0.6306 (mtp)
REVERT: R   40 MET cc_start: 0.7157 (mtt) cc_final: 0.6766 (mmt)
REVERT: R  124 LEU cc_start: 0.8672 (mt) cc_final: 0.8447 (tp)
REVERT: R  273 LYS cc_start: 0.8113 (tttt) cc_final: 0.7803 (tttp)
REVERT: N   90 ASP cc_start: 0.7148 (m-30) cc_final: 0.6885 (m-30)
REVERT: N  125 THR cc_start: 0.8320 (m) cc_final: 0.7543 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 250
  average time/residue: 0.1182
  time to fit residues: 37.1230
Evaluate side-chains
  136 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 135
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  292 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A  23 ASN
B  88 ASN
B 239 ASN
B 266 HIS
G  24 ASN
R  69 ASN
R 172 HIS
R 179 GLN
N   1 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.109907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.093403 restraints weight = 22716.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.096076 restraints weight = 12773.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.097891 restraints weight = 8674.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.099089 restraints weight = 6640.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.100010 restraints weight = 5489.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8302  Z= 0.139
  Angle     :  0.667  12.196  11266  Z= 0.345
  Chirality :  0.044   0.172   1280
  Planarity :  0.005   0.054   1436
  Dihedral  :  6.247  80.356   1150
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 11.00 %
    Favored  : 85.53 %
  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: -0.48 (0.25), residues: 1025
  helix:  0.85 (0.25), residues: 414
  sheet: -0.82 (0.31), residues: 220
  loop : -1.19 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  42 
 TYR   0.022   0.002   TYR A  37 
 PHE   0.019   0.002   PHE B 253 
 TRP   0.024   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8299)
  covalent geometry    : angle       0.66599 (11260)
  SS BOND              : bond        0.00966 (    3)
  SS BOND              : angle       1.98532 (    6)
  hydrogen bonds       : bond        0.04497 (  421)
  hydrogen bonds       : angle       5.33998 ( 1215)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 177
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ASP cc_start: 0.8806 (p0) cc_final: 0.7414 (p0)
REVERT: A  222 PHE cc_start: 0.5304 (t80) cc_final: 0.5101 (t80)
REVERT: A  333 ARG cc_start: 0.7957 (tpp80) cc_final: 0.7549 (tpp80)
REVERT: A  391 TYR cc_start: 0.8616 (m-10) cc_final: 0.8373 (m-10)
REVERT: B  321 THR cc_start: 0.8596 (p) cc_final: 0.8300 (p)
REVERT: G   38 MET cc_start: 0.7782 (tmm) cc_final: 0.7537 (tmm)
REVERT: G   48 ASP cc_start: 0.7786 (t0) cc_final: 0.7583 (t0)
REVERT: R   36 MET cc_start: 0.7119 (mmm) cc_final: 0.6273 (mtp)
REVERT: R   40 MET cc_start: 0.7204 (mtt) cc_final: 0.6976 (mmt)
REVERT: R  225 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8216 (tp30)
REVERT: R  273 LYS cc_start: 0.7894 (tttt) cc_final: 0.7646 (tttp)
REVERT: N   96 CYS cc_start: 0.5067 (p) cc_final: 0.4557 (p)
REVERT: N  120 GLN cc_start: 0.8096 (mp10) cc_final: 0.7713 (pm20)
REVERT: N  125 THR cc_start: 0.7282 (m) cc_final: 0.7075 (p)
  outliers start: 30
  outliers final: 18
  residues processed: 198
  average time/residue: 0.0941
  time to fit residues: 24.6651
Evaluate side-chains
  150 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain R residue   55 ILE
Chi-restraints excluded: chain R residue  129 VAL
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  133 PHE
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  179 GLN
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  295 VAL
Chi-restraints excluded: chain R residue  307 VAL
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain N residue  110 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 58 optimal weight:    0.0070
   chunk 14 optimal weight:    0.7980
   chunk 87 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0060
   chunk 33 optimal weight:    4.9990
   chunk 76 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0270
   chunk 93 optimal weight:    0.2980
   chunk 90 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 4 optimal weight:   10.0000
   overall best weight:    0.1872

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R  69 ASN
R 179 GLN
R 322 ASN
R 337 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.105537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.089773 restraints weight = 21572.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.092218 restraints weight = 12391.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.093947 restraints weight = 8415.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.095120 restraints weight = 6385.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.095846 restraints weight = 5248.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.4019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8302  Z= 0.120
  Angle     :  0.615  10.994  11266  Z= 0.314
  Chirality :  0.042   0.150   1280
  Planarity :  0.004   0.052   1436
  Dihedral  :  5.744  85.584   1150
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 14.58 %
    Favored  : 82.18 %
  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:  0.19 (0.26), residues: 1025
  helix:  1.52 (0.25), residues: 422
  sheet: -0.65 (0.31), residues: 224
  loop : -0.92 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B   8 
 TYR   0.031   0.001   TYR A 253 
 PHE   0.015   0.001   PHE B 253 
 TRP   0.019   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8299)
  covalent geometry    : angle       0.61460 (11260)
  SS BOND              : bond        0.00360 (    3)
  SS BOND              : angle       1.06521 (    6)
  hydrogen bonds       : bond        0.03971 (  421)
  hydrogen bonds       : angle       4.90152 ( 1215)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ASP cc_start: 0.7991 (p0) cc_final: 0.7761 (p0)
REVERT: A  212 PHE cc_start: 0.6121 (p90) cc_final: 0.5836 (p90)
REVERT: A  222 PHE cc_start: 0.5303 (t80) cc_final: 0.5080 (t80)
REVERT: A  278 ASN cc_start: 0.8542 (m-40) cc_final: 0.8260 (m-40)
REVERT: B   37 ILE cc_start: 0.8773 (mm) cc_final: 0.8551 (pt)
REVERT: B  158 VAL cc_start: 0.8511 (p) cc_final: 0.8218 (m)
REVERT: B  321 THR cc_start: 0.8559 (p) cc_final: 0.8018 (p)
REVERT: G   38 MET cc_start: 0.7872 (tmm) cc_final: 0.7640 (tmm)
REVERT: G   48 ASP cc_start: 0.7750 (t0) cc_final: 0.7085 (t0)
REVERT: G   51 LEU cc_start: 0.8061 (tt) cc_final: 0.7092 (mt)
REVERT: R   36 MET cc_start: 0.6841 (mmm) cc_final: 0.5989 (mtp)
REVERT: R  188 GLU cc_start: 0.7398 (pm20) cc_final: 0.6799 (tt0)
REVERT: R  204 SER cc_start: 0.8395 (m) cc_final: 0.7640 (t)
REVERT: R  225 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8171 (tp30)
REVERT: R  273 LYS cc_start: 0.7866 (tttt) cc_final: 0.7641 (ttpt)
REVERT: N   22 CYS cc_start: 0.5007 (t) cc_final: 0.4762 (t)
REVERT: N   78 THR cc_start: 0.6945 (OUTLIER) cc_final: 0.6674 (m)
REVERT: N  120 GLN cc_start: 0.7935 (mp10) cc_final: 0.7622 (pm20)
  outliers start: 28
  outliers final: 17
  residues processed: 169
  average time/residue: 0.0804
  time to fit residues: 18.2362
Evaluate side-chains
  140 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain R residue   31 VAL
Chi-restraints excluded: chain R residue   55 ILE
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  322 ASN
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  110 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0970
   chunk 25 optimal weight:    8.9990
   chunk 43 optimal weight:   10.0000
   chunk 77 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B 175 GLN
B 340 ASN
R  69 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.102944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.086944 restraints weight = 22348.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.089299 restraints weight = 12724.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.090994 restraints weight = 8742.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.092142 restraints weight = 6680.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.092932 restraints weight = 5521.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.4282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8302  Z= 0.143
  Angle     :  0.630  12.442  11266  Z= 0.319
  Chirality :  0.042   0.155   1280
  Planarity :  0.004   0.052   1436
  Dihedral  :  5.693  89.311   1150
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 15.97 %
    Favored  : 80.44 %
  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:  0.32 (0.26), residues: 1025
  helix:  1.73 (0.26), residues: 418
  sheet: -0.66 (0.32), residues: 226
  loop : -0.88 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B   8 
 TYR   0.014   0.001   TYR A 253 
 PHE   0.018   0.001   PHE B 253 
 TRP   0.018   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8299)
  covalent geometry    : angle       0.62975 (11260)
  SS BOND              : bond        0.00186 (    3)
  SS BOND              : angle       1.42383 (    6)
  hydrogen bonds       : bond        0.03969 (  421)
  hydrogen bonds       : angle       4.65046 ( 1215)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 132
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ASP cc_start: 0.8009 (p0) cc_final: 0.7778 (p0)
REVERT: A  222 PHE cc_start: 0.5275 (t80) cc_final: 0.5023 (t80)
REVERT: A  333 ARG cc_start: 0.7998 (tpp80) cc_final: 0.7774 (tpp80)
REVERT: B   15 LYS cc_start: 0.8879 (ttpp) cc_final: 0.8610 (tttt)
REVERT: B  188 MET cc_start: 0.8652 (mmm) cc_final: 0.8429 (mmp)
REVERT: G   21 MET cc_start: 0.7856 (ppp) cc_final: 0.7615 (ppp)
REVERT: G   22 GLU cc_start: 0.7743 (pp20) cc_final: 0.7447 (pp20)
REVERT: G   38 MET cc_start: 0.7983 (tmm) cc_final: 0.7706 (tmm)
REVERT: G   48 ASP cc_start: 0.7748 (t0) cc_final: 0.7222 (t0)
REVERT: G   51 LEU cc_start: 0.8118 (tt) cc_final: 0.7123 (mt)
REVERT: R   36 MET cc_start: 0.6734 (mmm) cc_final: 0.5928 (mtp)
REVERT: R   40 MET cc_start: 0.7963 (mmm) cc_final: 0.7518 (mmm)
REVERT: R  273 LYS cc_start: 0.7961 (tttt) cc_final: 0.7699 (ttpt)
REVERT: N   78 THR cc_start: 0.7133 (OUTLIER) cc_final: 0.6746 (m)
REVERT: N  120 GLN cc_start: 0.8002 (mp10) cc_final: 0.7743 (pm20)
  outliers start: 31
  outliers final: 23
  residues processed: 151
  average time/residue: 0.0884
  time to fit residues: 17.9534
Evaluate side-chains
  150 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   31 VAL
Chi-restraints excluded: chain R residue   55 ILE
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  133 PHE
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain N residue   91 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 89 optimal weight:    7.9990
   chunk 87 optimal weight:    1.9990
   chunk 25 optimal weight:    8.9990
   chunk 96 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0270
   chunk 7 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 68 optimal weight:    7.9990
   overall best weight:    1.8046

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
R  69 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.101446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.085057 restraints weight = 22567.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.087421 restraints weight = 13173.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.089077 restraints weight = 9109.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.090220 restraints weight = 7052.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.091004 restraints weight = 5879.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.4409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8302  Z= 0.164
  Angle     :  0.641  12.828  11266  Z= 0.327
  Chirality :  0.043   0.159   1280
  Planarity :  0.004   0.053   1436
  Dihedral  :  5.724  88.766   1150
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 16.78 %
    Favored  : 79.17 %
  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:  0.45 (0.26), residues: 1025
  helix:  1.76 (0.26), residues: 420
  sheet: -0.53 (0.32), residues: 230
  loop : -0.78 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B   8 
 TYR   0.011   0.002   TYR A 318 
 PHE   0.030   0.001   PHE B 199 
 TRP   0.020   0.002   TRP B 211 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 8299)
  covalent geometry    : angle       0.64070 (11260)
  SS BOND              : bond        0.00141 (    3)
  SS BOND              : angle       1.47354 (    6)
  hydrogen bonds       : bond        0.04024 (  421)
  hydrogen bonds       : angle       4.58249 ( 1215)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 132
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ASP cc_start: 0.8115 (p0) cc_final: 0.7914 (p0)
REVERT: A  222 PHE cc_start: 0.5342 (t80) cc_final: 0.4480 (t80)
REVERT: A  333 ARG cc_start: 0.8004 (tpp80) cc_final: 0.7793 (tpp80)
REVERT: B   15 LYS cc_start: 0.8867 (ttpp) cc_final: 0.8625 (tttt)
REVERT: G   21 MET cc_start: 0.7900 (ppp) cc_final: 0.7634 (ppp)
REVERT: G   22 GLU cc_start: 0.7869 (pp20) cc_final: 0.7577 (pp20)
REVERT: G   38 MET cc_start: 0.7997 (tmm) cc_final: 0.7720 (tmm)
REVERT: G   48 ASP cc_start: 0.7804 (t0) cc_final: 0.7362 (t0)
REVERT: G   51 LEU cc_start: 0.8178 (tt) cc_final: 0.7188 (mt)
REVERT: R   36 MET cc_start: 0.6651 (mmm) cc_final: 0.6010 (mtp)
REVERT: R   40 MET cc_start: 0.7929 (mmm) cc_final: 0.7515 (mmm)
REVERT: R  273 LYS cc_start: 0.8048 (tttt) cc_final: 0.7796 (ttpt)
REVERT: R  312 ASN cc_start: 0.8099 (t160) cc_final: 0.7790 (t0)
REVERT: N   78 THR cc_start: 0.7004 (OUTLIER) cc_final: 0.6722 (m)
  outliers start: 35
  outliers final: 25
  residues processed: 155
  average time/residue: 0.0923
  time to fit residues: 19.1051
Evaluate side-chains
  148 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   31 VAL
Chi-restraints excluded: chain R residue   55 ILE
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  133 PHE
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  278 ILE
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain N residue   91 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 98 optimal weight:    0.7980
   chunk 60 optimal weight:   10.0000
   chunk 88 optimal weight:    0.8980
   chunk 40 optimal weight:    0.1980
   chunk 1 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
R  69 ASN
** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.103685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.087728 restraints weight = 21666.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.090134 restraints weight = 12496.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.091780 restraints weight = 8506.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.092935 restraints weight = 6530.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.093716 restraints weight = 5388.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.4675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8302  Z= 0.122
  Angle     :  0.652  16.241  11266  Z= 0.319
  Chirality :  0.042   0.162   1280
  Planarity :  0.004   0.051   1436
  Dihedral  :  5.520  87.337   1150
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 17.82 %
    Favored  : 78.70 %
  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 (0.26), residues: 1025
  helix:  1.83 (0.26), residues: 420
  sheet: -0.43 (0.33), residues: 226
  loop : -0.82 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B   8 
 TYR   0.010   0.001   TYR A 391 
 PHE   0.033   0.001   PHE R 208 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8299)
  covalent geometry    : angle       0.65136 (11260)
  SS BOND              : bond        0.00203 (    3)
  SS BOND              : angle       1.13327 (    6)
  hydrogen bonds       : bond        0.03706 (  421)
  hydrogen bonds       : angle       4.44949 ( 1215)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 134
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ASP cc_start: 0.7815 (p0) cc_final: 0.7570 (p0)
REVERT: A  278 ASN cc_start: 0.8545 (m-40) cc_final: 0.8286 (m-40)
REVERT: G   21 MET cc_start: 0.7748 (ppp) cc_final: 0.7548 (ppp)
REVERT: G   22 GLU cc_start: 0.7864 (pp20) cc_final: 0.7613 (pp20)
REVERT: G   38 MET cc_start: 0.8008 (tmm) cc_final: 0.7721 (tmm)
REVERT: G   48 ASP cc_start: 0.7808 (t0) cc_final: 0.7426 (t0)
REVERT: G   51 LEU cc_start: 0.8127 (tt) cc_final: 0.7142 (mt)
REVERT: R   40 MET cc_start: 0.7950 (mmm) cc_final: 0.7546 (mmm)
REVERT: R  273 LYS cc_start: 0.8034 (tttt) cc_final: 0.7787 (ttpt)
REVERT: N   34 MET cc_start: 0.7173 (mtp) cc_final: 0.6891 (mtp)
REVERT: N   79 LEU cc_start: 0.8045 (mt) cc_final: 0.7762 (mp)
REVERT: N  120 GLN cc_start: 0.8056 (mp10) cc_final: 0.7768 (pm20)
  outliers start: 30
  outliers final: 21
  residues processed: 155
  average time/residue: 0.0841
  time to fit residues: 17.7795
Evaluate side-chains
  147 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   31 VAL
Chi-restraints excluded: chain R residue   55 ILE
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  133 PHE
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  278 ILE
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain N residue   91 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 38 optimal weight:    0.1980
   chunk 50 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 67 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 43 optimal weight:    9.9990
   chunk 92 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9990
   chunk 94 optimal weight:    3.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
R  69 ASN
** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.102594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.086665 restraints weight = 22124.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.089027 restraints weight = 12661.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.090707 restraints weight = 8620.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.091833 restraints weight = 6588.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.092509 restraints weight = 5454.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.4761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8302  Z= 0.143
  Angle     :  0.661  14.219  11266  Z= 0.325
  Chirality :  0.042   0.150   1280
  Planarity :  0.004   0.051   1436
  Dihedral  :  5.542  84.891   1150
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.98 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.27), residues: 1025
  helix:  1.84 (0.26), residues: 420
  sheet: -0.36 (0.32), residues: 227
  loop : -0.77 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B   8 
 TYR   0.018   0.001   TYR A 253 
 PHE   0.025   0.001   PHE R 208 
 TRP   0.016   0.002   TRP B 211 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 8299)
  covalent geometry    : angle       0.66065 (11260)
  SS BOND              : bond        0.00349 (    3)
  SS BOND              : angle       1.29910 (    6)
  hydrogen bonds       : bond        0.03767 (  421)
  hydrogen bonds       : angle       4.41287 ( 1215)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 127
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ASP cc_start: 0.7862 (p0) cc_final: 0.7660 (p0)
REVERT: G   21 MET cc_start: 0.7747 (ppp) cc_final: 0.7540 (ppp)
REVERT: G   22 GLU cc_start: 0.7930 (pp20) cc_final: 0.7671 (pp20)
REVERT: G   38 MET cc_start: 0.8022 (tmm) cc_final: 0.7734 (tmm)
REVERT: G   48 ASP cc_start: 0.7822 (t0) cc_final: 0.7516 (t0)
REVERT: G   51 LEU cc_start: 0.8190 (tt) cc_final: 0.7245 (mt)
REVERT: R   40 MET cc_start: 0.7927 (mmm) cc_final: 0.6708 (mmm)
REVERT: R  273 LYS cc_start: 0.8047 (tttt) cc_final: 0.7793 (ttpt)
  outliers start: 27
  outliers final: 24
  residues processed: 147
  average time/residue: 0.0912
  time to fit residues: 18.0824
Evaluate side-chains
  150 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   31 VAL
Chi-restraints excluded: chain R residue   55 ILE
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  133 PHE
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  278 ILE
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  310 LEU
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain N residue   91 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 97 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0070
   chunk 29 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 20 optimal weight:    0.3980
   chunk 71 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 96 optimal weight:    8.9990
   chunk 75 optimal weight:    8.9990
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
R  69 ASN
** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.104246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.088370 restraints weight = 21626.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.090774 restraints weight = 12351.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.092460 restraints weight = 8409.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.093586 restraints weight = 6416.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.094390 restraints weight = 5306.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.4937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8302  Z= 0.117
  Angle     :  0.656  14.436  11266  Z= 0.319
  Chirality :  0.042   0.147   1280
  Planarity :  0.004   0.050   1436
  Dihedral  :  5.415  83.362   1150
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 20.14 %
    Favored  : 77.43 %
  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:  0.62 (0.27), residues: 1025
  helix:  1.92 (0.26), residues: 422
  sheet: -0.26 (0.34), residues: 205
  loop : -0.84 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B   8 
 TYR   0.013   0.001   TYR A 253 
 PHE   0.020   0.001   PHE B 199 
 TRP   0.028   0.002   TRP B  82 
 HIS   0.002   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8299)
  covalent geometry    : angle       0.65575 (11260)
  SS BOND              : bond        0.00131 (    3)
  SS BOND              : angle       0.98623 (    6)
  hydrogen bonds       : bond        0.03587 (  421)
  hydrogen bonds       : angle       4.31466 ( 1215)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ASP cc_start: 0.7878 (p0) cc_final: 0.7632 (p0)
REVERT: A  278 ASN cc_start: 0.8549 (m-40) cc_final: 0.8285 (m-40)
REVERT: B  158 VAL cc_start: 0.8575 (p) cc_final: 0.8263 (m)
REVERT: G   22 GLU cc_start: 0.7831 (pp20) cc_final: 0.7586 (pp20)
REVERT: G   38 MET cc_start: 0.8032 (tmm) cc_final: 0.7741 (tmm)
REVERT: G   48 ASP cc_start: 0.7806 (t0) cc_final: 0.7496 (t0)
REVERT: G   51 LEU cc_start: 0.8152 (tt) cc_final: 0.7237 (mt)
REVERT: R   40 MET cc_start: 0.7960 (mmm) cc_final: 0.6728 (mmm)
REVERT: R   80 LEU cc_start: 0.8400 (tt) cc_final: 0.8133 (tp)
REVERT: R  273 LYS cc_start: 0.8014 (tttt) cc_final: 0.7777 (ttpt)
REVERT: N  120 GLN cc_start: 0.7983 (mp10) cc_final: 0.7654 (pm20)
  outliers start: 21
  outliers final: 19
  residues processed: 148
  average time/residue: 0.0855
  time to fit residues: 17.4242
Evaluate side-chains
  142 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   31 VAL
Chi-restraints excluded: chain R residue   55 ILE
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  133 PHE
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  278 ILE
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain N residue   91 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9990
   chunk 16 optimal weight:    0.2980
   chunk 51 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   chunk 21 optimal weight:    0.7980
   chunk 80 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** R 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 322 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 = 0.3801 r_free = 0.3801 target = 0.104434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.088376 restraints weight = 21819.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.090809 restraints weight = 12499.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.092505 restraints weight = 8503.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.093645 restraints weight = 6499.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.094331 restraints weight = 5386.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.5066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8302  Z= 0.119
  Angle     :  0.659  14.155  11266  Z= 0.321
  Chirality :  0.042   0.175   1280
  Planarity :  0.004   0.050   1436
  Dihedral  :  5.383  81.323   1150
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 19.56 %
    Favored  : 77.55 %
  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:  0.70 (0.27), residues: 1025
  helix:  1.96 (0.26), residues: 422
  sheet: -0.24 (0.33), residues: 220
  loop : -0.76 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B   8 
 TYR   0.013   0.001   TYR A 391 
 PHE   0.019   0.001   PHE B 199 
 TRP   0.033   0.002   TRP B  82 
 HIS   0.002   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8299)
  covalent geometry    : angle       0.65869 (11260)
  SS BOND              : bond        0.00166 (    3)
  SS BOND              : angle       0.85784 (    6)
  hydrogen bonds       : bond        0.03548 (  421)
  hydrogen bonds       : angle       4.26737 ( 1215)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ASP cc_start: 0.8014 (p0) cc_final: 0.7776 (p0)
REVERT: A  278 ASN cc_start: 0.8514 (m-40) cc_final: 0.8281 (m-40)
REVERT: B  158 VAL cc_start: 0.8588 (p) cc_final: 0.8287 (m)
REVERT: G   14 LYS cc_start: 0.9255 (pttp) cc_final: 0.8948 (ptmm)
REVERT: G   38 MET cc_start: 0.8029 (tmm) cc_final: 0.7729 (tmm)
REVERT: G   48 ASP cc_start: 0.7833 (t0) cc_final: 0.7478 (t0)
REVERT: G   51 LEU cc_start: 0.8158 (tt) cc_final: 0.7268 (mt)
REVERT: R   40 MET cc_start: 0.7967 (mmm) cc_final: 0.6733 (mmm)
REVERT: R  273 LYS cc_start: 0.7999 (tttt) cc_final: 0.7780 (ttpt)
REVERT: N    6 GLU cc_start: 0.6792 (mp0) cc_final: 0.6551 (mp0)
REVERT: N  120 GLN cc_start: 0.7979 (mp10) cc_final: 0.7660 (pm20)
  outliers start: 25
  outliers final: 24
  residues processed: 148
  average time/residue: 0.0925
  time to fit residues: 18.4073
Evaluate side-chains
  149 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   31 VAL
Chi-restraints excluded: chain R residue   55 ILE
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  133 PHE
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  278 ILE
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain N residue   91 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 94 optimal weight:    0.7980
   chunk 98 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   chunk 74 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** R 322 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 = 0.3791 r_free = 0.3791 target = 0.103824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.087886 restraints weight = 21737.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.090245 restraints weight = 12499.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.091910 restraints weight = 8557.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.093107 restraints weight = 6553.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.093769 restraints weight = 5388.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.5112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8302  Z= 0.141
  Angle     :  0.679  14.564  11266  Z= 0.332
  Chirality :  0.043   0.247   1280
  Planarity :  0.004   0.051   1436
  Dihedral  :  5.448  79.695   1150
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 19.56 %
    Favored  : 77.08 %
  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:  0.76 (0.27), residues: 1025
  helix:  1.92 (0.26), residues: 422
  sheet: -0.21 (0.33), residues: 229
  loop : -0.61 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 333 
 TYR   0.013   0.001   TYR A  37 
 PHE   0.024   0.001   PHE A 246 
 TRP   0.038   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8299)
  covalent geometry    : angle       0.67840 (11260)
  SS BOND              : bond        0.00239 (    3)
  SS BOND              : angle       1.06692 (    6)
  hydrogen bonds       : bond        0.03645 (  421)
  hydrogen bonds       : angle       4.27914 ( 1215)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 133
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  278 ASN cc_start: 0.8598 (m-40) cc_final: 0.8301 (m-40)
REVERT: B  158 VAL cc_start: 0.8636 (p) cc_final: 0.8313 (m)
REVERT: G   14 LYS cc_start: 0.9245 (pttp) cc_final: 0.8933 (ptmm)
REVERT: G   38 MET cc_start: 0.8037 (tmm) cc_final: 0.7741 (tmm)
REVERT: G   48 ASP cc_start: 0.7858 (t0) cc_final: 0.7656 (t0)
REVERT: G   51 LEU cc_start: 0.8075 (tt) cc_final: 0.7236 (mt)
REVERT: R   40 MET cc_start: 0.7996 (mmm) cc_final: 0.6753 (mmm)
REVERT: R  185 TYR cc_start: 0.5199 (m-10) cc_final: 0.4802 (m-10)
REVERT: R  273 LYS cc_start: 0.8051 (tttt) cc_final: 0.7809 (ttpt)
REVERT: R  312 ASN cc_start: 0.8086 (t160) cc_final: 0.7815 (t0)
REVERT: N    6 GLU cc_start: 0.6929 (mp0) cc_final: 0.6666 (mp0)
REVERT: N  120 GLN cc_start: 0.8015 (mp10) cc_final: 0.7622 (pm20)
  outliers start: 29
  outliers final: 28
  residues processed: 151
  average time/residue: 0.0852
  time to fit residues: 17.6246
Evaluate side-chains
  158 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   31 VAL
Chi-restraints excluded: chain R residue   55 ILE
Chi-restraints excluded: chain R residue  130 ASP
Chi-restraints excluded: chain R residue  133 PHE
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  206 VAL
Chi-restraints excluded: chain R residue  278 ILE
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  321 PHE
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain N residue   91 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9980
   chunk 25 optimal weight:   10.0000
   chunk 29 optimal weight:    0.0070
   chunk 51 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.9400

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
G  24 ASN
** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.106674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.090052 restraints weight = 22482.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.092502 restraints weight = 12899.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.094187 restraints weight = 8913.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.095309 restraints weight = 6922.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.096071 restraints weight = 5807.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.5182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8302  Z= 0.126
  Angle     :  0.674  14.641  11266  Z= 0.328
  Chirality :  0.042   0.224   1280
  Planarity :  0.004   0.051   1436
  Dihedral  :  5.429  79.132   1150
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 19.79 %
    Favored  : 76.85 %
  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:  0.78 (0.27), residues: 1025
  helix:  1.91 (0.26), residues: 422
  sheet: -0.22 (0.33), residues: 230
  loop : -0.55 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B   8 
 TYR   0.012   0.001   TYR A  37 
 PHE   0.025   0.001   PHE A 246 
 TRP   0.029   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8299)
  covalent geometry    : angle       0.67369 (11260)
  SS BOND              : bond        0.00189 (    3)
  SS BOND              : angle       0.88714 (    6)
  hydrogen bonds       : bond        0.03554 (  421)
  hydrogen bonds       : angle       4.23013 ( 1215)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1358.82 seconds
wall clock time: 24 minutes 8.74 seconds (1448.74 seconds total)