Starting phenix.real_space_refine
on Tue Sep 24 05:10:53 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gga_40000/09_2024/8gga_40000.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gga_40000/09_2024/8gga_40000.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gga_40000/09_2024/8gga_40000.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gga_40000/09_2024/8gga_40000.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gga_40000/09_2024/8gga_40000.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gga_40000/09_2024/8gga_40000.cif"
  }
  resolution = 3.5
  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=   0.021
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      41      5.16       5
     C    4438      2.51       5
     N    1224      2.21       5
     O    1289      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 6995
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2318
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 326, 2318
          Classifications: {'peptide': 326}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 102}
          Link IDs: {'PTRANS': 9, 'TRANS': 316}
          Chain breaks: 3
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 392
          Unresolved non-hydrogen angles: 488
          Unresolved non-hydrogen dihedrals: 319
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 10}
          Unresolved non-hydrogen planarities: 255
    Chain: "B"
      Number of atoms: 2454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2454
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 138
          Unresolved non-hydrogen angles: 170
          Unresolved non-hydrogen dihedrals: 106
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 113
    Chain: "G"
      Number of atoms: 352
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 352
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 78
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "R"
      Number of atoms: 1824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 269, 1824
          Classifications: {'peptide': 269}
          Incomplete info: {'truncation_to_alanine': 97}
          Link IDs: {'PTRANS': 7, 'TRANS': 261}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 345
          Unresolved non-hydrogen angles: 443
          Unresolved non-hydrogen dihedrals: 285
          Unresolved non-hydrogen chiralities: 39
          Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 3, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 173
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 9.01, per 1000 atoms: 1.29
  Number of scatterers: 6995
  At special positions: 0
  Unit cell: (83.2992, 135.361, 102.389, 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      41     16.00
     P       3     15.00
     O    1289      8.00
     N    1224      7.00
     C    4438      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.61
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1874

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 8 sheets defined
      48.5% alpha, 14.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 3.871A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LYS A  17 " --> pdb=" O   ARG A  13 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLN A  19 " --> pdb=" O   GLU A  15 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLN A  31 " --> pdb=" O   GLU A  27 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 63
      removed outlier: 3.642A  pdb=" N   VAL A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 111
      removed outlier: 3.637A  pdb=" N   GLU A 101 " --> pdb=" O   ASN A  97 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ILE A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   SER A 111 " --> pdb=" O   VAL A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 152
      removed outlier: 3.540A  pdb=" N   GLU A 148 " --> pdb=" O   PRO A 144 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ALA A 152 " --> pdb=" O   GLU A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 155
      No H-bonds generated for 'chain 'A' and resid 153 through 155'
    Processing helix  chain 'A' and resid 156 through 165
      removed outlier: 3.572A  pdb=" N   CYS A 162 " --> pdb=" O   GLY A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 180
    Processing helix  chain 'A' and resid 232 through 237
      removed outlier: 3.589A  pdb=" N   ILE A 235 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.747A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.976A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.602A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   SER A 349 " --> pdb=" O   PHE A 345 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 390
    Processing helix  chain 'B' and resid 5 through 25
      removed outlier: 3.743A  pdb=" N   GLN B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ARG B  19 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.542A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 132
      removed outlier: 3.987A  pdb=" N   ASN B 132 " --> pdb=" O   ARG B 129 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 24
      removed outlier: 3.693A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLU G  22 " --> pdb=" O   GLN G  18 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.634A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.750A  pdb=" N   GLY R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   VAL R  52 " --> pdb=" O   VAL R  48 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU R  53 " --> pdb=" O   PHE R  49 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 97
      removed outlier: 4.265A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.515A  pdb=" N   ILE R 121 " --> pdb=" O   VAL R 117 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLU R 122 " --> pdb=" O   THR R 118 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   CYS R 125 " --> pdb=" O   ILE R 121 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL R 126 " --> pdb=" O   GLU R 122 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   PHE R 133 " --> pdb=" O   VAL R 129 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA R 134 " --> pdb=" O   ASP R 130 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
      removed outlier: 3.526A  pdb=" N   LEU R 145 " --> pdb=" O   TYR R 141 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 172
      removed outlier: 3.658A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   SER R 165 " --> pdb=" O   SER R 161 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 181 through 187
    Processing helix  chain 'R' and resid 196 through 237
      removed outlier: 3.547A  pdb=" N   ALA R 200 " --> pdb=" O   ASN R 196 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   VAL R 210 " --> pdb=" O   VAL R 206 " (cutoff:3.500A)
      Proline residue:  R 211  - end of helix
      removed outlier: 3.540A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 3.945A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.931A  pdb=" N   VAL R 292 " --> pdb=" O   PRO R 288 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ASN R 293 " --> pdb=" O   PHE R 289 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   VAL R 295 " --> pdb=" O   ILE R 291 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 326
      removed outlier: 3.690A  pdb=" N   TYR R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213
      removed outlier: 6.237A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.626A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 9.203A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.725A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.688A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.703A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.756A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.853A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 3.956A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.730A  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 103
      removed outlier: 7.096A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.073A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER B 160 " --> pdb=" O   CYS B 148 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.756A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.007A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.821A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.705A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)

    353 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: 2.37

  Time building geometry restraints manager: 2.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2299
        1.34 -     1.46: 1053
        1.46 -     1.57: 3719
        1.57 -     1.69: 5
        1.69 -     1.81: 56
  Bond restraints: 7132
  Sorted by residual:
  bond pdb=" N   THR A 204 "
       pdb=" CA  THR A 204 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.041 1.24e-02 6.50e+03 1.08e+01
  bond pdb=" N   VAL A 224 "
       pdb=" CA  VAL A 224 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.19e-02 7.06e+03 8.65e+00
  bond pdb=" N   ILE A 207 "
       pdb=" CA  ILE A 207 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.036 1.25e-02 6.40e+03 8.39e+00
  bond pdb=" N   SER A 205 "
       pdb=" CA  SER A 205 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.20e-02 6.94e+03 8.27e+00
  bond pdb=" N   PHE R 133 "
       pdb=" CA  PHE R 133 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.034 1.21e-02 6.83e+03 8.13e+00
  ... (remaining 7127 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 9603
        2.37 -     4.74: 136
        4.74 -     7.10: 13
        7.10 -     9.47: 8
        9.47 -    11.84: 2
  Bond angle restraints: 9762
  Sorted by residual:
  angle pdb=" C   ASP A 223 "
        pdb=" CA  ASP A 223 "
        pdb=" CB  ASP A 223 "
      ideal   model   delta    sigma   weight residual
     110.62  101.55    9.07 1.51e+00 4.39e-01 3.60e+01
  angle pdb=" N   ARG A 231 "
        pdb=" CA  ARG A 231 "
        pdb=" C   ARG A 231 "
      ideal   model   delta    sigma   weight residual
     113.43  107.03    6.40 1.26e+00 6.30e-01 2.58e+01
  angle pdb=" CA  LEU A 203 "
        pdb=" C   LEU A 203 "
        pdb=" O   LEU A 203 "
      ideal   model   delta    sigma   weight residual
     121.28  116.55    4.73 1.18e+00 7.18e-01 1.61e+01
  angle pdb=" CA  GLY A 206 "
        pdb=" C   GLY A 206 "
        pdb=" O   GLY A 206 "
      ideal   model   delta    sigma   weight residual
     121.58  118.00    3.58 9.00e-01 1.23e+00 1.58e+01
  angle pdb=" PA  GTP A 401 "
        pdb=" O3A GTP A 401 "
        pdb=" PB  GTP A 401 "
      ideal   model   delta    sigma   weight residual
     120.50  132.34  -11.84 3.00e+00 1.11e-01 1.56e+01
  ... (remaining 9757 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.13: 4009
       28.13 -    56.25: 127
       56.25 -    84.38: 8
       84.38 -   112.51: 2
      112.51 -   140.64: 3
  Dihedral angle restraints: 4149
    sinusoidal: 1269
      harmonic: 2880
  Sorted by residual:
  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
     303.79  163.16  140.64     1      2.00e+01 2.50e-03 4.26e+01
  dihedral pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" O3A GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -158.46 -132.27     1      2.00e+01 2.50e-03 4.01e+01
  dihedral pdb=" O2G GTP A 401 "
           pdb=" O3B GTP A 401 "
           pdb=" PG  GTP A 401 "
           pdb=" PB  GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.30  -65.39 -117.31     1      2.00e+01 2.50e-03 3.50e+01
  ... (remaining 4146 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 892
       0.047 -    0.094: 203
       0.094 -    0.140: 65
       0.140 -    0.187: 7
       0.187 -    0.234: 2
  Chirality restraints: 1169
  Sorted by residual:
  chirality pdb=" CA  ASP A 223 "
            pdb=" N   ASP A 223 "
            pdb=" C   ASP A 223 "
            pdb=" CB  ASP A 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CA  VAL A 202 "
            pdb=" N   VAL A 202 "
            pdb=" C   VAL A 202 "
            pdb=" CB  VAL A 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 9.27e-01
  chirality pdb=" CA  ARG A 201 "
            pdb=" N   ARG A 201 "
            pdb=" C   ARG A 201 "
            pdb=" CB  ARG A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.00e-01
  ... (remaining 1166 not shown)

  Planarity restraints: 1247
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG R 131 "    0.019 2.00e-02 2.50e+03   3.82e-02 1.46e+01
        pdb=" C   ARG R 131 "   -0.066 2.00e-02 2.50e+03
        pdb=" O   ARG R 131 "    0.025 2.00e-02 2.50e+03
        pdb=" N   TYR R 132 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 198 "    0.010 2.00e-02 2.50e+03   1.94e-02 3.76e+00
        pdb=" C   LEU A 198 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   LEU A 198 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ARG A 199 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 167 "   -0.030 5.00e-02 4.00e+02   4.60e-02 3.38e+00
        pdb=" N   PRO R 168 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO R 168 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO R 168 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1244 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 942
        2.75 -     3.29: 6582
        3.29 -     3.83: 10783
        3.83 -     4.36: 11692
        4.36 -     4.90: 21588
  Nonbonded interactions: 51587
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" ND2 ASN R  51 "
            pdb=" O   ALA R  76 "
     model   vdw
     2.355 3.120
  nonbonded pdb=" ND2 ASN A  23 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.359 3.120
  nonbonded pdb=" OD2 ASP B 212 "
            pdb=" NH2 ARG B 219 "
     model   vdw
     2.372 3.120
  ... (remaining 51582 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 group one per residue
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:             8.380
  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:          0.340
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     26.900
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:3.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
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   0.055   7132  Z= 0.245
  Angle     :  0.667  11.840   9762  Z= 0.378
  Chirality :  0.045   0.234   1169
  Planarity :  0.005   0.073   1247
  Dihedral  : 14.504 140.637   2275
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  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: -0.34 (0.27), residues: 968
  helix:  1.15 (0.26), residues: 416
  sheet: -1.14 (0.44), residues: 163
  loop : -1.29 (0.28), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 109 
 HIS   0.010   0.001   HIS R 296 
 PHE   0.010   0.001   PHE B 235 
 TYR   0.012   0.001   TYR R 132 
 ARG   0.004   0.000   ARG A 356 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.819 
Fit side-chains
REVERT: A  177 TYR cc_start: 0.7961 (t80) cc_final: 0.7056 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1689
  time to fit residues: 19.6884
Evaluate side-chains
  64 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 72 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 45 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A  19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7132  Z= 0.198
  Angle     :  0.504   6.070   9762  Z= 0.276
  Chirality :  0.042   0.143   1169
  Planarity :  0.003   0.035   1247
  Dihedral  :  8.296 125.799   1073
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.62 %
    Favored  : 89.55 %
  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:  0.04 (0.27), residues: 968
  helix:  1.58 (0.26), residues: 430
  sheet: -1.03 (0.44), residues: 155
  loop : -1.31 (0.29), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 339 
 HIS   0.012   0.001   HIS R 296 
 PHE   0.013   0.002   PHE R 223 
 TYR   0.011   0.001   TYR R 308 
 ARG   0.003   0.000   ARG A 333 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.804 
Fit side-chains
REVERT: A  177 TYR cc_start: 0.7906 (t80) cc_final: 0.7439 (t80)
  outliers start: 5
  outliers final: 4
  residues processed: 76
  average time/residue: 0.1475
  time to fit residues: 16.5138
Evaluate side-chains
  72 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  117 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 27 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 94 optimal weight:    0.7980
   chunk 77 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 70 optimal weight:    8.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   7132  Z= 0.170
  Angle     :  0.464   6.349   9762  Z= 0.252
  Chirality :  0.042   0.142   1169
  Planarity :  0.003   0.035   1247
  Dihedral  :  7.342 124.572   1073
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 13.76 %
    Favored  : 85.57 %
  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:  0.32 (0.28), residues: 968
  helix:  1.87 (0.26), residues: 429
  sheet: -0.77 (0.42), residues: 170
  loop : -1.30 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 339 
 HIS   0.008   0.001   HIS R 296 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.010   0.001   TYR R 308 
 ARG   0.002   0.000   ARG A 356 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.774 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.8607 (m-80) cc_final: 0.8239 (m-80)
REVERT: B   75 GLN cc_start: 0.8246 (mt0) cc_final: 0.7921 (mt0)
  outliers start: 4
  outliers final: 2
  residues processed: 74
  average time/residue: 0.1473
  time to fit residues: 15.9798
Evaluate side-chains
  70 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain R residue  115 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    4.9990
   chunk 65 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0010
   chunk 9 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0570
   chunk 92 optimal weight:    0.5980
   chunk 83 optimal weight:    0.0970
   chunk 25 optimal weight:    0.9980
   chunk 77 optimal weight:    0.5980
   overall best weight:    0.2702

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   7132  Z= 0.107
  Angle     :  0.428   6.287   9762  Z= 0.229
  Chirality :  0.040   0.134   1169
  Planarity :  0.003   0.031   1247
  Dihedral  :  6.721 125.151   1073
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 13.93 %
    Favored  : 84.58 %
  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:  0.51 (0.28), residues: 968
  helix:  2.07 (0.26), residues: 429
  sheet: -0.57 (0.43), residues: 159
  loop : -1.31 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 109 
 HIS   0.007   0.001   HIS R 296 
 PHE   0.011   0.001   PHE R 282 
 TYR   0.014   0.001   TYR R 174 
 ARG   0.001   0.000   ARG A 356 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.767 
Fit side-chains
  outliers start: 9
  outliers final: 4
  residues processed: 75
  average time/residue: 0.1430
  time to fit residues: 15.9121
Evaluate side-chains
  71 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  195 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 47 optimal weight:    0.3980
   chunk 83 optimal weight:    7.9990
   chunk 23 optimal weight:    6.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   7132  Z= 0.171
  Angle     :  0.460   6.609   9762  Z= 0.247
  Chirality :  0.041   0.144   1169
  Planarity :  0.003   0.032   1247
  Dihedral  :  6.706 125.379   1073
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 15.59 %
    Favored  : 82.92 %
  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:  0.61 (0.28), residues: 968
  helix:  2.15 (0.26), residues: 429
  sheet: -0.50 (0.41), residues: 173
  loop : -1.28 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 296 
 PHE   0.012   0.001   PHE B 235 
 TYR   0.014   0.001   TYR A 177 
 ARG   0.002   0.000   ARG A 280 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.772 
Fit side-chains
  outliers start: 9
  outliers final: 5
  residues processed: 74
  average time/residue: 0.1470
  time to fit residues: 16.1792
Evaluate side-chains
  73 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  117 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    0.0670
   chunk 18 optimal weight:    0.4980
   chunk 54 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   chunk 77 optimal weight:    0.6980
   chunk 43 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0270
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.4576

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   7132  Z= 0.120
  Angle     :  0.430   6.624   9762  Z= 0.230
  Chirality :  0.040   0.135   1169
  Planarity :  0.003   0.031   1247
  Dihedral  :  6.643 126.822   1073
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 15.75 %
    Favored  : 82.75 %
  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:  0.76 (0.28), residues: 968
  helix:  2.28 (0.26), residues: 423
  sheet: -0.44 (0.41), residues: 174
  loop : -1.14 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 296 
 PHE   0.009   0.001   PHE B 199 
 TYR   0.009   0.001   TYR R 174 
 ARG   0.002   0.000   ARG A 356 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.767 
Fit side-chains
  outliers start: 9
  outliers final: 5
  residues processed: 77
  average time/residue: 0.1401
  time to fit residues: 16.1677
Evaluate side-chains
  77 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  195 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 52 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 92 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7132  Z= 0.199
  Angle     :  0.478   6.677   9762  Z= 0.258
  Chirality :  0.042   0.144   1169
  Planarity :  0.003   0.033   1247
  Dihedral  :  6.705 123.134   1073
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 16.58 %
    Favored  : 81.92 %
  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:  0.67 (0.28), residues: 968
  helix:  2.23 (0.26), residues: 424
  sheet: -0.43 (0.41), residues: 174
  loop : -1.26 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 296 
 PHE   0.014   0.001   PHE B 235 
 TYR   0.016   0.001   TYR A 177 
 ARG   0.002   0.000   ARG A 280 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.714 
Fit side-chains
  outliers start: 9
  outliers final: 6
  residues processed: 74
  average time/residue: 0.1386
  time to fit residues: 15.1818
Evaluate side-chains
  75 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  282 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 18 optimal weight:    0.3980
   chunk 17 optimal weight:    1.9990
   chunk 58 optimal weight:    0.2980
   chunk 63 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 8 optimal weight:   20.0000
   chunk 72 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 88 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  18 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7132  Z= 0.147
  Angle     :  0.448   6.853   9762  Z= 0.240
  Chirality :  0.041   0.135   1169
  Planarity :  0.003   0.033   1247
  Dihedral  :  6.645 124.687   1073
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 17.41 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.79 (0.28), residues: 968
  helix:  2.30 (0.26), residues: 424
  sheet: -0.36 (0.42), residues: 173
  loop : -1.17 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 296 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.010   0.001   TYR R 308 
 ARG   0.001   0.000   ARG A 280 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.917 
Fit side-chains
  outliers start: 8
  outliers final: 7
  residues processed: 73
  average time/residue: 0.1589
  time to fit residues: 17.2026
Evaluate side-chains
  76 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 ARG
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  282 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 37 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 81 optimal weight:    9.9990
   chunk 85 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  18 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   7132  Z= 0.167
  Angle     :  0.458   6.662   9762  Z= 0.245
  Chirality :  0.041   0.140   1169
  Planarity :  0.003   0.033   1247
  Dihedral  :  6.619 122.196   1073
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 17.58 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.78 (0.28), residues: 968
  helix:  2.30 (0.26), residues: 424
  sheet: -0.36 (0.42), residues: 173
  loop : -1.19 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 296 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.018   0.001   TYR A 177 
 ARG   0.002   0.000   ARG A 280 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.828 
Fit side-chains
  outliers start: 8
  outliers final: 5
  residues processed: 73
  average time/residue: 0.1448
  time to fit residues: 15.8825
Evaluate side-chains
  73 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  282 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 63 optimal weight:    0.0770
   chunk 95 optimal weight:    3.9990
   chunk 88 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   chunk 58 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 60 optimal weight:    0.7980
   chunk 81 optimal weight:    9.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   7132  Z= 0.136
  Angle     :  0.446   6.650   9762  Z= 0.238
  Chirality :  0.041   0.136   1169
  Planarity :  0.003   0.032   1247
  Dihedral  :  6.553 122.400   1073
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 18.57 %
    Favored  : 80.60 %
  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:  0.86 (0.28), residues: 968
  helix:  2.35 (0.26), residues: 424
  sheet: -0.29 (0.42), residues: 173
  loop : -1.15 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R 296 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.009   0.001   TYR R 308 
 ARG   0.001   0.000   ARG A 280 

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.797 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 72
  average time/residue: 0.1419
  time to fit residues: 15.3466
Evaluate side-chains
  71 residues out of total 855 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  115 LEU
Chi-restraints excluded: chain R residue  282 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 70 optimal weight:    7.9990
   chunk 11 optimal weight:    0.4980
   chunk 21 optimal weight:    5.9990
   chunk 76 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 78 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 66 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    2.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.143031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.105359 restraints weight = 10421.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.107756 restraints weight = 7214.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.109210 restraints weight = 5728.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7132  Z= 0.361
  Angle     :  0.574   6.721   9762  Z= 0.310
  Chirality :  0.045   0.151   1169
  Planarity :  0.004   0.034   1247
  Dihedral  :  6.924 117.815   1073
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 18.08 %
    Favored  : 80.60 %
  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:  0.41 (0.28), residues: 968
  helix:  2.00 (0.26), residues: 427
  sheet: -0.65 (0.42), residues: 169
  loop : -1.35 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 339 
 HIS   0.006   0.001   HIS R 296 
 PHE   0.020   0.002   PHE B 199 
 TYR   0.018   0.002   TYR A 177 
 ARG   0.003   0.000   ARG A 280 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1594.16 seconds
wall clock time: 29 minutes 29.47 seconds (1769.47 seconds total)