Starting phenix.real_space_refine
on Fri Oct 10 14:15:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8unp_42412/10_2025/8unp_42412.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8unp_42412/10_2025/8unp_42412.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8unp_42412/10_2025/8unp_42412.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8unp_42412/10_2025/8unp_42412.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8unp_42412/10_2025/8unp_42412.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8unp_42412/10_2025/8unp_42412.map"
  }
  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=   0.027
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    4225      2.51       5
     N    1130      2.21       5
     O    1158      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6559
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1724
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 237, 1712
          Classifications: {'peptide': 237}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 69}
          Link IDs: {'PTRANS': 5, 'TRANS': 231}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 266
          Unresolved non-hydrogen angles: 323
          Unresolved non-hydrogen dihedrals: 209
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLU:plan': 15, 'ASP:plan': 10, 'GLN:plan1': 8, 'ARG:plan': 12, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 191
      Conformer: "B"
        Number of residues, atoms: 237, 1712
          Classifications: {'peptide': 237}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 69}
          Link IDs: {'PTRANS': 5, 'TRANS': 231}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 266
          Unresolved non-hydrogen angles: 323
          Unresolved non-hydrogen dihedrals: 209
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLU:plan': 15, 'ASP:plan': 10, 'GLN:plan1': 8, 'ARG:plan': 12, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 191
          bond proxies already assigned to first conformer: 1731
    Chain: "B"
      Number of atoms: 2357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2357
          Classifications: {'peptide': 331}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 5, 'TRANS': 325}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 187
          Unresolved non-hydrogen angles: 229
          Unresolved non-hydrogen dihedrals: 145
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 8, 'GLU:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 12}
          Unresolved non-hydrogen planarities: 144
    Chain: "G"
      Number of atoms: 335
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 335
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 85
          Unresolved non-hydrogen angles: 102
          Unresolved non-hydrogen dihedrals: 70
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 43
    Chain: "R"
      Number of atoms: 2095
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2095
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 57}
          Link IDs: {'PTRANS': 7, 'TRANS': 276}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 197
          Unresolved non-hydrogen angles: 247
          Unresolved non-hydrogen dihedrals: 156
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 8, 'ASP:plan': 6, 'GLN:plan1': 5, 'ASN:plan1': 3, 'ARG:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 108
    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: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR A 360 " occ=0.51
      ... (22 atoms not shown)
      pdb=" OH BTYR A 360 " occ=0.49
  Time building chain proxies: 2.08, per 1000 atoms: 0.32
  Number of scatterers: 6559
  At special positions: 0
  Unit cell: (84.1669, 133.626, 96.3147, 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    1158      8.00
     N    1130      7.00
     C    4225      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03

  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: 0.57
  Conformation dependent library (CDL) restraints added in 332.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1720

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 8 sheets defined
      47.6% alpha, 17.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 40
      removed outlier: 3.540A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 4.037A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 3.842A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.115A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 3.572A  pdb=" N   ARG A 317 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   TYR A 318 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.635A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ARG A 336 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 7 through 26
      removed outlier: 4.208A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   LEU B  14 " --> pdb=" O   GLU B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 10 through 24
      removed outlier: 3.683A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU G  19 " --> pdb=" O   LEU G  15 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.699A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.569A  pdb=" N   LEU R  45 " --> pdb=" O   SER R  41 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA R  46 " --> pdb=" O   LEU R  42 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE R  58 " --> pdb=" O   VAL R  54 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 97
      removed outlier: 4.071A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR R  73 " --> pdb=" O   ASN R  69 " (cutoff:3.500A)
      removed outlier: 4.374A  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 102 through 120
    Processing helix  chain 'R' and resid 121 through 137
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 164
      removed outlier: 3.829A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 171
      removed outlier: 3.719A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.703A  pdb=" N   SER R 204 " --> pdb=" O   ALA R 200 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 238
      removed outlier: 3.729A  pdb=" N   VAL R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   MET R 215 " --> pdb=" O   PRO R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 3.854A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.376A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 3.590A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      removed outlier: 3.801A  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 208 through 214
      removed outlier: 7.218A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.283A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.074A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.487A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.357A  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 51
      removed outlier: 6.735A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLY B 330 " --> pdb=" O   CYS B 317 " (cutoff:3.500A)
      removed outlier: 3.546A  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: 3.859A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL B  71 " --> pdb=" O   HIS B  62 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.695A  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: 7.097A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.038A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.144A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.747A  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: 6.941A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.844A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.690A  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: 3.891A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.936A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 5.022A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)

    348 hydrogen bonds defined for protein.
    1020 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: 0.98

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1303
        1.33 -     1.45: 1701
        1.45 -     1.57: 3635
        1.57 -     1.69: 5
        1.69 -     1.81: 59
  Bond restraints: 6703
  Sorted by residual:
  bond pdb=" CA  GLN A  12 "
       pdb=" C   GLN A  12 "
    ideal  model  delta    sigma   weight residual
    1.523  1.452  0.071 1.41e-02 5.03e+03 2.53e+01
  bond pdb=" CA  ASP A 223 "
       pdb=" C   ASP A 223 "
    ideal  model  delta    sigma   weight residual
    1.523  1.468  0.055 1.23e-02 6.61e+03 1.98e+01
  bond pdb=" CA  THR A 325 "
       pdb=" C   THR A 325 "
    ideal  model  delta    sigma   weight residual
    1.523  1.468  0.055 1.24e-02 6.50e+03 1.98e+01
  bond pdb=" C5  GTP A 401 "
       pdb=" C6  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.477 -0.087 2.00e-02 2.50e+03 1.89e+01
  bond pdb=" C4  GTP A 401 "
       pdb=" C5  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.469 -0.079 2.00e-02 2.50e+03 1.54e+01
  ... (remaining 6698 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.87: 9050
        2.87 -     5.74: 110
        5.74 -     8.61: 9
        8.61 -    11.49: 6
       11.49 -    14.36: 2
  Bond angle restraints: 9177
  Sorted by residual:
  angle pdb=" N   GLN A  12 "
        pdb=" CA  GLN A  12 "
        pdb=" C   GLN A  12 "
      ideal   model   delta    sigma   weight residual
     113.16   99.62   13.54 1.24e+00 6.50e-01 1.19e+02
  angle pdb=" N   ARG A 228 "
        pdb=" CA  ARG A 228 "
        pdb=" C   ARG A 228 "
      ideal   model   delta    sigma   weight residual
     110.10  124.46  -14.36 1.49e+00 4.50e-01 9.28e+01
  angle pdb=" N   ILE R  58 "
        pdb=" CA  ILE R  58 "
        pdb=" C   ILE R  58 "
      ideal   model   delta    sigma   weight residual
     110.62  101.44    9.18 1.02e+00 9.61e-01 8.09e+01
  angle pdb=" N   THR A 263 "
        pdb=" CA  THR A 263 "
        pdb=" C   THR A 263 "
      ideal   model   delta    sigma   weight residual
     110.53  100.96    9.57 1.32e+00 5.74e-01 5.26e+01
  angle pdb=" N   ARG A 231 "
        pdb=" CA  ARG A 231 "
        pdb=" C   ARG A 231 "
      ideal   model   delta    sigma   weight residual
     110.23  100.03   10.20 1.45e+00 4.76e-01 4.95e+01
  ... (remaining 9172 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.82: 3801
       33.82 -    67.63: 48
       67.63 -   101.45: 1
      101.45 -   135.27: 2
      135.27 -   169.08: 3
  Dihedral angle restraints: 3855
    sinusoidal: 1208
      harmonic: 2647
  Sorted by residual:
  dihedral pdb=" O5' GTP A 401 "
           pdb=" O3A GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" PB  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     274.12  105.04  169.08     1      2.00e+01 2.50e-03 4.76e+01
  dihedral pdb=" C4' GTP A 401 "
           pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     260.87  100.64  160.23     1      2.00e+01 2.50e-03 4.66e+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
     291.08  152.69  138.39     1      2.00e+01 2.50e-03 4.19e+01
  ... (remaining 3852 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 819
       0.044 -    0.088: 206
       0.088 -    0.132: 70
       0.132 -    0.176: 7
       0.176 -    0.219: 1
  Chirality restraints: 1103
  Sorted by residual:
  chirality pdb=" CA  ARG A 228 "
            pdb=" N   ARG A 228 "
            pdb=" C   ARG A 228 "
            pdb=" CB  ARG A 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  VAL R  44 "
            pdb=" N   VAL R  44 "
            pdb=" C   VAL R  44 "
            pdb=" CB  VAL R  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.76e-01
  chirality pdb=" CA  ILE R  58 "
            pdb=" N   ILE R  58 "
            pdb=" C   ILE R  58 "
            pdb=" CB  ILE R  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.65e-01
  ... (remaining 1100 not shown)

  Planarity restraints: 1145
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 320 "    0.053 5.00e-02 4.00e+02   8.08e-02 1.04e+01
        pdb=" N   PRO A 321 "   -0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO A 321 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 321 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R  42 "    0.013 2.00e-02 2.50e+03   2.48e-02 6.16e+00
        pdb=" C   LEU R  42 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   LEU R  42 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ILE R  43 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R  33 "   -0.012 2.00e-02 2.50e+03   2.42e-02 5.85e+00
        pdb=" C   VAL R  33 "    0.042 2.00e-02 2.50e+03
        pdb=" O   VAL R  33 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   VAL R  34 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1142 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 804
        2.75 -     3.28: 6231
        3.28 -     3.82: 10286
        3.82 -     4.36: 11339
        4.36 -     4.90: 20929
  Nonbonded interactions: 49589
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A  55 "
            pdb=" O2A GTP A 401 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" N   GLN A  12 "
            pdb=" N   ARG A  13 "
     model   vdw
     2.246 2.560
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OD1 ASN A 239 "
            pdb=" NZ  LYS B  57 "
     model   vdw
     2.307 3.120
  ... (remaining 49584 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=0.49 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.290
  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:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.050
  Find NCS groups from input model:        0.020
  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:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
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      :  0.006   0.087   6704  Z= 0.343
  Angle     :  0.795  14.357   9179  Z= 0.502
  Chirality :  0.044   0.219   1103
  Planarity :  0.004   0.081   1145
  Dihedral  : 13.788 169.085   2132
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  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:  0.82 (0.29), residues: 889
  helix:  1.96 (0.27), residues: 400
  sheet:  0.16 (0.40), residues: 171
  loop : -1.06 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.019   0.001   TYR B  59 
 PHE   0.018   0.001   PHE A 222 
 TRP   0.021   0.001   TRP R 313 
 HIS   0.010   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 6703)
  covalent geometry    : angle       0.79534 ( 9177)
  SS BOND              : bond        0.00029 (    1)
  SS BOND              : angle       0.83043 (    2)
  hydrogen bonds       : bond        0.18874 (  348)
  hydrogen bonds       : angle       6.77609 ( 1020)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  267 GLN cc_start: 0.8277 (tp-100) cc_final: 0.7739 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1081
  time to fit residues: 13.3002
Evaluate side-chains
  72 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.4980
   chunk 74 optimal weight:    0.2980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
A 220 HIS
A 254 ASN
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 241 HIS
R 322 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.126044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.099211 restraints weight = 33137.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 4.39
r_work: 0.3075 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.1065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6704  Z= 0.116
  Angle     :  0.495   7.177   9179  Z= 0.265
  Chirality :  0.041   0.150   1103
  Planarity :  0.003   0.038   1145
  Dihedral  : 10.626 178.968    990
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  7.88 %
    Favored  : 91.44 %
  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 aren not related in a simple way.
  whole:  1.15 (0.29), residues: 889
  helix:  2.20 (0.26), residues: 410
  sheet:  0.16 (0.39), residues: 180
  loop : -0.88 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  42 
 TYR   0.013   0.001   TYR B  59 
 PHE   0.016   0.001   PHE R  61 
 TRP   0.008   0.001   TRP B 297 
 HIS   0.006   0.001   HIS R 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 6703)
  covalent geometry    : angle       0.49542 ( 9177)
  SS BOND              : bond        0.00040 (    1)
  SS BOND              : angle       0.52280 (    2)
  hydrogen bonds       : bond        0.05064 (  348)
  hydrogen bonds       : angle       4.61074 ( 1020)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A  267 GLN cc_start: 0.8051 (tp-100) cc_final: 0.7620 (tp-100)
REVERT: A  311 TYR cc_start: 0.8356 (m-80) cc_final: 0.8153 (m-80)
REVERT: R   65 GLN cc_start: 0.8612 (mp10) cc_final: 0.8389 (mp10)
  outliers start: 4
  outliers final: 2
  residues processed: 80
  average time/residue: 0.0714
  time to fit residues: 7.8532
Evaluate side-chains
  76 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain B residue  156 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 67 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
R 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.122501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.094678 restraints weight = 35507.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 4.61
r_work: 0.2978 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2976
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2976 r_free = 0.2976    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2976 r_free = 0.2976    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2976
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.1262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6704  Z= 0.139
  Angle     :  0.499   7.375   9179  Z= 0.264
  Chirality :  0.041   0.138   1103
  Planarity :  0.003   0.038   1145
  Dihedral  : 10.436 179.297    990
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 10.10 %
    Favored  : 89.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.29), residues: 889
  helix:  2.23 (0.26), residues: 410
  sheet:  0.03 (0.38), residues: 188
  loop : -0.88 (0.34), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 221 
 TYR   0.011   0.001   TYR B  59 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.009   0.001   TRP B 339 
 HIS   0.005   0.001   HIS R 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6703)
  covalent geometry    : angle       0.49916 ( 9177)
  SS BOND              : bond        0.00079 (    1)
  SS BOND              : angle       0.35566 (    2)
  hydrogen bonds       : bond        0.05075 (  348)
  hydrogen bonds       : angle       4.34024 ( 1020)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.184 
Fit side-chains
  outliers start: 4
  outliers final: 4
  residues processed: 76
  average time/residue: 0.0845
  time to fit residues: 8.4982
Evaluate side-chains
  75 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain R residue  143 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 72 optimal weight:    9.9990
   chunk 1 optimal weight:    7.9990
   chunk 12 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
R 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.122310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.094268 restraints weight = 34529.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 4.58
r_work: 0.2937 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2946
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2946 r_free = 0.2946    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2946
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6704  Z= 0.164
  Angle     :  0.520   7.714   9179  Z= 0.276
  Chirality :  0.042   0.173   1103
  Planarity :  0.003   0.040   1145
  Dihedral  : 10.354 178.144    990
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 11.30 %
    Favored  : 86.64 %
  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: 889
  helix:  2.19 (0.27), residues: 410
  sheet:  0.04 (0.39), residues: 187
  loop : -0.95 (0.34), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 221 
 TYR   0.024   0.001   TYR B  59 
 PHE   0.014   0.001   PHE R 101 
 TRP   0.009   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6703)
  covalent geometry    : angle       0.52031 ( 9177)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       0.31513 (    2)
  hydrogen bonds       : bond        0.05401 (  348)
  hydrogen bonds       : angle       4.27220 ( 1020)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.247 
Fit side-chains
REVERT: B  259 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8480 (pt0)
  outliers start: 12
  outliers final: 8
  residues processed: 85
  average time/residue: 0.0727
  time to fit residues: 8.4346
Evaluate side-chains
  83 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain G residue   15 LEU
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  236 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 8 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
R 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.121351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.095097 restraints weight = 37959.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 4.73
r_work: 0.2982 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2981
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2981 r_free = 0.2981    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2981 r_free = 0.2981    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2981
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   6704  Z= 0.164
  Angle     :  0.514   7.726   9179  Z= 0.271
  Chirality :  0.042   0.179   1103
  Planarity :  0.003   0.042   1145
  Dihedral  : 10.320 177.862    990
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 2.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.01 %
    Favored  : 84.59 %
  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:  0.91 (0.29), residues: 889
  helix:  2.04 (0.26), residues: 418
  sheet: -0.02 (0.39), residues: 187
  loop : -1.14 (0.34), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 221 
 TYR   0.020   0.001   TYR B  59 
 PHE   0.012   0.001   PHE R 101 
 TRP   0.009   0.001   TRP B 339 
 HIS   0.006   0.001   HIS R 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 6703)
  covalent geometry    : angle       0.51355 ( 9177)
  SS BOND              : bond        0.00123 (    1)
  SS BOND              : angle       0.35022 (    2)
  hydrogen bonds       : bond        0.05268 (  348)
  hydrogen bonds       : angle       4.22247 ( 1020)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.263 
Fit side-chains
REVERT: B  234 PHE cc_start: 0.9220 (OUTLIER) cc_final: 0.7942 (t80)
REVERT: B  259 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8497 (pt0)
  outliers start: 14
  outliers final: 12
  residues processed: 86
  average time/residue: 0.0812
  time to fit residues: 9.5874
Evaluate side-chains
  89 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   15 LEU
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  236 SER
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 25 optimal weight:    9.9990
   chunk 36 optimal weight:    4.9990
   chunk 88 optimal weight:    0.7980
   chunk 7 optimal weight:    7.9990
   chunk 21 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0270
   overall best weight:    0.9040

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R 241 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.123472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.097078 restraints weight = 40674.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 4.96
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3178
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.1696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   6704  Z= 0.113
  Angle     :  0.473   7.565   9179  Z= 0.249
  Chirality :  0.041   0.185   1103
  Planarity :  0.003   0.042   1145
  Dihedral  : 10.234 177.939    990
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 2.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 13.18 %
    Favored  : 84.08 %
  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 aren not related in a simple way.
  whole:  1.04 (0.29), residues: 889
  helix:  2.16 (0.27), residues: 418
  sheet:  0.04 (0.39), residues: 186
  loop : -1.08 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 221 
 TYR   0.010   0.001   TYR B  59 
 PHE   0.009   0.001   PHE B 241 
 TRP   0.008   0.001   TRP B 339 
 HIS   0.006   0.001   HIS R 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6703)
  covalent geometry    : angle       0.47264 ( 9177)
  SS BOND              : bond        0.00042 (    1)
  SS BOND              : angle       0.41329 (    2)
  hydrogen bonds       : bond        0.04403 (  348)
  hydrogen bonds       : angle       4.01194 ( 1020)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.268 
Fit side-chains
REVERT: B  259 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8291 (pt0)
  outliers start: 16
  outliers final: 12
  residues processed: 89
  average time/residue: 0.0819
  time to fit residues: 9.9809
Evaluate side-chains
  89 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  236 GLN
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   15 LEU
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  236 SER
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 25 optimal weight:    0.2980
   chunk 53 optimal weight:    0.3980
   chunk 60 optimal weight:    0.9980
   chunk 59 optimal weight:    0.4980
   chunk 28 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 80 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0670
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:
R 241 HIS
R 322 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.126717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.100750 restraints weight = 32699.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 4.51
r_work: 0.3074 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3083
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3083
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6704  Z= 0.085
  Angle     :  0.447   7.728   9179  Z= 0.233
  Chirality :  0.040   0.196   1103
  Planarity :  0.003   0.040   1145
  Dihedral  : 10.111 177.885    990
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.55 %
    Favored  : 83.39 %
  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:  1.26 (0.29), residues: 889
  helix:  2.47 (0.27), residues: 405
  sheet:  0.10 (0.39), residues: 179
  loop : -0.97 (0.33), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 221 
 TYR   0.011   0.001   TYR R 219 
 PHE   0.009   0.001   PHE B 241 
 TRP   0.008   0.001   TRP A 277 
 HIS   0.007   0.001   HIS R 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00168 ( 6703)
  covalent geometry    : angle       0.44654 ( 9177)
  SS BOND              : bond        0.00014 (    1)
  SS BOND              : angle       0.59536 (    2)
  hydrogen bonds       : bond        0.03393 (  348)
  hydrogen bonds       : angle       3.76347 ( 1020)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.243 
Fit side-chains
REVERT: B  259 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8378 (pt0)
  outliers start: 12
  outliers final: 7
  residues processed: 95
  average time/residue: 0.0782
  time to fit residues: 10.2259
Evaluate side-chains
  84 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0030
   chunk 53 optimal weight:    0.0030
   chunk 14 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 58 optimal weight:    0.5980
   chunk 79 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 87 optimal weight:    0.6980
   overall best weight:    0.4200

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

Flipped N/Q/H residues before XYZ refinement:
R 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.125910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.098615 restraints weight = 34831.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 4.78
r_work: 0.3031 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3019
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3019
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6704  Z= 0.088
  Angle     :  0.452   8.340   9179  Z= 0.234
  Chirality :  0.040   0.195   1103
  Planarity :  0.003   0.038   1145
  Dihedral  : 10.056 177.506    990
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.58 %
    Favored  : 82.36 %
  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: 889
  helix:  2.47 (0.27), residues: 405
  sheet:  0.08 (0.39), residues: 180
  loop : -0.95 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 221 
 TYR   0.007   0.001   TYR A 339 
 PHE   0.008   0.001   PHE B 241 
 TRP   0.006   0.001   TRP A 277 
 HIS   0.006   0.001   HIS R 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00181 ( 6703)
  covalent geometry    : angle       0.45212 ( 9177)
  SS BOND              : bond        0.00027 (    1)
  SS BOND              : angle       0.45148 (    2)
  hydrogen bonds       : bond        0.03420 (  348)
  hydrogen bonds       : angle       3.70290 ( 1020)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.182 
Fit side-chains
REVERT: B  156 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8084 (mt0)
REVERT: B  259 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8374 (pt0)
  outliers start: 12
  outliers final: 7
  residues processed: 92
  average time/residue: 0.0929
  time to fit residues: 11.1368
Evaluate side-chains
  89 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  236 SER
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
R 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.124210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.098339 restraints weight = 33090.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 4.48
r_work: 0.3034 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3050
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3050
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6704  Z= 0.120
  Angle     :  0.478   8.508   9179  Z= 0.250
  Chirality :  0.041   0.196   1103
  Planarity :  0.003   0.038   1145
  Dihedral  : 10.079 177.187    990
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 16.44 %
    Favored  : 81.85 %
  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:  1.30 (0.29), residues: 889
  helix:  2.38 (0.27), residues: 411
  sheet:  0.09 (0.38), residues: 186
  loop : -0.84 (0.34), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 221 
 TYR   0.008   0.001   TYR A 339 
 PHE   0.010   0.001   PHE B 241 
 TRP   0.007   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6703)
  covalent geometry    : angle       0.47785 ( 9177)
  SS BOND              : bond        0.00034 (    1)
  SS BOND              : angle       0.29225 (    2)
  hydrogen bonds       : bond        0.04288 (  348)
  hydrogen bonds       : angle       3.81636 ( 1020)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A  294 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8142 (mm110)
REVERT: A  349 SER cc_start: 0.9171 (p) cc_final: 0.8900 (p)
REVERT: B  234 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8045 (t80)
REVERT: B  259 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8489 (pt0)
  outliers start: 10
  outliers final: 8
  residues processed: 87
  average time/residue: 0.0775
  time to fit residues: 9.2535
Evaluate side-chains
  87 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  236 SER
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 15 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9980
   chunk 73 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
R 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.125712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.099278 restraints weight = 46971.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 5.50
r_work: 0.3041 rms_B_bonded: 5.31 restraints_weight: 2.0000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3034
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3034
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
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   0.034   6704  Z= 0.098
  Angle     :  0.458   8.807   9179  Z= 0.238
  Chirality :  0.040   0.201   1103
  Planarity :  0.003   0.039   1145
  Dihedral  : 10.054 177.470    990
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 2.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 16.61 %
    Favored  : 81.68 %
  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 aren not related in a simple way.
  whole:  1.29 (0.29), residues: 889
  helix:  2.47 (0.27), residues: 405
  sheet:  0.15 (0.39), residues: 178
  loop : -0.94 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 221 
 TYR   0.008   0.001   TYR A 339 
 PHE   0.009   0.001   PHE B 241 
 TRP   0.006   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 6703)
  covalent geometry    : angle       0.45802 ( 9177)
  SS BOND              : bond        0.00003 (    1)
  SS BOND              : angle       0.40558 (    2)
  hydrogen bonds       : bond        0.03751 (  348)
  hydrogen bonds       : angle       3.73571 ( 1020)

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

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

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1778 Ramachandran restraints generated.
    889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A  294 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8171 (mm110)
REVERT: A  349 SER cc_start: 0.9083 (p) cc_final: 0.8877 (p)
REVERT: B  234 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.7928 (t80)
REVERT: B  259 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8482 (pt0)
REVERT: R  140 LYS cc_start: 0.8341 (mtmt) cc_final: 0.8023 (mtpt)
  outliers start: 10
  outliers final: 8
  residues processed: 90
  average time/residue: 0.0917
  time to fit residues: 10.7798
Evaluate side-chains
  90 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  236 SER
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 7 optimal weight:    9.9990
   chunk 77 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0000
   chunk 29 optimal weight:    0.8980
   chunk 85 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
R 241 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.126485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.100645 restraints weight = 32680.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 4.43
r_work: 0.3070 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3086
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3086 r_free = 0.3086    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3086 r_free = 0.3086    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3086
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6704  Z= 0.091
  Angle     :  0.450   8.660   9179  Z= 0.234
  Chirality :  0.040   0.202   1103
  Planarity :  0.003   0.038   1145
  Dihedral  : 10.002 177.029    990
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 16.78 %
    Favored  : 81.68 %
  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 aren not related in a simple way.
  whole:  1.33 (0.29), residues: 889
  helix:  2.52 (0.27), residues: 405
  sheet:  0.11 (0.38), residues: 181
  loop : -0.91 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 221 
 TYR   0.007   0.001   TYR A 339 
 PHE   0.009   0.001   PHE B 241 
 TRP   0.006   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00194 ( 6703)
  covalent geometry    : angle       0.45010 ( 9177)
  SS BOND              : bond        0.00029 (    1)
  SS BOND              : angle       0.44538 (    2)
  hydrogen bonds       : bond        0.03544 (  348)
  hydrogen bonds       : angle       3.66852 ( 1020)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1826.89 seconds
wall clock time: 31 minutes 56.23 seconds (1916.23 seconds total)