Starting phenix.real_space_refine
on Fri Aug 22 18:10:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gfv_29985/08_2025/8gfv_29985.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gfv_29985/08_2025/8gfv_29985.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gfv_29985/08_2025/8gfv_29985.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gfv_29985/08_2025/8gfv_29985.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gfv_29985/08_2025/8gfv_29985.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gfv_29985/08_2025/8gfv_29985.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.033
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      44      5.16       5
     C    4299      2.51       5
     N    1156      2.21       5
     O    1200      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6702
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1771
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 231, 1759
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 165
          Unresolved non-hydrogen angles: 200
          Unresolved non-hydrogen dihedrals: 133
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 6, 'ASN:plan1': 1, 'GLU:plan': 13, 'ASP:plan': 8, 'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 119
      Conformer: "B"
        Number of residues, atoms: 231, 1759
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 165
          Unresolved non-hydrogen angles: 200
          Unresolved non-hydrogen dihedrals: 133
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 6, 'ASN:plan1': 1, 'GLU:plan': 13, 'ASP:plan': 8, 'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 119
          bond proxies already assigned to first conformer: 1779
    Chain: "B"
      Number of atoms: 2405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2405
          Classifications: {'peptide': 329}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 5, 'TRANS': 323}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 122
          Unresolved non-hydrogen angles: 148
          Unresolved non-hydrogen dihedrals: 96
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 7, 'GLN:plan1': 4, 'GLU:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 97
    Chain: "G"
      Number of atoms: 332
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 332
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 77
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 32
    Chain: "R"
      Number of atoms: 2144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2144
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 142
          Unresolved non-hydrogen dihedrals: 94
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 4, 'ASN:plan1': 3, 'ARG:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 72
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "R"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          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: 2.29, per 1000 atoms: 0.34
  Number of scatterers: 6702
  At special positions: 0
  Unit cell: (82.4315, 133.626, 99.7855, 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      44     16.00
     P       3     15.00
     O    1200      8.00
     N    1156      7.00
     C    4299      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " 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 501.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1690

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 8 sheets defined
      48.5% alpha, 17.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 40
      removed outlier: 3.801A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.817A  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: 3.852A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 3.733A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ALA A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.287A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 3.596A  pdb=" N   ARG A 317 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.572A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.604A  pdb=" N   PHE A 376 " --> pdb=" O   ILE A 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 25
      removed outlier: 3.606A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 13 through 22
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.507A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'R' and resid 36 through 61
      removed outlier: 3.624A  pdb=" N   GLY R  50 " --> pdb=" O   ALA R  46 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 66
      removed outlier: 5.362A  pdb=" N   THR R  66 " --> pdb=" O   ARG R  63 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 97
      removed outlier: 4.123A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.727A  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 137
      removed outlier: 3.891A  pdb=" N   ILE R 121 " --> pdb=" O   VAL R 117 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   GLU R 122 " --> pdb=" O   THR R 118 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 166
      removed outlier: 3.793A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 171
      removed outlier: 3.592A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 175
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.751A  pdb=" N   SER R 204 " --> pdb=" O   ALA R 200 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 238
      removed outlier: 3.742A  pdb=" N   VAL R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   MET R 215 " --> pdb=" O   PRO R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 287
      removed outlier: 3.731A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 288 through 299
      removed outlier: 4.704A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.607A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 318 through 320
      No H-bonds generated for 'chain 'R' and resid 318 through 320'
    Processing helix  chain 'R' and resid 321 through 327
    Processing helix  chain 'R' and resid 329 through 339
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213
      removed outlier: 7.136A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.183A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.171A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.459A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   VAL A 287 " --> pdb=" O  ATYR A 360 " (cutoff:3.500A)
      removed outlier: 8.009A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.681A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.857A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.610A  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: 3.569A  pdb=" N   THR B 102 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.236A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.660A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.888A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.317A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.782A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.745A  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: 3.728A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)

    350 hydrogen bonds defined for protein.
    1011 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: 0.74

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2117
        1.34 -     1.46: 1109
        1.46 -     1.57: 3553
        1.57 -     1.69: 5
        1.69 -     1.81: 61
  Bond restraints: 6845
  Sorted by residual:
  bond pdb=" C5  GTP A 401 "
       pdb=" C6  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.476 -0.086 2.00e-02 2.50e+03 1.83e+01
  bond pdb=" C4  GTP A 401 "
       pdb=" C5  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.460 -0.070 2.00e-02 2.50e+03 1.22e+01
  bond pdb=" C4  GTP A 401 "
       pdb=" N9  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.375  1.324  0.051 2.00e-02 2.50e+03 6.61e+00
  bond pdb=" CA  SER A  51 "
       pdb=" C   SER A  51 "
    ideal  model  delta    sigma   weight residual
    1.523  1.491  0.032 1.30e-02 5.92e+03 6.13e+00
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.446 -0.049 2.00e-02 2.50e+03 6.01e+00
  ... (remaining 6840 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 9247
        2.19 -     4.39: 75
        4.39 -     6.58: 17
        6.58 -     8.77: 3
        8.77 -    10.97: 2
  Bond angle restraints: 9344
  Sorted by residual:
  angle pdb=" N   GLY A  49 "
        pdb=" CA  GLY A  49 "
        pdb=" C   GLY A  49 "
      ideal   model   delta    sigma   weight residual
     111.54  118.36   -6.82 1.36e+00 5.41e-01 2.51e+01
  angle pdb=" O1B GTP A 401 "
        pdb=" PB  GTP A 401 "
        pdb=" O2B GTP A 401 "
      ideal   model   delta    sigma   weight residual
     109.50  120.47  -10.97 3.00e+00 1.11e-01 1.34e+01
  angle pdb=" O1A GTP A 401 "
        pdb=" PA  GTP A 401 "
        pdb=" O2A GTP A 401 "
      ideal   model   delta    sigma   weight residual
     109.50  119.81  -10.31 3.00e+00 1.11e-01 1.18e+01
  angle pdb=" N   GLY A  52 "
        pdb=" CA  GLY A  52 "
        pdb=" C   GLY A  52 "
      ideal   model   delta    sigma   weight residual
     113.18  106.37    6.81 2.37e+00 1.78e-01 8.26e+00
  angle pdb=" CA  GLY A  49 "
        pdb=" C   GLY A  49 "
        pdb=" O   GLY A  49 "
      ideal   model   delta    sigma   weight residual
     121.58  119.25    2.33 9.00e-01 1.23e+00 6.68e+00
  ... (remaining 9339 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.41: 3893
       32.41 -    64.82: 79
       64.82 -    97.23: 5
       97.23 -   129.64: 0
      129.64 -   162.05: 3
  Dihedral angle restraints: 3980
    sinusoidal: 1375
      harmonic: 2605
  Sorted by residual:
  dihedral pdb=" CB  CYS R 184 "
           pdb=" SG  CYS R 184 "
           pdb=" SG  CYS R 190 "
           pdb=" CB  CYS R 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  152.46  -59.46     1      1.00e+01 1.00e-02 4.72e+01
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -57.46  162.05     1      2.00e+01 2.50e-03 4.68e+01
  dihedral pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" O3A GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27  -92.40  161.67     1      2.00e+01 2.50e-03 4.68e+01
  ... (remaining 3977 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 656
       0.029 -    0.057: 276
       0.057 -    0.086: 109
       0.086 -    0.115: 53
       0.115 -    0.144: 11
  Chirality restraints: 1105
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.54   -0.14 2.00e-01 2.50e+01 5.16e-01
  chirality pdb=" CA  ILE A 207 "
            pdb=" N   ILE A 207 "
            pdb=" C   ILE A 207 "
            pdb=" CB  ILE A 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.58e-01
  chirality pdb=" CA  ILE A 244 "
            pdb=" N   ILE A 244 "
            pdb=" C   ILE A 244 "
            pdb=" CB  ILE A 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 1102 not shown)

  Planarity restraints: 1167
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "    0.022 5.00e-02 4.00e+02   3.34e-02 1.78e+00
        pdb=" N   PRO G  49 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 210 "    0.022 5.00e-02 4.00e+02   3.33e-02 1.78e+00
        pdb=" N   PRO R 211 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO R 211 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO R 211 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "    0.019 5.00e-02 4.00e+02   2.89e-02 1.34e+00
        pdb=" N   PRO B 194 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1164 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1753
        2.80 -     3.33: 5976
        3.33 -     3.85: 10440
        3.85 -     4.38: 11659
        4.38 -     4.90: 21766
  Nonbonded interactions: 51594
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 343 "
            pdb=" NH2 ARG R 239 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" O   SER R 111 "
            pdb=" OG  SER R 165 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" OH  TYR R 209 "
            pdb=" O   PHE R 290 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.347 3.040
  nonbonded pdb=" OH  TYR R 219 "
            pdb=" O   HOH R 601 "
     model   vdw
     2.397 3.040
  ... (remaining 51589 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:             2.940
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     8.350
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
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      :  0.004   0.086   6847  Z= 0.197
  Angle     :  0.578  10.967   9348  Z= 0.297
  Chirality :  0.041   0.144   1105
  Planarity :  0.003   0.033   1167
  Dihedral  : 14.483 162.053   2284
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 2.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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:  1.20 (0.29), residues: 879
  helix:  2.01 (0.27), residues: 389
  sheet:  0.79 (0.41), residues: 169
  loop : -0.71 (0.32), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  38 
 TYR   0.008   0.001   TYR A 339 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.013   0.001   TRP R 109 
 HIS   0.011   0.002   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 6845)
  covalent geometry    : angle       0.57769 ( 9344)
  SS BOND              : bond        0.00301 (    2)
  SS BOND              : angle       0.73888 (    4)
  hydrogen bonds       : bond        0.18494 (  350)
  hydrogen bonds       : angle       6.25557 ( 1011)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.214 
Fit side-chains
REVERT: R  113 ASP cc_start: 0.8709 (t70) cc_final: 0.8436 (t0)
REVERT: R  231 GLN cc_start: 0.8333 (tm-30) cc_final: 0.7971 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0933
  time to fit residues: 12.4797
Evaluate side-chains
  88 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.1980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0050
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
A 236 GLN
B  75 GLN
R 296 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.123800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.098606 restraints weight = 34654.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 3.72
r_work: 0.2922 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2865
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2865 r_free = 0.2865    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2865 r_free = 0.2865    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2865
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.0880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6847  Z= 0.105
  Angle     :  0.473   6.550   9348  Z= 0.255
  Chirality :  0.040   0.131   1105
  Planarity :  0.003   0.033   1167
  Dihedral  :  9.716 177.229    985
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 2.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  6.04 %
    Favored  : 93.65 %
  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:  1.50 (0.29), residues: 879
  helix:  2.25 (0.27), residues: 392
  sheet:  0.91 (0.41), residues: 175
  loop : -0.58 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  38 
 TYR   0.008   0.001   TYR A 339 
 PHE   0.015   0.001   PHE A 212 
 TRP   0.008   0.001   TRP B 297 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 6845)
  covalent geometry    : angle       0.47252 ( 9344)
  SS BOND              : bond        0.00242 (    2)
  SS BOND              : angle       0.61988 (    4)
  hydrogen bonds       : bond        0.04476 (  350)
  hydrogen bonds       : angle       4.46149 ( 1011)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7507 (mt-10)
REVERT: A   38 ARG cc_start: 0.8545 (mmm-85) cc_final: 0.8179 (mtm110)
REVERT: A  330 GLU cc_start: 0.7497 (pt0) cc_final: 0.7236 (pt0)
REVERT: B  258 ASP cc_start: 0.8011 (t0) cc_final: 0.7791 (t0)
REVERT: R  231 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8291 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 99
  average time/residue: 0.1036
  time to fit residues: 13.2005
Evaluate side-chains
  88 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 31 optimal weight:    0.1980
   chunk 26 optimal weight:    4.9990
   chunk 35 optimal weight:    0.5980
   chunk 20 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.122018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.096859 restraints weight = 35554.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 3.88
r_work: 0.2889 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2832
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2832
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.1038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6847  Z= 0.121
  Angle     :  0.469   6.184   9348  Z= 0.252
  Chirality :  0.041   0.132   1105
  Planarity :  0.003   0.033   1167
  Dihedral  :  8.504 160.209    985
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 1.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  8.20 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.49 (0.29), residues: 879
  helix:  2.25 (0.27), residues: 393
  sheet:  0.78 (0.40), residues: 177
  loop : -0.53 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 283 
 TYR   0.008   0.001   TYR A  37 
 PHE   0.015   0.001   PHE A 212 
 TRP   0.008   0.001   TRP B 297 
 HIS   0.008   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6845)
  covalent geometry    : angle       0.46879 ( 9344)
  SS BOND              : bond        0.00215 (    2)
  SS BOND              : angle       0.57059 (    4)
  hydrogen bonds       : bond        0.04487 (  350)
  hydrogen bonds       : angle       4.17605 ( 1011)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8653 (mmm-85) cc_final: 0.8206 (mtm-85)
REVERT: B  258 ASP cc_start: 0.8036 (t0) cc_final: 0.7834 (t0)
REVERT: R  231 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8366 (tm-30)
  outliers start: 7
  outliers final: 5
  residues processed: 91
  average time/residue: 0.1091
  time to fit residues: 12.8536
Evaluate side-chains
  90 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 57 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 84 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.122407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.096146 restraints weight = 25818.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 3.35
r_work: 0.2895 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2880
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2880
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.1177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6847  Z= 0.111
  Angle     :  0.457   6.604   9348  Z= 0.245
  Chirality :  0.040   0.132   1105
  Planarity :  0.003   0.035   1167
  Dihedral  :  8.063 153.884    985
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 1.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  8.82 %
    Favored  : 90.09 %
  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:  1.56 (0.29), residues: 879
  helix:  2.29 (0.27), residues: 393
  sheet:  0.80 (0.40), residues: 175
  loop : -0.45 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 283 
 TYR   0.008   0.001   TYR A  37 
 PHE   0.015   0.001   PHE A 212 
 TRP   0.007   0.001   TRP B 297 
 HIS   0.008   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6845)
  covalent geometry    : angle       0.45727 ( 9344)
  SS BOND              : bond        0.00218 (    2)
  SS BOND              : angle       0.57568 (    4)
  hydrogen bonds       : bond        0.04172 (  350)
  hydrogen bonds       : angle       4.04166 ( 1011)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8675 (mmm-85) cc_final: 0.8266 (mtm-85)
REVERT: B  258 ASP cc_start: 0.7977 (t0) cc_final: 0.7776 (t0)
REVERT: R  231 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8294 (tm-30)
  outliers start: 7
  outliers final: 7
  residues processed: 94
  average time/residue: 0.0993
  time to fit residues: 12.0455
Evaluate side-chains
  95 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 70 optimal weight:    0.4980
   chunk 9 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.120874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.093966 restraints weight = 31389.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 3.55
r_work: 0.2836 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2753
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2753 r_free = 0.2753    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2753 r_free = 0.2753    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2753
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6847  Z= 0.143
  Angle     :  0.480   6.875   9348  Z= 0.258
  Chirality :  0.041   0.134   1105
  Planarity :  0.003   0.040   1167
  Dihedral  :  8.013 151.415    985
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 1.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  9.29 %
    Favored  : 89.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.29), residues: 879
  helix:  2.29 (0.27), residues: 390
  sheet:  0.69 (0.40), residues: 175
  loop : -0.52 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 239 
 TYR   0.009   0.001   TYR A 339 
 PHE   0.015   0.001   PHE A 212 
 TRP   0.007   0.001   TRP B 297 
 HIS   0.009   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6845)
  covalent geometry    : angle       0.48000 ( 9344)
  SS BOND              : bond        0.00225 (    2)
  SS BOND              : angle       0.61739 (    4)
  hydrogen bonds       : bond        0.04763 (  350)
  hydrogen bonds       : angle       4.11129 ( 1011)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8695 (mmm-85) cc_final: 0.8219 (mtm-85)
REVERT: B  234 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8184 (t80)
REVERT: R  231 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8341 (tm-30)
  outliers start: 11
  outliers final: 9
  residues processed: 92
  average time/residue: 0.1019
  time to fit residues: 12.1152
Evaluate side-chains
  95 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0970
   chunk 9 optimal weight:    0.7980
   chunk 76 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.122858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.097375 restraints weight = 29866.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 3.30
r_work: 0.2911 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2880
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2880 r_free = 0.2880    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2880
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.1335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6847  Z= 0.101
  Angle     :  0.442   6.968   9348  Z= 0.237
  Chirality :  0.040   0.131   1105
  Planarity :  0.003   0.036   1167
  Dihedral  :  7.840 149.155    985
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 10.68 %
    Favored  : 87.77 %
  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:  1.56 (0.29), residues: 879
  helix:  2.35 (0.27), residues: 393
  sheet:  0.66 (0.39), residues: 175
  loop : -0.44 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 283 
 TYR   0.008   0.001   TYR A 339 
 PHE   0.015   0.001   PHE A 212 
 TRP   0.007   0.001   TRP B 297 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 6845)
  covalent geometry    : angle       0.44162 ( 9344)
  SS BOND              : bond        0.00214 (    2)
  SS BOND              : angle       0.56635 (    4)
  hydrogen bonds       : bond        0.03861 (  350)
  hydrogen bonds       : angle       3.93162 ( 1011)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8685 (mmm-85) cc_final: 0.8279 (mtm-85)
REVERT: B  234 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8119 (t80)
REVERT: R  231 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8308 (tm-30)
  outliers start: 10
  outliers final: 8
  residues processed: 95
  average time/residue: 0.0981
  time to fit residues: 12.1463
Evaluate side-chains
  92 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 59 optimal weight:    0.0570
   chunk 5 optimal weight:    5.9990
   chunk 37 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.8902

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.121879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.095930 restraints weight = 36525.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 3.82
r_work: 0.2874 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2857
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2857
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6847  Z= 0.114
  Angle     :  0.463   8.137   9348  Z= 0.246
  Chirality :  0.040   0.131   1105
  Planarity :  0.003   0.042   1167
  Dihedral  :  7.824 148.284    985
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 1.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 10.84 %
    Favored  : 87.46 %
  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:  1.52 (0.29), residues: 879
  helix:  2.29 (0.27), residues: 393
  sheet:  0.65 (0.39), residues: 175
  loop : -0.45 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 239 
 TYR   0.008   0.001   TYR R 132 
 PHE   0.015   0.001   PHE A 212 
 TRP   0.007   0.001   TRP B 297 
 HIS   0.012   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6845)
  covalent geometry    : angle       0.46290 ( 9344)
  SS BOND              : bond        0.00214 (    2)
  SS BOND              : angle       0.57471 (    4)
  hydrogen bonds       : bond        0.04128 (  350)
  hydrogen bonds       : angle       3.94720 ( 1011)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8714 (mmm-85) cc_final: 0.8263 (mtm-85)
REVERT: B  234 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8183 (t80)
REVERT: R  231 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8396 (tm-30)
  outliers start: 11
  outliers final: 10
  residues processed: 89
  average time/residue: 0.0947
  time to fit residues: 10.8280
Evaluate side-chains
  95 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 83 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.122598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.096710 restraints weight = 34126.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 3.72
r_work: 0.2875 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2832
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2832 r_free = 0.2832    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2832
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6847  Z= 0.105
  Angle     :  0.454   7.791   9348  Z= 0.241
  Chirality :  0.040   0.131   1105
  Planarity :  0.003   0.043   1167
  Dihedral  :  7.777 147.110    985
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 1.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.15 %
    Favored  : 87.15 %
  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:  1.56 (0.29), residues: 879
  helix:  2.36 (0.27), residues: 392
  sheet:  0.68 (0.39), residues: 175
  loop : -0.46 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 239 
 TYR   0.008   0.001   TYR A 339 
 PHE   0.016   0.001   PHE A 212 
 TRP   0.007   0.001   TRP B 297 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 6845)
  covalent geometry    : angle       0.45351 ( 9344)
  SS BOND              : bond        0.00216 (    2)
  SS BOND              : angle       0.56075 (    4)
  hydrogen bonds       : bond        0.03916 (  350)
  hydrogen bonds       : angle       3.89304 ( 1011)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8695 (mmm-85) cc_final: 0.8265 (mtm-85)
REVERT: B  234 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8163 (t80)
REVERT: R  231 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8377 (tm-30)
  outliers start: 11
  outliers final: 9
  residues processed: 90
  average time/residue: 0.0967
  time to fit residues: 11.3474
Evaluate side-chains
  92 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9980
   chunk 35 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.120856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.095396 restraints weight = 32029.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 3.54
r_work: 0.2868 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2840
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2840 r_free = 0.2840    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2840
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.1351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6847  Z= 0.130
  Angle     :  0.479   7.670   9348  Z= 0.256
  Chirality :  0.041   0.134   1105
  Planarity :  0.003   0.047   1167
  Dihedral  :  7.828 146.789    985
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 1.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 10.99 %
    Favored  : 87.31 %
  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:  1.50 (0.29), residues: 879
  helix:  2.27 (0.27), residues: 393
  sheet:  0.67 (0.39), residues: 175
  loop : -0.46 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 239 
 TYR   0.008   0.001   TYR R 132 
 PHE   0.017   0.001   PHE A 212 
 TRP   0.006   0.001   TRP B 297 
 HIS   0.008   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6845)
  covalent geometry    : angle       0.47875 ( 9344)
  SS BOND              : bond        0.00223 (    2)
  SS BOND              : angle       0.58950 (    4)
  hydrogen bonds       : bond        0.04463 (  350)
  hydrogen bonds       : angle       3.97337 ( 1011)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8694 (mmm-85) cc_final: 0.8278 (mtm-85)
REVERT: B  234 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8217 (t80)
REVERT: R  231 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8356 (tm-30)
  outliers start: 11
  outliers final: 10
  residues processed: 91
  average time/residue: 0.0944
  time to fit residues: 11.2338
Evaluate side-chains
  94 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  365 CYS
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 70 optimal weight:    0.0970
   chunk 9 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.122909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.097327 restraints weight = 31652.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 3.60
r_work: 0.2897 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2912
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2912 r_free = 0.2912    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2912 r_free = 0.2912    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2912
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8645
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6847  Z= 0.101
  Angle     :  0.453   7.587   9348  Z= 0.242
  Chirality :  0.040   0.130   1105
  Planarity :  0.003   0.043   1167
  Dihedral  :  7.757 145.500    985
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 1.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 11.61 %
    Favored  : 86.84 %
  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:  1.57 (0.29), residues: 879
  helix:  2.37 (0.27), residues: 392
  sheet:  0.69 (0.39), residues: 175
  loop : -0.47 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 239 
 TYR   0.008   0.001   TYR A 339 
 PHE   0.017   0.001   PHE A 212 
 TRP   0.007   0.001   TRP B 297 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 6845)
  covalent geometry    : angle       0.45330 ( 9344)
  SS BOND              : bond        0.00210 (    2)
  SS BOND              : angle       0.56428 (    4)
  hydrogen bonds       : bond        0.03816 (  350)
  hydrogen bonds       : angle       3.87040 ( 1011)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.8684 (mmm-85) cc_final: 0.8254 (mtm-85)
REVERT: B  234 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8056 (t80)
REVERT: R  231 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8344 (tm-30)
  outliers start: 10
  outliers final: 9
  residues processed: 89
  average time/residue: 0.1024
  time to fit residues: 11.6972
Evaluate side-chains
  89 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.4980
   chunk 44 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 66 optimal weight:    0.3980
   chunk 8 optimal weight:    3.9990
   chunk 57 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.122769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.097039 restraints weight = 28582.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 3.26
r_work: 0.2918 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2918
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2918 r_free = 0.2918    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2918 r_free = 0.2918    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2918
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.1463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6847  Z= 0.104
  Angle     :  0.464   7.477   9348  Z= 0.248
  Chirality :  0.040   0.131   1105
  Planarity :  0.003   0.042   1167
  Dihedral  :  7.738 145.010    985
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 1.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 11.46 %
    Favored  : 86.84 %
  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:  1.58 (0.29), residues: 879
  helix:  2.37 (0.27), residues: 392
  sheet:  0.69 (0.39), residues: 175
  loop : -0.46 (0.35), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG R 239 
 TYR   0.008   0.001   TYR A 339 
 PHE   0.017   0.001   PHE A 212 
 TRP   0.007   0.001   TRP B 297 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 6845)
  covalent geometry    : angle       0.46376 ( 9344)
  SS BOND              : bond        0.00213 (    2)
  SS BOND              : angle       0.55631 (    4)
  hydrogen bonds       : bond        0.03845 (  350)
  hydrogen bonds       : angle       3.86734 ( 1011)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1842.32 seconds
wall clock time: 32 minutes 11.13 seconds (1931.13 seconds total)