Starting phenix.real_space_refine
on Fri Aug 22 18:16:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gfw_29986/08_2025/8gfw_29986.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gfw_29986/08_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_29986/08_2025/8gfw_29986.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gfw_29986/08_2025/8gfw_29986.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gfw_29986/08_2025/8gfw_29986.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gfw_29986/08_2025/8gfw_29986.cif"
  }
  resolution = 3.0
  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=   0.034
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): 0.00s

  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: 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: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 13, 'PHE:plan': 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: {'ARG:plan': 8, 'GLN:plan1': 4, 'GLU:plan': 5, '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: {'ARG:plan': 2, 'GLU:plan': 3, '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: {'GLU:plan': 8, 'ASP:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 2, 'GLN:plan1': 4, 'HIS:plan': 1}
          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: 1.49, per 1000 atoms: 0.22
  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: 0.46
  Conformation dependent library (CDL) restraints added in 315.6 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.19
  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: 0.81

  Time building geometry restraints manager: 0.63 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:             2.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.180
  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:8.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.810
-------------------------------------------------------------------------------
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   6893  Z= 0.199
  Angle     :  0.578  11.969   9408  Z= 0.306
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (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
 ARG   0.005   0.000   ARG B 197 
 TYR   0.020   0.001   TYR B  59 
 PHE   0.013   0.001   PHE R 101 
 TRP   0.010   0.001   TRP R 105 
 HIS   0.007   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 6891)
  covalent geometry    : angle       0.57418 ( 9404)
  SS BOND              : bond        0.00277 (    2)
  SS BOND              : angle       3.19494 (    4)
  hydrogen bonds       : bond        0.19409 (  352)
  hydrogen bonds       : angle       6.28951 ( 1023)

*********************** 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  : 0.182 
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: 0.4401
  time to fit residues: 45.7865
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  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.4980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3447 r_free = 0.3447 target = 0.125708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.100874 restraints weight = 9169.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 1.98
r_work: 0.3004 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.1019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6893  Z= 0.127
  Angle     :  0.491   5.660   9408  Z= 0.265
  Chirality :  0.041   0.132   1109
  Planarity :  0.003   0.038   1177
  Dihedral  : 10.008 167.671    992
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 1.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  :  7.22 %
    Favored  : 90.48 %
  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:  1.21 (0.29), residues: 886
  helix:  1.84 (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
 ARG   0.006   0.000   ARG R 228 
 TYR   0.013   0.001   TYR B  59 
 PHE   0.013   0.001   PHE A 212 
 TRP   0.010   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6891)
  covalent geometry    : angle       0.48969 ( 9404)
  SS BOND              : bond        0.00308 (    2)
  SS BOND              : angle       1.92454 (    4)
  hydrogen bonds       : bond        0.05361 (  352)
  hydrogen bonds       : angle       4.67219 ( 1023)

*********************** 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
  104 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8327 (mptp)
REVERT: B   22 ARG cc_start: 0.6855 (OUTLIER) cc_final: 0.5422 (mtp180)
REVERT: B  175 GLN cc_start: 0.8684 (pt0) cc_final: 0.8406 (pt0)
  outliers start: 15
  outliers final: 3
  residues processed: 96
  average time/residue: 0.4344
  time to fit residues: 44.0865
Evaluate side-chains
  84 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue  137 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 37 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    0.7980
   chunk 85 optimal weight:    0.0870
   chunk 77 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0060
   chunk 26 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.5776

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3468 r_free = 0.3468 target = 0.127565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.102935 restraints weight = 9102.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 1.96
r_work: 0.3036 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6893  Z= 0.102
  Angle     :  0.448   6.432   9408  Z= 0.240
  Chirality :  0.040   0.131   1109
  Planarity :  0.003   0.029   1177
  Dihedral  :  9.408 166.132    992
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 1.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.37 %
    Favored  : 86.94 %
  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:  1.38 (0.29), residues: 886
  helix:  1.99 (0.27), residues: 395
  sheet:  1.03 (0.44), residues: 162
  loop : -0.46 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 197 
 TYR   0.008   0.001   TYR R 132 
 PHE   0.010   0.001   PHE A 212 
 TRP   0.007   0.001   TRP B 169 
 HIS   0.006   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 6891)
  covalent geometry    : angle       0.44677 ( 9404)
  SS BOND              : bond        0.00358 (    2)
  SS BOND              : angle       1.49758 (    4)
  hydrogen bonds       : bond        0.04264 (  352)
  hydrogen bonds       : angle       4.21832 ( 1023)

*********************** 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
  97 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.270 
Fit side-chains
REVERT: B   22 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.5342 (mtp180)
REVERT: B  175 GLN cc_start: 0.8619 (pt0) cc_final: 0.8369 (pt0)
REVERT: R  228 ARG cc_start: 0.7862 (mtp85) cc_final: 0.7192 (mtt-85)
  outliers start: 11
  outliers final: 4
  residues processed: 91
  average time/residue: 0.4588
  time to fit residues: 43.9588
Evaluate side-chains
  79 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
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  145 LEU
Chi-restraints excluded: chain R residue  195 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0270
   chunk 72 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0060
   chunk 58 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.5054

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3472 r_free = 0.3472 target = 0.128033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.103369 restraints weight = 9206.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 1.98
r_work: 0.2999 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6893  Z= 0.095
  Angle     :  0.439   6.704   9408  Z= 0.233
  Chirality :  0.040   0.129   1109
  Planarity :  0.003   0.028   1177
  Dihedral  :  9.270 168.109    992
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 1.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 11.83 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.29), residues: 886
  helix:  2.16 (0.27), residues: 390
  sheet:  0.94 (0.43), residues: 169
  loop : -0.21 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 197 
 TYR   0.008   0.001   TYR R 132 
 PHE   0.010   0.001   PHE B 241 
 TRP   0.007   0.001   TRP B  99 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 ( 6891)
  covalent geometry    : angle       0.43831 ( 9404)
  SS BOND              : bond        0.00338 (    2)
  SS BOND              : angle       1.33712 (    4)
  hydrogen bonds       : bond        0.03947 (  352)
  hydrogen bonds       : angle       4.08445 ( 1023)

*********************** 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: 16
    poor density    : 81
  time to evaluate  : 0.251 
Fit side-chains
REVERT: B   22 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6584 (mtt180)
REVERT: B  175 GLN cc_start: 0.8570 (pt0) cc_final: 0.8326 (pt0)
  outliers start: 16
  outliers final: 8
  residues processed: 88
  average time/residue: 0.4397
  time to fit residues: 40.8154
Evaluate side-chains
  84 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  163 ASP
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 40 optimal weight:    7.9990
   chunk 30 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 88 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3454 r_free = 0.3454 target = 0.126627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.101724 restraints weight = 9222.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 1.99
r_work: 0.2990 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2865 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6893  Z= 0.108
  Angle     :  0.453   6.794   9408  Z= 0.241
  Chirality :  0.040   0.128   1109
  Planarity :  0.003   0.028   1177
  Dihedral  :  9.214 167.826    992
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 1.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 12.29 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: 886
  helix:  2.12 (0.27), residues: 390
  sheet:  0.92 (0.42), residues: 175
  loop : -0.21 (0.33), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 197 
 TYR   0.010   0.001   TYR R 132 
 PHE   0.010   0.001   PHE B 241 
 TRP   0.006   0.001   TRP B  99 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6891)
  covalent geometry    : angle       0.45196 ( 9404)
  SS BOND              : bond        0.00323 (    2)
  SS BOND              : angle       1.37401 (    4)
  hydrogen bonds       : bond        0.04270 (  352)
  hydrogen bonds       : angle       4.06167 ( 1023)

*********************** 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
  91 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A   46 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8572 (mp)
REVERT: B  175 GLN cc_start: 0.8599 (pt0) cc_final: 0.8369 (pt0)
REVERT: R  228 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7215 (mtt-85)
  outliers start: 19
  outliers final: 9
  residues processed: 81
  average time/residue: 0.4776
  time to fit residues: 40.8833
Evaluate side-chains
  82 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.3382 r_free = 0.3382 target = 0.120841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.095793 restraints weight = 9269.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 2.02
r_work: 0.2920 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.1565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6893  Z= 0.173
  Angle     :  0.518   6.870   9408  Z= 0.277
  Chirality :  0.042   0.138   1109
  Planarity :  0.003   0.031   1177
  Dihedral  :  9.356 166.075    992
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.29), residues: 886
  helix:  1.87 (0.27), residues: 396
  sheet:  0.91 (0.41), residues: 179
  loop : -0.45 (0.33), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 197 
 TYR   0.015   0.001   TYR R 132 
 PHE   0.013   0.002   PHE B 234 
 TRP   0.009   0.001   TRP B  63 
 HIS   0.004   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 6891)
  covalent geometry    : angle       0.51652 ( 9404)
  SS BOND              : bond        0.00343 (    2)
  SS BOND              : angle       1.63038 (    4)
  hydrogen bonds       : bond        0.05663 (  352)
  hydrogen bonds       : angle       4.31244 ( 1023)

*********************** 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
  91 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A   46 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8616 (mt)
REVERT: A  386 MET cc_start: 0.8932 (tmm) cc_final: 0.8699 (ttm)
REVERT: B  175 GLN cc_start: 0.8621 (pt0) cc_final: 0.8358 (pt0)
  outliers start: 15
  outliers final: 11
  residues processed: 83
  average time/residue: 0.4414
  time to fit residues: 38.8302
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  : 0.184 
-------------------------------------------------------------------------------
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  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  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 57 optimal weight:    2.9990
   chunk 78 optimal weight:    0.5980
   chunk 6 optimal weight:    0.2980
   chunk 13 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9980
   chunk 56 optimal weight:    9.9990
   chunk 61 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 81 optimal weight:    3.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3443 r_free = 0.3443 target = 0.125703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.101063 restraints weight = 9105.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 1.96
r_work: 0.2963 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2841 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6893  Z= 0.105
  Angle     :  0.457   6.818   9408  Z= 0.244
  Chirality :  0.040   0.128   1109
  Planarity :  0.003   0.028   1177
  Dihedral  :  9.192 165.686    992
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 1.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 13.36 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.29), residues: 886
  helix:  1.98 (0.27), residues: 396
  sheet:  0.87 (0.41), residues: 175
  loop : -0.37 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 228 
 TYR   0.009   0.001   TYR R 132 
 PHE   0.011   0.001   PHE B 241 
 TRP   0.008   0.001   TRP B  99 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 6891)
  covalent geometry    : angle       0.45585 ( 9404)
  SS BOND              : bond        0.00441 (    2)
  SS BOND              : angle       1.30144 (    4)
  hydrogen bonds       : bond        0.04247 (  352)
  hydrogen bonds       : angle       4.11417 ( 1023)

*********************** 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
  93 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.189 
Fit side-chains
REVERT: B  175 GLN cc_start: 0.8605 (pt0) cc_final: 0.8360 (pt0)
REVERT: R  228 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7164 (mtt-85)
  outliers start: 16
  outliers final: 10
  residues processed: 86
  average time/residue: 0.4106
  time to fit residues: 37.6074
Evaluate side-chains
  82 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    0.4980
   chunk 72 optimal weight:    0.9980
   chunk 68 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.2182

-------------------------------------------------------------------------------
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 = 0.3394 r_free = 0.3394 target = 0.121796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.096691 restraints weight = 9220.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 2.02
r_work: 0.2930 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2806 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6893  Z= 0.145
  Angle     :  0.503   6.908   9408  Z= 0.268
  Chirality :  0.041   0.134   1109
  Planarity :  0.003   0.029   1177
  Dihedral  :  9.228 164.941    992
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 13.67 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.29), residues: 886
  helix:  1.89 (0.27), residues: 395
  sheet:  0.84 (0.41), residues: 175
  loop : -0.45 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 228 
 TYR   0.015   0.001   TYR R 132 
 PHE   0.012   0.001   PHE B 241 
 TRP   0.007   0.001   TRP B  63 
 HIS   0.003   0.001   HIS R 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 6891)
  covalent geometry    : angle       0.50240 ( 9404)
  SS BOND              : bond        0.00334 (    2)
  SS BOND              : angle       1.30138 (    4)
  hydrogen bonds       : bond        0.05091 (  352)
  hydrogen bonds       : angle       4.20945 ( 1023)

*********************** 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
  91 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.197 
Fit side-chains
REVERT: B  175 GLN cc_start: 0.8615 (pt0) cc_final: 0.8344 (pt0)
  outliers start: 15
  outliers final: 12
  residues processed: 84
  average time/residue: 0.4472
  time to fit residues: 39.8216
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  : 0.289 
-------------------------------------------------------------------------------
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 27 optimal weight:    8.9990
   chunk 72 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.3425 r_free = 0.3425 target = 0.124227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.099581 restraints weight = 9239.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 1.96
r_work: 0.2927 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2804 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.1729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6893  Z= 0.120
  Angle     :  0.478   6.912   9408  Z= 0.255
  Chirality :  0.041   0.129   1109
  Planarity :  0.003   0.028   1177
  Dihedral  :  9.120 163.815    992
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 14.13 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.33 (0.29), residues: 886
  helix:  1.93 (0.27), residues: 395
  sheet:  0.82 (0.41), residues: 175
  loop : -0.40 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 228 
 TYR   0.012   0.001   TYR R 132 
 PHE   0.011   0.001   PHE B 241 
 TRP   0.008   0.001   TRP B  99 
 HIS   0.004   0.001   HIS R 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 6891)
  covalent geometry    : angle       0.47684 ( 9404)
  SS BOND              : bond        0.00307 (    2)
  SS BOND              : angle       1.30993 (    4)
  hydrogen bonds       : bond        0.04599 (  352)
  hydrogen bonds       : angle       4.15552 ( 1023)

*********************** 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: 14
    poor density    : 77
  time to evaluate  : 0.270 
Fit side-chains
REVERT: B  175 GLN cc_start: 0.8614 (pt0) cc_final: 0.8361 (pt0)
REVERT: B  234 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.7753 (t80)
REVERT: R  228 ARG cc_start: 0.7910 (mtp85) cc_final: 0.7224 (mtt-85)
  outliers start: 14
  outliers final: 10
  residues processed: 84
  average time/residue: 0.4522
  time to fit residues: 40.3220
Evaluate side-chains
  85 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
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  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 53 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 78 optimal weight:    0.0060
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.6996

-------------------------------------------------------------------------------
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 = 0.3450 r_free = 0.3450 target = 0.126136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.101213 restraints weight = 9156.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 2.03
r_work: 0.2916 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2790 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6893  Z= 0.108
  Angle     :  0.469   6.945   9408  Z= 0.250
  Chirality :  0.040   0.128   1109
  Planarity :  0.003   0.028   1177
  Dihedral  :  9.071 163.345    992
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 1.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.59 %
    Favored  : 83.41 %
  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:  1.46 (0.29), residues: 886
  helix:  2.09 (0.27), residues: 389
  sheet:  0.80 (0.41), residues: 175
  loop : -0.30 (0.33), residues: 322

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 6891)
  covalent geometry    : angle       0.46878 ( 9404)
  SS BOND              : bond        0.00248 (    2)
  SS BOND              : angle       1.26077 (    4)
  hydrogen bonds       : bond        0.04232 (  352)
  hydrogen bonds       : angle       4.08923 ( 1023)

********************** 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
  91 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.151 
Fit side-chains
REVERT: B  175 GLN cc_start: 0.8644 (pt0) cc_final: 0.8387 (pt0)
REVERT: B  234 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.7726 (t80)
REVERT: R  228 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7378 (ttm110)
  outliers start: 13
  outliers final: 10
  residues processed: 84
  average time/residue: 0.4783
  time to fit residues: 42.4591
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  : 0.166 
-------------------------------------------------------------------------------
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  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 21 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 79 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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
A 239 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.123546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.098759 restraints weight = 9194.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 2.01
r_work: 0.2918 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6893  Z= 0.110
  Angle     :  0.470   7.012   9408  Z= 0.250
  Chirality :  0.040   0.129   1109
  Planarity :  0.003   0.028   1177
  Dihedral  :  8.986 162.853    992
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 1.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 14.59 %
    Favored  : 83.26 %
  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:  1.44 (0.29), residues: 886
  helix:  2.09 (0.27), residues: 389
  sheet:  0.77 (0.41), residues: 175
  loop : -0.32 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 228 
 TYR   0.011   0.001   TYR R 132 
 PHE   0.011   0.001   PHE B 241 
 TRP   0.008   0.001   TRP B  99 
 HIS   0.006   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 6891)
  covalent geometry    : angle       0.46913 ( 9404)
  SS BOND              : bond        0.00290 (    2)
  SS BOND              : angle       1.26148 (    4)
  hydrogen bonds       : bond        0.04273 (  352)
  hydrogen bonds       : angle       4.07676 ( 1023)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1904.69 seconds
wall clock time: 33 minutes 14.41 seconds (1994.41 seconds total)