Starting phenix.real_space_refine
on Fri Aug 22 17:50:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gg8_29998/08_2025/8gg8_29998.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gg8_29998/08_2025/8gg8_29998.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gg8_29998/08_2025/8gg8_29998.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gg8_29998/08_2025/8gg8_29998.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gg8_29998/08_2025/8gg8_29998.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gg8_29998/08_2025/8gg8_29998.cif"
  }
  resolution = 3.3
  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=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      43      5.16       5
     C    4219      2.51       5
     N    1145      2.21       5
     O    1201      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6611
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 241, 1803
          Classifications: {'peptide': 241}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 52}
          Link IDs: {'PTRANS': 6, 'TRANS': 234}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 203
          Unresolved non-hydrogen angles: 248
          Unresolved non-hydrogen dihedrals: 160
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 7, 'ASN:plan1': 2, 'GLU:plan': 14, 'ASP:plan': 8, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 150
    Chain: "B"
      Number of atoms: 2428
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2428
          Classifications: {'peptide': 332}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 5, 'TRANS': 326}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 119
          Unresolved non-hydrogen angles: 144
          Unresolved non-hydrogen dihedrals: 94
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 4, 'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 90
    Chain: "G"
      Number of atoms: 332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 332
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "R"
      Number of atoms: 2001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2001
          Classifications: {'peptide': 283}
          Incomplete info: {'truncation_to_alanine': 77}
          Link IDs: {'PTRANS': 7, 'TRANS': 275}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 290
          Unresolved non-hydrogen angles: 368
          Unresolved non-hydrogen dihedrals: 241
          Unresolved non-hydrogen chiralities: 28
          Planarities with less than four sites: {'TRP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 9, 'GLN:plan1': 6, 'ASN:plan1': 3, 'ARG:plan': 6, 'ASP:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 158
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.62, per 1000 atoms: 0.25
  Number of scatterers: 6611
  At special positions: 0
  Unit cell: (82.4315, 134.493, 98.0501, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      43     16.00
     P       3     15.00
     O    1201      8.00
     N    1145      7.00
     C    4219      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 444.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1714

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 8 sheets defined
      46.8% alpha, 16.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 3.577A  pdb=" N   LYS A  24 " --> pdb=" O   ARG A  20 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLN A  31 " --> pdb=" O   GLU A  27 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 3.557A  pdb=" N   ILE A  62 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU A  63 " --> pdb=" O   GLN A  59 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   HIS A  64 " --> pdb=" O   MET A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.774A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.332A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.776A  pdb=" N   ALA A 337 " --> pdb=" O   ARG A 333 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 4.509A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 26
      removed outlier: 3.527A  pdb=" N   ILE B  18 " --> pdb=" O   LEU B  14 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.750A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 14 through 24
      removed outlier: 3.583A  pdb=" N   LYS G  20 " --> pdb=" O   VAL G  16 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLU G  22 " --> pdb=" O   GLN G  18 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.657A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.772A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.791A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ILE R  47 " --> pdb=" O   ILE R  43 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU R  53 " --> pdb=" O   PHE R  49 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ALA R  59 " --> pdb=" O   ILE R  55 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 3.725A  pdb=" N   TYR R  70 " --> pdb=" O   THR R  66 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 104 through 137
      removed outlier: 3.576A  pdb=" N   GLU R 122 " --> pdb=" O   THR R 118 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   CYS R 125 " --> pdb=" O   ILE R 121 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.462A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 164
      removed outlier: 3.543A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 165 through 171
      removed outlier: 3.809A  pdb=" N   ILE R 169 " --> pdb=" O   SER R 165 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 238
      removed outlier: 3.649A  pdb=" N   VAL R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 3.535A  pdb=" N   ILE R 278 " --> pdb=" O   THR R 274 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   CYS R 285 " --> pdb=" O   THR R 281 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.752A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ILE R 298 " --> pdb=" O   ILE R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 326
      removed outlier: 3.729A  pdb=" N   TYR R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ILE R 314 " --> pdb=" O   LEU R 310 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   GLY R 315 " --> pdb=" O   LEU R 311 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   TYR R 316 " --> pdb=" O   ASN R 312 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 339
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 3.548A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   VAL A 214 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 9.422A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.506A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.687A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.881A  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 62
      removed outlier: 3.664A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ALA B  73 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.096A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.918A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.092A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.253A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.969A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.193A  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: 6.646A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.015A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   SER B 201 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.817A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.942A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.957A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.633A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)

    327 hydrogen bonds defined for protein.
    963 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: 0.92

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2150
        1.34 -     1.46: 1210
        1.46 -     1.57: 3327
        1.57 -     1.69: 6
        1.69 -     1.81: 59
  Bond restraints: 6752
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.451 -0.054 2.00e-02 2.50e+03 7.26e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.575 -0.052 2.00e-02 2.50e+03 6.67e+00
  bond pdb=" CA  LEU A 393 "
       pdb=" C   LEU A 393 "
    ideal  model  delta    sigma   weight residual
    1.528  1.492  0.036 1.45e-02 4.76e+03 6.11e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.442 -0.048 2.00e-02 2.50e+03 5.84e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.566 -0.046 2.00e-02 2.50e+03 5.19e+00
  ... (remaining 6747 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 9033
        1.37 -     2.75: 147
        2.75 -     4.12: 36
        4.12 -     5.50: 13
        5.50 -     6.87: 3
  Bond angle restraints: 9232
  Sorted by residual:
  angle pdb=" N   MET R  40 "
        pdb=" CA  MET R  40 "
        pdb=" C   MET R  40 "
      ideal   model   delta    sigma   weight residual
     111.28  106.42    4.86 1.09e+00 8.42e-01 1.98e+01
  angle pdb=" C   ILE R  43 "
        pdb=" N   VAL R  44 "
        pdb=" CA  VAL R  44 "
      ideal   model   delta    sigma   weight residual
     121.65  117.12    4.53 1.48e+00 4.57e-01 9.36e+00
  angle pdb=" C   VAL R  34 "
        pdb=" CA  VAL R  34 "
        pdb=" CB  VAL R  34 "
      ideal   model   delta    sigma   weight residual
     112.14  108.06    4.08 1.35e+00 5.49e-01 9.14e+00
  angle pdb=" C   VAL R  39 "
        pdb=" CA  VAL R  39 "
        pdb=" CB  VAL R  39 "
      ideal   model   delta    sigma   weight residual
     112.14  108.36    3.78 1.35e+00 5.49e-01 7.83e+00
  angle pdb=" C   VAL R  33 "
        pdb=" CA  VAL R  33 "
        pdb=" CB  VAL R  33 "
      ideal   model   delta    sigma   weight residual
     112.14  108.59    3.55 1.35e+00 5.49e-01 6.93e+00
  ... (remaining 9227 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.55: 3623
       18.55 -    37.09: 251
       37.09 -    55.64: 30
       55.64 -    74.19: 7
       74.19 -    92.73: 6
  Dihedral angle restraints: 3917
    sinusoidal: 1277
      harmonic: 2640
  Sorted by residual:
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59   11.86   92.73     1      2.00e+01 2.50e-03 2.51e+01
  dihedral pdb=" O3B GTP A 401 "
           pdb=" O3A GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PA  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -68.92 -149.84   80.92     1      2.00e+01 2.50e-03 2.02e+01
  dihedral pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" O3A GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27  145.80  -76.53     1      2.00e+01 2.50e-03 1.84e+01
  ... (remaining 3914 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 705
       0.031 -    0.062: 262
       0.062 -    0.093: 73
       0.093 -    0.123: 53
       0.123 -    0.154: 3
  Chirality restraints: 1096
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.55   -0.15 2.00e-01 2.50e+01 5.94e-01
  chirality pdb=" CB  VAL R 317 "
            pdb=" CA  VAL R 317 "
            pdb=" CG1 VAL R 317 "
            pdb=" CG2 VAL R 317 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.73e-01
  chirality pdb=" CA  TRP R 286 "
            pdb=" N   TRP R 286 "
            pdb=" C   TRP R 286 "
            pdb=" CB  TRP R 286 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.05e-01
  ... (remaining 1093 not shown)

  Planarity restraints: 1167
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 392 "    0.008 2.00e-02 2.50e+03   1.64e-02 2.68e+00
        pdb=" C   GLU A 392 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   GLU A 392 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU A 393 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "    0.020 5.00e-02 4.00e+02   3.08e-02 1.52e+00
        pdb=" N   PRO B 194 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 331 "    0.019 5.00e-02 4.00e+02   2.91e-02 1.36e+00
        pdb=" N   PRO A 332 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 332 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 332 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1164 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1601
        2.79 -     3.32: 5962
        3.32 -     3.85: 10286
        3.85 -     4.37: 11139
        4.37 -     4.90: 20875
  Nonbonded interactions: 49863
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" N   GLU A 259 "
            pdb=" OE1 GLU A 259 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" OXT LEU A 394 "
            pdb=" CB  ALA R 226 "
     model   vdw
     2.339 3.460
  nonbonded pdb=" O   LYS B  57 "
            pdb=" OG  SER B  74 "
     model   vdw
     2.344 3.040
  nonbonded pdb=" NE2 GLN G  18 "
            pdb=" OE2 GLU G  22 "
     model   vdw
     2.388 3.120
  ... (remaining 49858 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.200
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6752  Z= 0.149
  Angle     :  0.503   6.869   9232  Z= 0.277
  Chirality :  0.040   0.154   1096
  Planarity :  0.003   0.031   1167
  Dihedral  : 13.451  92.735   2203
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.82 %
    Favored  : 99.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.28), residues: 890
  helix:  1.88 (0.26), residues: 374
  sheet: -0.04 (0.47), residues: 144
  loop : -1.08 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 175 
 TYR   0.013   0.001   TYR B 111 
 PHE   0.019   0.001   PHE B 234 
 TRP   0.007   0.001   TRP R 313 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6752)
  covalent geometry    : angle       0.50285 ( 9232)
  hydrogen bonds       : bond        0.20828 (  327)
  hydrogen bonds       : angle       6.52298 (  963)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.170 
Fit side-chains
REVERT: R  286 TRP cc_start: 0.7370 (OUTLIER) cc_final: 0.6847 (t-100)
REVERT: R  319 SER cc_start: 0.8181 (m) cc_final: 0.7818 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0622
  time to fit residues: 8.2539
Evaluate side-chains
  80 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  286 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.146205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.117322 restraints weight = 9301.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.29
r_work: 0.3334 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6752  Z= 0.127
  Angle     :  0.496   6.965   9232  Z= 0.267
  Chirality :  0.042   0.173   1096
  Planarity :  0.003   0.032   1167
  Dihedral  :  7.361  92.656    994
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  7.55 %
    Favored  : 91.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.28), residues: 890
  helix:  2.13 (0.26), residues: 382
  sheet: -0.17 (0.42), residues: 168
  loop : -1.00 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 385 
 TYR   0.034   0.001   TYR R 185 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.007   0.001   TRP R 313 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6752)
  covalent geometry    : angle       0.49576 ( 9232)
  hydrogen bonds       : bond        0.05405 (  327)
  hydrogen bonds       : angle       4.46416 (  963)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.214 
Fit side-chains
  outliers start: 7
  outliers final: 5
  residues processed: 90
  average time/residue: 0.0655
  time to fit residues: 8.1364
Evaluate side-chains
  86 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  286 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 81 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.145034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.116096 restraints weight = 9273.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 2.29
r_work: 0.3317 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6752  Z= 0.128
  Angle     :  0.485   7.131   9232  Z= 0.260
  Chirality :  0.041   0.145   1096
  Planarity :  0.003   0.033   1167
  Dihedral  :  7.470  93.245    994
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 11.17 %
    Favored  : 87.85 %
  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 aren not related in a simple way.
  whole:  0.87 (0.29), residues: 890
  helix:  2.26 (0.27), residues: 388
  sheet: -0.08 (0.43), residues: 161
  loop : -1.11 (0.31), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 131 
 TYR   0.042   0.001   TYR R 185 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.007   0.001   TRP B 339 
 HIS   0.005   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6752)
  covalent geometry    : angle       0.48518 ( 9232)
  hydrogen bonds       : bond        0.04855 (  327)
  hydrogen bonds       : angle       4.14831 (  963)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.161 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 87
  average time/residue: 0.0752
  time to fit residues: 8.9138
Evaluate side-chains
  84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  286 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0040
   chunk 70 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 7 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   chunk 42 optimal weight:    0.4980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.8594

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
B 142 HIS

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 = 0.144691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.115697 restraints weight = 9351.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.31
r_work: 0.3343 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6752  Z= 0.126
  Angle     :  0.485   7.148   9232  Z= 0.260
  Chirality :  0.041   0.143   1096
  Planarity :  0.003   0.033   1167
  Dihedral  :  7.473  93.971    994
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.81 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.29), residues: 890
  helix:  2.30 (0.27), residues: 389
  sheet: -0.06 (0.42), residues: 162
  loop : -1.14 (0.31), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 385 
 TYR   0.039   0.001   TYR R 185 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.013   0.001   TRP R 286 
 HIS   0.004   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6752)
  covalent geometry    : angle       0.48499 ( 9232)
  hydrogen bonds       : bond        0.04526 (  327)
  hydrogen bonds       : angle       4.02105 (  963)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.203 
Fit side-chains
  outliers start: 9
  outliers final: 8
  residues processed: 86
  average time/residue: 0.0555
  time to fit residues: 6.6628
Evaluate side-chains
  84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  286 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 52 optimal weight:    0.4980
   chunk 84 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 80 optimal weight:    0.0270
   chunk 3 optimal weight:    0.7980
   chunk 67 optimal weight:    0.2980
   chunk 64 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0970
   overall best weight:    0.3036

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
B 142 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.148935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.120486 restraints weight = 9356.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.22
r_work: 0.3373 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6752  Z= 0.087
  Angle     :  0.434   6.849   9232  Z= 0.232
  Chirality :  0.040   0.137   1096
  Planarity :  0.003   0.030   1167
  Dihedral  :  7.277  92.898    994
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 13.96 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.29), residues: 890
  helix:  2.56 (0.27), residues: 389
  sheet:  0.09 (0.42), residues: 163
  loop : -1.08 (0.31), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 385 
 TYR   0.035   0.001   TYR R 185 
 PHE   0.008   0.001   PHE B 199 
 TRP   0.008   0.001   TRP R 286 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00173 ( 6752)
  covalent geometry    : angle       0.43419 ( 9232)
  hydrogen bonds       : bond        0.03448 (  327)
  hydrogen bonds       : angle       3.74578 (  963)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.181 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 94
  average time/residue: 0.0583
  time to fit residues: 7.7990
Evaluate side-chains
  87 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  286 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 88 optimal weight:    3.9990
   chunk 44 optimal weight:    0.3980
   chunk 83 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 218 ASN
B  17 GLN
B 142 HIS
R 229 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.146044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.117559 restraints weight = 9386.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.25
r_work: 0.3326 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6752  Z= 0.126
  Angle     :  0.483   7.000   9232  Z= 0.258
  Chirality :  0.041   0.140   1096
  Planarity :  0.003   0.032   1167
  Dihedral  :  7.346  93.232    994
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 13.79 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.29), residues: 890
  helix:  2.51 (0.27), residues: 389
  sheet:  0.03 (0.42), residues: 163
  loop : -1.07 (0.31), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 175 
 TYR   0.008   0.001   TYR B 105 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.010   0.001   TRP R 286 
 HIS   0.011   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6752)
  covalent geometry    : angle       0.48332 ( 9232)
  hydrogen bonds       : bond        0.04140 (  327)
  hydrogen bonds       : angle       3.78305 (  963)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.152 
Fit side-chains
  outliers start: 13
  outliers final: 11
  residues processed: 85
  average time/residue: 0.0569
  time to fit residues: 6.7902
Evaluate side-chains
  87 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  286 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 8 optimal weight:    0.4980
   chunk 74 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 68 optimal weight:    6.9990
   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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.145481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.116837 restraints weight = 9265.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.26
r_work: 0.3317 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6752  Z= 0.127
  Angle     :  0.485   7.074   9232  Z= 0.259
  Chirality :  0.041   0.137   1096
  Planarity :  0.003   0.033   1167
  Dihedral  :  7.393  93.573    994
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 14.45 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.29), residues: 890
  helix:  2.50 (0.27), residues: 389
  sheet:  0.01 (0.42), residues: 162
  loop : -1.08 (0.30), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 314 
 TYR   0.008   0.001   TYR B 105 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.010   0.001   TRP R 286 
 HIS   0.011   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6752)
  covalent geometry    : angle       0.48512 ( 9232)
  hydrogen bonds       : bond        0.04264 (  327)
  hydrogen bonds       : angle       3.79538 (  963)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.204 
Fit side-chains
  outliers start: 13
  outliers final: 11
  residues processed: 87
  average time/residue: 0.0537
  time to fit residues: 6.6999
Evaluate side-chains
  89 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  286 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0010
   chunk 89 optimal weight:    1.9990
   chunk 76 optimal weight:    0.4980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.147374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.118574 restraints weight = 9398.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.28
r_work: 0.3346 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6752  Z= 0.099
  Angle     :  0.453   6.912   9232  Z= 0.244
  Chirality :  0.040   0.135   1096
  Planarity :  0.003   0.032   1167
  Dihedral  :  7.286  93.081    994
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 14.94 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.29), residues: 890
  helix:  2.56 (0.27), residues: 391
  sheet:  0.07 (0.42), residues: 163
  loop : -1.01 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 385 
 TYR   0.006   0.001   TYR A 339 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.009   0.001   TRP R 286 
 HIS   0.008   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 6752)
  covalent geometry    : angle       0.45330 ( 9232)
  hydrogen bonds       : bond        0.03705 (  327)
  hydrogen bonds       : angle       3.69470 (  963)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.177 
Fit side-chains
  outliers start: 10
  outliers final: 9
  residues processed: 90
  average time/residue: 0.0611
  time to fit residues: 7.5600
Evaluate side-chains
  88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  286 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 67 optimal weight:    0.2980
   chunk 7 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 46 optimal weight:    0.7980
   chunk 14 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:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 218 ASN
B  17 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.146182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.117487 restraints weight = 9404.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.25
r_work: 0.3329 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6752  Z= 0.113
  Angle     :  0.475   6.966   9232  Z= 0.254
  Chirality :  0.041   0.134   1096
  Planarity :  0.003   0.032   1167
  Dihedral  :  7.286  92.979    994
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 15.60 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.29), residues: 890
  helix:  2.52 (0.27), residues: 391
  sheet:  0.04 (0.41), residues: 163
  loop : -1.03 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 175 
 TYR   0.007   0.001   TYR B 105 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.009   0.001   TRP R 286 
 HIS   0.002   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 6752)
  covalent geometry    : angle       0.47466 ( 9232)
  hydrogen bonds       : bond        0.03974 (  327)
  hydrogen bonds       : angle       3.72261 (  963)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.174 
Fit side-chains
  outliers start: 10
  outliers final: 10
  residues processed: 84
  average time/residue: 0.0642
  time to fit residues: 7.3871
Evaluate side-chains
  87 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  286 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 88 optimal weight:    0.0060
   chunk 33 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 21 optimal weight:    0.4980
   chunk 3 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 103 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.147546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.118986 restraints weight = 9384.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.26
r_work: 0.3347 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.1921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6752  Z= 0.100
  Angle     :  0.461   6.869   9232  Z= 0.247
  Chirality :  0.040   0.134   1096
  Planarity :  0.003   0.031   1167
  Dihedral  :  7.238  92.417    994
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 15.93 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.29), residues: 890
  helix:  2.59 (0.27), residues: 391
  sheet:  0.08 (0.42), residues: 163
  loop : -0.99 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.007   0.001   TYR B  59 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.009   0.001   TRP R 286 
 HIS   0.002   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 6752)
  covalent geometry    : angle       0.46084 ( 9232)
  hydrogen bonds       : bond        0.03648 (  327)
  hydrogen bonds       : angle       3.65576 (  963)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.138 
Fit side-chains
  outliers start: 11
  outliers final: 11
  residues processed: 86
  average time/residue: 0.0574
  time to fit residues: 6.7383
Evaluate side-chains
  88 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  111 SER
Chi-restraints excluded: chain R residue  218 VAL
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  286 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.2980
   chunk 30 optimal weight:    0.4980
   chunk 72 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0030
   chunk 66 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.4590

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
R 103 ASN
R 229 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.148186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.119566 restraints weight = 9308.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 2.23
r_work: 0.3360 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3222 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6752  Z= 0.096
  Angle     :  0.454   6.785   9232  Z= 0.244
  Chirality :  0.040   0.133   1096
  Planarity :  0.003   0.031   1167
  Dihedral  :  7.119  91.375    994
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 16.26 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.29), residues: 890
  helix:  2.61 (0.27), residues: 391
  sheet:  0.13 (0.42), residues: 164
  loop : -0.98 (0.31), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 175 
 TYR   0.013   0.001   TYR B 111 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.008   0.001   TRP R 286 
 HIS   0.002   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 6752)
  covalent geometry    : angle       0.45380 ( 9232)
  hydrogen bonds       : bond        0.03468 (  327)
  hydrogen bonds       : angle       3.59171 (  963)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1549.50 seconds
wall clock time: 27 minutes 8.55 seconds (1628.55 seconds total)