Starting phenix.real_space_refine
on Tue Feb 11 22:46:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gfw_29986/02_2025/8gfw_29986.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gfw_29986/02_2025/8gfw_29986.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gfw_29986/02_2025/8gfw_29986.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gfw_29986/02_2025/8gfw_29986.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gfw_29986/02_2025/8gfw_29986.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gfw_29986/02_2025/8gfw_29986.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.034
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      45      5.16       5
     C    4322      2.51       5
     N    1168      2.21       5
     O    1211      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6749
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1779
          Classifications: {'peptide': 232}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 152
          Unresolved non-hydrogen angles: 185
          Unresolved non-hydrogen dihedrals: 122
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 104
    Chain: "B"
      Number of atoms: 2417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2417
          Classifications: {'peptide': 333}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 5, 'TRANS': 327}
          Unresolved non-hydrogen bonds: 142
          Unresolved non-hydrogen angles: 174
          Unresolved non-hydrogen dihedrals: 110
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 10}
          Unresolved non-hydrogen planarities: 115
    Chain: "G"
      Number of atoms: 364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 364
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "R"
      Number of atoms: 2137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2137
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 124
          Unresolved non-hydrogen angles: 150
          Unresolved non-hydrogen dihedrals: 100
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 81
    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: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 4.35, per 1000 atoms: 0.64
  Number of scatterers: 6749
  At special positions: 0
  Unit cell: (82.4315, 130.155, 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      45     16.00
     P       3     15.00
     O    1211      8.00
     N    1168      7.00
     C    4322      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: 1.67
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1702

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      47.0% alpha, 18.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 4.088A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ALA A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLN A  31 " --> pdb=" O   GLU A  27 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
      removed outlier: 3.641A  pdb=" N   MET A  60 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 4.061A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.557A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
      removed outlier: 3.586A  pdb=" N   ASP A 310 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.631A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.930A  pdb=" N   VAL A 375 " --> pdb=" O   ASN A 371 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   PHE A 376 " --> pdb=" O   ILE A 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 26
      removed outlier: 3.680A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 10 through 22
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'R' and resid 36 through 61
      removed outlier: 3.615A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 3.668A  pdb=" N   TYR R  70 " --> pdb=" O   THR R  66 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.376A  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: 3.511A  pdb=" N   ILE R 121 " --> pdb=" O   VAL R 117 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   CYS R 125 " --> pdb=" O   ILE R 121 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE R 135 " --> pdb=" O   ARG R 131 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER R 137 " --> pdb=" O   PHE R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 164
      removed outlier: 3.566A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 165 through 171
      removed outlier: 3.596A  pdb=" N   ILE R 169 " --> pdb=" O   SER R 165 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 238
      removed outlier: 3.515A  pdb=" N   ALA R 200 " --> pdb=" O   ASN R 196 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   SER R 204 " --> pdb=" O   ALA R 200 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   VAL R 210 " --> pdb=" O   VAL R 206 " (cutoff:3.500A)
      Proline residue:  R 211  - end of helix
      removed outlier: 3.642A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 3.690A  pdb=" N   THR R 274 " --> pdb=" O   LYS R 270 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   ILE R 277 " --> pdb=" O   LYS R 273 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.317A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 318
      removed outlier: 3.606A  pdb=" N   TYR R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE R 309 " --> pdb=" O   LYS R 305 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LEU R 310 " --> pdb=" O   GLU R 306 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 321 through 327
    Processing helix  chain 'R' and resid 329 through 340
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.569A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.717A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.095A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.930A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.591A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.600A  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: 3.924A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.141A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.023A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.850A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.579A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.456A  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: 6.818A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.245A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.295A  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: 3.744A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.713A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    352 hydrogen bonds defined for protein.
    1023 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.90

  Time building geometry restraints manager: 1.90 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1467
        1.33 -     1.45: 1579
        1.45 -     1.57: 3777
        1.57 -     1.69: 5
        1.69 -     1.81: 63
  Bond restraints: 6891
  Sorted by residual:
  bond pdb=" C5  GTP A 401 "
       pdb=" C6  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.467 -0.077 2.00e-02 2.50e+03 1.47e+01
  bond pdb=" C4  GTP A 401 "
       pdb=" C5  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.459 -0.069 2.00e-02 2.50e+03 1.18e+01
  bond pdb=" C4  GTP A 401 "
       pdb=" N9  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.375  1.323  0.052 2.00e-02 2.50e+03 6.73e+00
  bond pdb=" C6  GTP A 401 "
       pdb=" N1  GTP A 401 "
    ideal  model  delta    sigma   weight residual
    1.380  1.329  0.051 2.00e-02 2.50e+03 6.60e+00
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.447 -0.050 2.00e-02 2.50e+03 6.32e+00
  ... (remaining 6886 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 9322
        2.39 -     4.79: 69
        4.79 -     7.18: 11
        7.18 -     9.57: 0
        9.57 -    11.97: 2
  Bond angle restraints: 9404
  Sorted by residual:
  angle pdb=" N   ARG R 239 "
        pdb=" CA  ARG R 239 "
        pdb=" C   ARG R 239 "
      ideal   model   delta    sigma   weight residual
     111.71  116.73   -5.02 1.15e+00 7.56e-01 1.91e+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  121.47  -11.97 3.00e+00 1.11e-01 1.59e+01
  angle pdb=" N   VAL R  81 "
        pdb=" CA  VAL R  81 "
        pdb=" C   VAL R  81 "
      ideal   model   delta    sigma   weight residual
     110.72  106.75    3.97 1.01e+00 9.80e-01 1.54e+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  120.07  -10.57 3.00e+00 1.11e-01 1.24e+01
  angle pdb=" N   LEU R 340 "
        pdb=" CA  LEU R 340 "
        pdb=" C   LEU R 340 "
      ideal   model   delta    sigma   weight residual
     110.55  106.70    3.85 1.35e+00 5.49e-01 8.15e+00
  ... (remaining 9399 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.64: 3968
       35.64 -    71.28: 43
       71.28 -   106.91: 0
      106.91 -   142.55: 2
      142.55 -   178.19: 2
  Dihedral angle restraints: 4015
    sinusoidal: 1392
      harmonic: 2623
  Sorted by residual:
  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 -112.54 -178.19     1      2.00e+01 2.50e-03 4.80e+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  -60.12  164.71     1      2.00e+01 2.50e-03 4.72e+01
  dihedral pdb=" O3A GTP A 401 "
           pdb=" O3B GTP A 401 "
           pdb=" PB  GTP A 401 "
           pdb=" PG  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.21 -179.15  122.94     1      2.00e+01 2.50e-03 3.71e+01
  ... (remaining 4012 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 652
       0.029 -    0.059: 294
       0.059 -    0.088: 108
       0.088 -    0.118: 46
       0.118 -    0.147: 9
  Chirality restraints: 1109
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.55   -0.15 2.00e-01 2.50e+01 5.41e-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 4.28e-01
  chirality pdb=" CA  ILE B 157 "
            pdb=" N   ILE B 157 "
            pdb=" C   ILE B 157 "
            pdb=" CB  ILE B 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.06e-01
  ... (remaining 1106 not shown)

  Planarity restraints: 1177
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 205 "    0.009 2.00e-02 2.50e+03   1.78e-02 3.17e+00
        pdb=" C   ILE R 205 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   ILE R 205 "    0.012 2.00e-02 2.50e+03
        pdb=" N   VAL R 206 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R  76 "    0.009 2.00e-02 2.50e+03   1.69e-02 2.86e+00
        pdb=" C   ALA R  76 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ALA R  76 "    0.011 2.00e-02 2.50e+03
        pdb=" N   CYS R  77 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "    0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO B 194 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1174 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 483
        2.74 -     3.28: 6362
        3.28 -     3.82: 10565
        3.82 -     4.36: 12206
        4.36 -     4.90: 22590
  Nonbonded interactions: 52206
  Sorted by model distance:
  nonbonded pdb=" OH  TYR R 219 "
            pdb=" O   HOH R 601 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OD1 ASP R 113 "
            pdb=" OH  TYR R 316 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OD2 ASP R 113 "
            pdb=" OAM G1I R 501 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" NE2 GLN G  18 "
            pdb=" OE2 GLU G  22 "
     model   vdw
     2.341 3.120
  ... (remaining 52201 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.970
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
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   0.077   6891  Z= 0.274
  Angle     :  0.574  11.969   9404  Z= 0.304
  Chirality :  0.042   0.147   1109
  Planarity :  0.003   0.030   1177
  Dihedral  : 13.587 178.192   2307
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.29), residues: 886
  helix:  1.63 (0.27), residues: 392
  sheet:  0.73 (0.44), residues: 160
  loop : -0.63 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 105 
 HIS   0.007   0.001   HIS B 183 
 PHE   0.013   0.001   PHE R 101 
 TYR   0.020   0.001   TYR B  59 
 ARG   0.005   0.000   ARG B 197 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.725 
Fit side-chains
REVERT: B  175 GLN cc_start: 0.8501 (pt0) cc_final: 0.8129 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 1.2236
  time to fit residues: 127.7107
Evaluate side-chains
  75 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 45 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 371 ASN
B  75 GLN
R  51 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.125222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.100679 restraints weight = 8983.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 1.95
r_work: 0.3003 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.1017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6891  Z= 0.194
  Angle     :  0.494   5.687   9404  Z= 0.266
  Chirality :  0.042   0.132   1109
  Planarity :  0.003   0.039   1177
  Dihedral  : 10.001 167.800    992
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  :  7.53 %
    Favored  : 90.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.29), residues: 886
  helix:  1.83 (0.27), residues: 393
  sheet:  0.80 (0.42), residues: 175
  loop : -0.47 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 169 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.013   0.001   TYR B  59 
 ARG   0.005   0.000   ARG R 228 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.789 
Fit side-chains
REVERT: B   22 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.5426 (mtp180)
REVERT: B  175 GLN cc_start: 0.8673 (pt0) cc_final: 0.8410 (pt0)
  outliers start: 15
  outliers final: 2
  residues processed: 97
  average time/residue: 1.1860
  time to fit residues: 121.4770
Evaluate side-chains
  83 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0020
   chunk 84 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 88 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN
R  51 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.126009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.101077 restraints weight = 9197.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 2.02
r_work: 0.2968 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6891  Z= 0.159
  Angle     :  0.459   6.205   9404  Z= 0.247
  Chirality :  0.040   0.130   1109
  Planarity :  0.003   0.029   1177
  Dihedral  :  9.542 166.372    992
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.52 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.29), residues: 886
  helix:  1.92 (0.27), residues: 395
  sheet:  0.92 (0.42), residues: 174
  loop : -0.39 (0.33), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.009   0.001   TYR R 132 
 ARG   0.005   0.000   ARG B 197 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.778 
Fit side-chains
REVERT: B   22 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.5344 (mtp180)
REVERT: B  175 GLN cc_start: 0.8635 (pt0) cc_final: 0.8372 (pt0)
REVERT: R  228 ARG cc_start: 0.7912 (mtp85) cc_final: 0.7219 (mtt-85)
  outliers start: 11
  outliers final: 5
  residues processed: 90
  average time/residue: 1.2208
  time to fit residues: 116.1391
Evaluate side-chains
  80 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 40 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    0.6980
   chunk 85 optimal weight:    0.5980
   chunk 57 optimal weight:    8.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN
R  51 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.121375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.096249 restraints weight = 9157.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 2.02
r_work: 0.2924 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6891  Z= 0.263
  Angle     :  0.512   6.593   9404  Z= 0.274
  Chirality :  0.042   0.137   1109
  Planarity :  0.003   0.031   1177
  Dihedral  :  9.510 165.956    992
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 11.52 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.29), residues: 886
  helix:  1.78 (0.27), residues: 396
  sheet:  0.88 (0.42), residues: 174
  loop : -0.42 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  63 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.013   0.002   PHE A 212 
 TYR   0.016   0.001   TYR R 132 
 ARG   0.005   0.000   ARG B 197 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.707 
Fit side-chains
REVERT: A   46 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8603 (mt)
REVERT: B  175 GLN cc_start: 0.8626 (pt0) cc_final: 0.8370 (pt0)
REVERT: B  217 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8171 (pmt)
  outliers start: 19
  outliers final: 10
  residues processed: 86
  average time/residue: 1.2077
  time to fit residues: 109.6039
Evaluate side-chains
  86 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0070
   chunk 23 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0030
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.2014

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
B 340 ASN
R  51 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.121744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.096738 restraints weight = 9096.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 2.01
r_work: 0.2918 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.1504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6891  Z= 0.224
  Angle     :  0.491   6.690   9404  Z= 0.262
  Chirality :  0.041   0.134   1109
  Planarity :  0.003   0.030   1177
  Dihedral  :  9.422 165.917    992
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 1.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 12.14 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.29), residues: 886
  helix:  1.79 (0.27), residues: 396
  sheet:  0.86 (0.42), residues: 175
  loop : -0.47 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  99 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.013   0.001   TYR R 132 
 ARG   0.004   0.000   ARG B 197 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.731 
Fit side-chains
REVERT: A  386 MET cc_start: 0.8933 (tmm) cc_final: 0.8691 (ttm)
REVERT: B  175 GLN cc_start: 0.8604 (pt0) cc_final: 0.8328 (pt0)
REVERT: B  217 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8144 (pmt)
  outliers start: 19
  outliers final: 11
  residues processed: 85
  average time/residue: 1.1756
  time to fit residues: 105.7102
Evaluate side-chains
  86 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0970
   chunk 80 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 35 optimal weight:    8.9990
   chunk 55 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN
B 340 ASN
R  51 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.121781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.096693 restraints weight = 9133.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 2.02
r_work: 0.2958 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.1581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6891  Z= 0.218
  Angle     :  0.489   6.778   9404  Z= 0.263
  Chirality :  0.041   0.134   1109
  Planarity :  0.003   0.029   1177
  Dihedral  :  9.412 165.692    992
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 1.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 13.06 %
    Favored  : 84.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.29), residues: 886
  helix:  1.80 (0.27), residues: 394
  sheet:  0.83 (0.42), residues: 175
  loop : -0.54 (0.33), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  99 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.012   0.001   PHE B 241 
 TYR   0.013   0.001   TYR R 132 
 ARG   0.004   0.000   ARG B 197 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.745 
Fit side-chains
REVERT: A  386 MET cc_start: 0.8947 (tmm) cc_final: 0.8714 (ttm)
REVERT: B  175 GLN cc_start: 0.8644 (pt0) cc_final: 0.8379 (pt0)
REVERT: B  217 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8178 (pmt)
REVERT: R  228 ARG cc_start: 0.7907 (mtp85) cc_final: 0.7142 (mtt-85)
  outliers start: 19
  outliers final: 12
  residues processed: 87
  average time/residue: 1.1222
  time to fit residues: 103.5146
Evaluate side-chains
  89 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   chunk 79 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0770
   chunk 28 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN
B 340 ASN
R  51 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.125190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.100596 restraints weight = 9092.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 1.95
r_work: 0.2986 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2863 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.1671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6891  Z= 0.156
  Angle     :  0.459   6.820   9404  Z= 0.246
  Chirality :  0.040   0.129   1109
  Planarity :  0.003   0.029   1177
  Dihedral  :  9.273 165.459    992
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 0.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 13.67 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.29), residues: 886
  helix:  1.96 (0.27), residues: 395
  sheet:  0.86 (0.42), residues: 175
  loop : -0.44 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  99 
 HIS   0.003   0.001   HIS R 296 
 PHE   0.011   0.001   PHE B 241 
 TYR   0.009   0.001   TYR R 132 
 ARG   0.004   0.000   ARG B 197 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.758 
Fit side-chains
REVERT: B  175 GLN cc_start: 0.8606 (pt0) cc_final: 0.8379 (pt0)
REVERT: B  217 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8231 (pmt)
REVERT: R  228 ARG cc_start: 0.7856 (mtp85) cc_final: 0.7425 (ttm110)
  outliers start: 16
  outliers final: 10
  residues processed: 87
  average time/residue: 1.0556
  time to fit residues: 97.6368
Evaluate side-chains
  87 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   chunk 74 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN
B 340 ASN
R  51 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.120429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.095313 restraints weight = 9201.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 2.02
r_work: 0.2911 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2785 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6891  Z= 0.273
  Angle     :  0.519   6.918   9404  Z= 0.278
  Chirality :  0.042   0.137   1109
  Planarity :  0.003   0.032   1177
  Dihedral  :  9.333 163.729    992
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 1.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 13.67 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.29), residues: 886
  helix:  1.76 (0.27), residues: 400
  sheet:  0.88 (0.41), residues: 173
  loop : -0.55 (0.33), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  63 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.013   0.002   PHE B 241 
 TYR   0.015   0.001   TYR R 132 
 ARG   0.003   0.000   ARG B 197 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.752 
Fit side-chains
REVERT: A  265 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6150 (mmt90)
REVERT: A  386 MET cc_start: 0.8946 (tmm) cc_final: 0.8722 (ttm)
REVERT: B  175 GLN cc_start: 0.8643 (pt0) cc_final: 0.8373 (pt0)
REVERT: B  217 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8156 (pmt)
REVERT: B  234 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.7781 (t80)
  outliers start: 17
  outliers final: 10
  residues processed: 88
  average time/residue: 1.2026
  time to fit residues: 112.5735
Evaluate side-chains
  92 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   chunk 83 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0470
   chunk 50 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.9880

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.123389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.098664 restraints weight = 9187.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 1.95
r_work: 0.2968 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6891  Z= 0.196
  Angle     :  0.487   6.893   9404  Z= 0.260
  Chirality :  0.041   0.130   1109
  Planarity :  0.003   0.029   1177
  Dihedral  :  9.204 162.782    992
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.75 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.29), residues: 886
  helix:  1.87 (0.27), residues: 398
  sheet:  0.83 (0.41), residues: 174
  loop : -0.57 (0.33), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  99 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.012   0.001   PHE B 241 
 TYR   0.012   0.001   TYR R 132 
 ARG   0.006   0.000   ARG R 228 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.819 
Fit side-chains
REVERT: A  265 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6253 (mmt90)
REVERT: A  386 MET cc_start: 0.8954 (tmm) cc_final: 0.8721 (ttm)
REVERT: B  175 GLN cc_start: 0.8644 (pt0) cc_final: 0.8409 (pt0)
REVERT: B  217 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8163 (pmt)
REVERT: B  234 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.7792 (t80)
REVERT: R  228 ARG cc_start: 0.7995 (mtp85) cc_final: 0.7266 (mtt-85)
  outliers start: 17
  outliers final: 11
  residues processed: 81
  average time/residue: 1.1551
  time to fit residues: 99.0505
Evaluate side-chains
  87 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  161 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 80 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.124640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.099813 restraints weight = 9301.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 1.98
r_work: 0.2958 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6891  Z= 0.164
  Angle     :  0.470   6.937   9404  Z= 0.252
  Chirality :  0.040   0.129   1109
  Planarity :  0.003   0.029   1177
  Dihedral  :  9.127 162.046    992
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.90 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.29), residues: 886
  helix:  1.94 (0.27), residues: 395
  sheet:  0.78 (0.41), residues: 175
  loop : -0.49 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  99 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.011   0.001   PHE B 241 
 TYR   0.010   0.001   TYR R 132 
 ARG   0.006   0.000   ARG R 228 

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.779 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8248 (tp40) cc_final: 0.7906 (tm-30)
REVERT: A  265 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6234 (mmt90)
REVERT: B  175 GLN cc_start: 0.8623 (pt0) cc_final: 0.8389 (pt0)
REVERT: B  217 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8171 (pmt)
REVERT: B  234 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.7767 (t80)
REVERT: R  228 ARG cc_start: 0.7924 (mtp85) cc_final: 0.7221 (mtt-85)
  outliers start: 15
  outliers final: 10
  residues processed: 85
  average time/residue: 1.2055
  time to fit residues: 108.3128
Evaluate side-chains
  87 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  163 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  145 LEU
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  227 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 83 optimal weight:    0.5980
   chunk 86 optimal weight:    0.1980
   chunk 29 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 59 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 61 optimal weight:    4.9990
   chunk 14 optimal weight:    0.5980
   chunk 50 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.127248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.102151 restraints weight = 9202.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 2.05
r_work: 0.2944 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2817 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6891  Z= 0.142
  Angle     :  0.464   8.221   9404  Z= 0.246
  Chirality :  0.040   0.130   1109
  Planarity :  0.003   0.028   1177
  Dihedral  :  9.012 161.569    992
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 15.36 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.29), residues: 886
  helix:  2.10 (0.27), residues: 390
  sheet:  0.77 (0.41), residues: 175
  loop : -0.33 (0.33), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  99 
 HIS   0.004   0.001   HIS R 296 
 PHE   0.011   0.001   PHE A 212 
 TYR   0.008   0.001   TYR R 132 
 ARG   0.005   0.000   ARG R 228 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4578.75 seconds
wall clock time: 81 minutes 33.02 seconds (4893.02 seconds total)