Starting phenix.real_space_refine
on Fri Feb 14 11:46:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qau_18304/02_2025/8qau_18304.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qau_18304/02_2025/8qau_18304.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qau_18304/02_2025/8qau_18304.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qau_18304/02_2025/8qau_18304.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qau_18304/02_2025/8qau_18304.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qau_18304/02_2025/8qau_18304.cif"
  }
  resolution = 3.54
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 142 atoms to isotropic.
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: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      1      5.21       5
     S      59      5.16       5
     C    6370      2.51       5
     N    1749      2.21       5
     O    1953      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10137
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "C"
      Number of atoms: 3373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 431, 3373
          Classifications: {'peptide': 431}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 410}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3359
          Classifications: {'peptide': 427}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406}
    Chain: "A"
      Number of atoms: 1700
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1700
          Classifications: {'peptide': 253}
          Incomplete info: {'truncation_to_alanine': 124}
          Link IDs: {'PTRANS': 8, 'TRANS': 244}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 461
          Unresolved non-hydrogen angles: 585
          Unresolved non-hydrogen dihedrals: 380
          Unresolved non-hydrogen chiralities: 36
          Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 268
    Chain: "B"
      Number of atoms: 1440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1440
          Classifications: {'peptide': 207}
          Incomplete info: {'truncation_to_alanine': 73}
          Link IDs: {'PTRANS': 4, 'TRANS': 202}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 269
          Unresolved non-hydrogen angles: 336
          Unresolved non-hydrogen dihedrals: 215
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 168
    Chain: "E"
      Number of atoms: 142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 142
          Classifications: {'peptide': 29}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 1, 'TRANS': 27}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 73
          Unresolved non-hydrogen angles: 92
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "C"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 62
          Unusual residues: {'TA1': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.62, per 1000 atoms: 0.65
  Number of scatterers: 10137
  At special positions: 0
  Unit cell: (171.72, 101.76, 118.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      59     16.00
     P       5     15.00
     Mg      1     11.99
     O    1953      8.00
     N    1749      7.00
     C    6370      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.93
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2534

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 5 sheets defined
      62.6% alpha, 8.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'C' and resid 9 through 28
      removed outlier: 3.756A  pdb=" N   GLN C  15 " --> pdb=" O   GLN C  11 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 51
      removed outlier: 3.625A  pdb=" N   ASN C  50 " --> pdb=" O   ASP C  47 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   THR C  51 " --> pdb=" O   SER C  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 47 through 51'
    Processing helix  chain 'C' and resid 72 through 81
    Processing helix  chain 'C' and resid 102 through 108
    Processing helix  chain 'C' and resid 110 through 113
    Processing helix  chain 'C' and resid 114 through 129
      removed outlier: 3.790A  pdb=" N   GLN C 128 " --> pdb=" O   LYS C 124 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   CYS C 129 " --> pdb=" O   LEU C 125 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 161
      removed outlier: 4.336A  pdb=" N   THR C 150 " --> pdb=" O   GLY C 146 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 182 through 190
    Processing helix  chain 'C' and resid 190 through 196
      removed outlier: 3.947A  pdb=" N   GLU C 196 " --> pdb=" O   HIS C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 205 through 216
    Processing helix  chain 'C' and resid 223 through 240
      removed outlier: 3.979A  pdb=" N   LEU C 227 " --> pdb=" O   THR C 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 241 through 243
      No H-bonds generated for 'chain 'C' and resid 241 through 243'
    Processing helix  chain 'C' and resid 251 through 260
    Processing helix  chain 'C' and resid 277 through 284
    Processing helix  chain 'C' and resid 287 through 296
      removed outlier: 3.589A  pdb=" N   PHE C 296 " --> pdb=" O   THR C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 297 through 301
    Processing helix  chain 'C' and resid 306 through 310
    Processing helix  chain 'C' and resid 324 through 338
    Processing helix  chain 'C' and resid 384 through 400
      removed outlier: 3.675A  pdb=" N   TRP C 388 " --> pdb=" O   ILE C 384 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ARG C 390 " --> pdb=" O   GLU C 386 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU C 391 " --> pdb=" O   ALA C 387 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ASP C 396 " --> pdb=" O   ASP C 392 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   MET C 398 " --> pdb=" O   LYS C 394 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 410
    Processing helix  chain 'C' and resid 415 through 432
      removed outlier: 4.001A  pdb=" N   SER C 419 " --> pdb=" O   GLU C 415 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   LYS C 430 " --> pdb=" O   ALA C 426 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 10 through 28
    Processing helix  chain 'D' and resid 46 through 49
    Processing helix  chain 'D' and resid 69 through 78
      removed outlier: 4.627A  pdb=" N   MET D  73 " --> pdb=" O   GLU D  69 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   SER D  78 " --> pdb=" O   ASP D  74 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 81 through 85
      removed outlier: 3.637A  pdb=" N   ILE D  84 " --> pdb=" O   PHE D  81 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   PHE D  85 " --> pdb=" O   GLY D  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 81 through 85'
    Processing helix  chain 'D' and resid 86 through 90
    Processing helix  chain 'D' and resid 100 through 106
    Processing helix  chain 'D' and resid 109 through 126
      removed outlier: 4.230A  pdb=" N   ASP D 114 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   SER D 115 " --> pdb=" O   GLU D 111 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   VAL D 119 " --> pdb=" O   SER D 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 142 through 159
    Processing helix  chain 'D' and resid 180 through 195
      removed outlier: 3.536A  pdb=" N   ASN D 184 " --> pdb=" O   VAL D 180 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   HIS D 190 " --> pdb=" O   THR D 186 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLN D 191 " --> pdb=" O   LEU D 187 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLU D 194 " --> pdb=" O   HIS D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 204 through 214
    Processing helix  chain 'D' and resid 221 through 237
      removed outlier: 3.643A  pdb=" N   LEU D 225 " --> pdb=" O   THR D 221 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   THR D 237 " --> pdb=" O   MET D 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 237 through 242
      removed outlier: 3.823A  pdb=" N   ARG D 241 " --> pdb=" O   THR D 237 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 249 through 258
    Processing helix  chain 'D' and resid 285 through 294
      removed outlier: 3.739A  pdb=" N   PHE D 294 " --> pdb=" O   THR D 290 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 304 through 308
    Processing helix  chain 'D' and resid 322 through 337
      removed outlier: 3.670A  pdb=" N   VAL D 326 " --> pdb=" O   SER D 322 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 374 through 390
      removed outlier: 3.601A  pdb=" N   PHE D 378 " --> pdb=" O   ILE D 374 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   ILE D 381 " --> pdb=" O   LEU D 377 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 394 through 402
      removed outlier: 4.232A  pdb=" N   TYR D 398 " --> pdb=" O   PHE D 394 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 404 through 427
      removed outlier: 4.373A  pdb=" N   PHE D 408 " --> pdb=" O   ASP D 404 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   THR D 409 " --> pdb=" O   GLU D 405 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   TYR D 425 " --> pdb=" O   GLU D 421 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLN D 426 " --> pdb=" O   TYR D 422 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ASP D 427 " --> pdb=" O   GLN D 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 139
      removed outlier: 3.538A  pdb=" N   ASN A 139 " --> pdb=" O   TYR A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 145
    Processing helix  chain 'A' and resid 150 through 156
    Processing helix  chain 'A' and resid 158 through 172
    Processing helix  chain 'A' and resid 182 through 194
    Processing helix  chain 'A' and resid 198 through 202
    Processing helix  chain 'A' and resid 203 through 209
    Processing helix  chain 'A' and resid 214 through 255
      removed outlier: 5.001A  pdb=" N   GLY A 220 " --> pdb=" O   HIS A 216 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   LYS A 238 " --> pdb=" O   MET A 234 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ASP A 240 " --> pdb=" O   LEU A 236 " (cutoff:3.500A)
      removed outlier: 4.792A  pdb=" N   GLU A 250 " --> pdb=" O   GLN A 246 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   ILE A 251 " --> pdb=" O   ASN A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 292
      removed outlier: 3.933A  pdb=" N   LYS A 292 " --> pdb=" O   LYS A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 365
    Processing helix  chain 'B' and resid 12 through 24
      removed outlier: 3.855A  pdb=" N   LEU B  16 " --> pdb=" O   ASP B  12 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ASP B  24 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'B' and resid 37 through 53
      removed outlier: 4.320A  pdb=" N   MET B  53 " --> pdb=" O   ILE B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 70
      removed outlier: 3.754A  pdb=" N   LEU B  60 " --> pdb=" O   SER B  56 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   GLU B  67 " --> pdb=" O   SER B  63 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   THR B  68 " --> pdb=" O   SER B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 101
    Processing helix  chain 'B' and resid 107 through 113
      removed outlier: 3.774A  pdb=" N   LEU B 111 " --> pdb=" O   ASN B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 140
    Processing helix  chain 'B' and resid 140 through 169
      removed outlier: 3.577A  pdb=" N   ILE B 144 " --> pdb=" O   CYS B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 207
    Processing helix  chain 'E' and resid 257 through 267
    Processing sheet with id=AA1, first strand: chain 'C' and resid 92 through 93
      removed outlier: 8.036A  pdb=" N   ILE C  93 " --> pdb=" O   ALA C  65 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   PHE C  67 " --> pdb=" O   ILE C  93 " (cutoff:3.500A)
      removed outlier: 8.638A  pdb=" N   VAL C  66 " --> pdb=" O   CYS C   4 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   SER C   6 " --> pdb=" O   VAL C  66 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   VAL C  68 " --> pdb=" O   SER C   6 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   HIS C   8 " --> pdb=" O   VAL C  68 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   GLU C   3 " --> pdb=" O   GLY C 134 " (cutoff:3.500A)
      removed outlier: 8.397A  pdb=" N   SER C 136 " --> pdb=" O   GLU C   3 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ILE C   5 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 7.778A  pdb=" N   PHE C 138 " --> pdb=" O   ILE C   5 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ILE C   7 " --> pdb=" O   PHE C 138 " (cutoff:3.500A)
      removed outlier: 9.222A  pdb=" N   SER C 165 " --> pdb=" O   GLY C 131 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   GLN C 133 " --> pdb=" O   SER C 165 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   LEU C 167 " --> pdb=" O   GLN C 133 " (cutoff:3.500A)
      removed outlier: 5.884A  pdb=" N   PHE C 135 " --> pdb=" O   LEU C 167 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   PHE C 169 " --> pdb=" O   PHE C 135 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   VAL C 137 " --> pdb=" O   PHE C 169 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 55
    Processing sheet with id=AA3, first strand: chain 'C' and resid 269 through 273
    Processing sheet with id=AA4, first strand: chain 'D' and resid 91 through 92
      removed outlier: 7.974A  pdb=" N   VAL D  91 " --> pdb=" O   ALA D  63 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   LEU D  65 " --> pdb=" O   VAL D  91 " (cutoff:3.500A)
      removed outlier: 8.390A  pdb=" N   ILE D  64 " --> pdb=" O   ILE D   4 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   HIS D   6 " --> pdb=" O   ILE D  64 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   VAL D  66 " --> pdb=" O   HIS D   6 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   GLN D   8 " --> pdb=" O   VAL D  66 " (cutoff:3.500A)
      removed outlier: 5.686A  pdb=" N   GLU D   3 " --> pdb=" O   LEU D 130 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLY D 132 " --> pdb=" O   GLU D   3 " (cutoff:3.500A)
      removed outlier: 5.146A  pdb=" N   SER D 138 " --> pdb=" O   ALA D   9 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   GLN D 131 " --> pdb=" O   ILE D 163 " (cutoff:3.500A)
      removed outlier: 7.508A  pdb=" N   ASN D 165 " --> pdb=" O   GLN D 131 " (cutoff:3.500A)
      removed outlier: 5.509A  pdb=" N   PHE D 133 " --> pdb=" O   ASN D 165 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   PHE D 167 " --> pdb=" O   PHE D 133 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   LEU D 135 " --> pdb=" O   PHE D 167 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   VAL D 169 " --> pdb=" O   LEU D 135 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   HIS D 137 " --> pdb=" O   VAL D 169 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   MET D 164 " --> pdb=" O   GLU D 198 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   TYR D 200 " --> pdb=" O   MET D 164 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   THR D 166 " --> pdb=" O   TYR D 200 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   ILE D 202 " --> pdb=" O   THR D 166 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   SER D 168 " --> pdb=" O   ILE D 202 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   THR D 199 " --> pdb=" O   PHE D 266 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   CYS D 201 " --> pdb=" O   PRO D 268 " (cutoff:3.500A)
      removed outlier: 10.614A  pdb=" N   PHE D 270 " --> pdb=" O   CYS D 201 " (cutoff:3.500A)
      removed outlier: 14.092A  pdb=" N   ASP D 203 " --> pdb=" O   PHE D 270 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   PHE D 265 " --> pdb=" O   SER D 371 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   SER D 371 " --> pdb=" O   PHE D 265 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 51 through 54

    608 hydrogen bonds defined for protein.
    1779 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: 3.10

  Time building geometry restraints manager: 3.30 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1818
        1.32 -     1.44: 2651
        1.44 -     1.57: 5764
        1.57 -     1.69: 13
        1.69 -     1.81: 94
  Bond restraints: 10340
  Sorted by residual:
  bond pdb=" CG  PRO C  32 "
       pdb=" CD  PRO C  32 "
    ideal  model  delta    sigma   weight residual
    1.503  1.265  0.238 3.40e-02 8.65e+02 4.91e+01
  bond pdb=" N   PRO C  32 "
       pdb=" CD  PRO C  32 "
    ideal  model  delta    sigma   weight residual
    1.473  1.507 -0.034 1.40e-02 5.10e+03 6.02e+00
  bond pdb=" CB  PRO C  32 "
       pdb=" CG  PRO C  32 "
    ideal  model  delta    sigma   weight residual
    1.492  1.597 -0.105 5.00e-02 4.00e+02 4.40e+00
  bond pdb=" CG  GLU A 131 "
       pdb=" CD  GLU A 131 "
    ideal  model  delta    sigma   weight residual
    1.516  1.484  0.032 2.50e-02 1.60e+03 1.64e+00
  bond pdb=" CD  GLU A 131 "
       pdb=" OE1 GLU A 131 "
    ideal  model  delta    sigma   weight residual
    1.249  1.225  0.024 1.90e-02 2.77e+03 1.58e+00
  ... (remaining 10335 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.31: 13986
        3.31 -     6.62: 82
        6.62 -     9.92: 9
        9.92 -    13.23: 0
       13.23 -    16.54: 2
  Bond angle restraints: 14079
  Sorted by residual:
  angle pdb=" CA  PRO C  32 "
        pdb=" N   PRO C  32 "
        pdb=" CD  PRO C  32 "
      ideal   model   delta    sigma   weight residual
     112.00   95.46   16.54 1.40e+00 5.10e-01 1.40e+02
  angle pdb=" N   PRO C  32 "
        pdb=" CD  PRO C  32 "
        pdb=" CG  PRO C  32 "
      ideal   model   delta    sigma   weight residual
     103.20   89.05   14.15 1.50e+00 4.44e-01 8.89e+01
  angle pdb=" CA  PRO C  32 "
        pdb=" CB  PRO C  32 "
        pdb=" CG  PRO C  32 "
      ideal   model   delta    sigma   weight residual
     104.50   94.58    9.92 1.90e+00 2.77e-01 2.73e+01
  angle pdb=" CA  MET B 108 "
        pdb=" CB  MET B 108 "
        pdb=" CG  MET B 108 "
      ideal   model   delta    sigma   weight residual
     114.10  121.77   -7.67 2.00e+00 2.50e-01 1.47e+01
  angle pdb=" N   GLY C  10 "
        pdb=" CA  GLY C  10 "
        pdb=" C   GLY C  10 "
      ideal   model   delta    sigma   weight residual
     113.18  122.13   -8.95 2.37e+00 1.78e-01 1.43e+01
  ... (remaining 14074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.23: 6038
       32.23 -    64.46: 154
       64.46 -    96.70: 29
       96.70 -   128.93: 5
      128.93 -   161.16: 11
  Dihedral angle restraints: 6237
    sinusoidal: 2318
      harmonic: 3919
  Sorted by residual:
  dihedral pdb=" C5' GDP D 501 "
           pdb=" O5' GDP D 501 "
           pdb=" PA  GDP D 501 "
           pdb=" O3A GDP D 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.98   37.05  142.93     1      2.00e+01 2.50e-03 4.32e+01
  dihedral pdb=" CA  VAL C   9 "
           pdb=" C   VAL C   9 "
           pdb=" N   GLY C  10 "
           pdb=" CA  GLY C  10 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -149.55  -30.45     0      5.00e+00 4.00e-02 3.71e+01
  dihedral pdb=" C8  GTP C 501 "
           pdb=" C1' GTP C 501 "
           pdb=" N9  GTP C 501 "
           pdb=" O4' GTP C 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -10.71  115.31     1      2.00e+01 2.50e-03 3.43e+01
  ... (remaining 6234 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1293
       0.052 -    0.105: 255
       0.105 -    0.157: 36
       0.157 -    0.209: 3
       0.209 -    0.262: 1
  Chirality restraints: 1588
  Sorted by residual:
  chirality pdb=" C10 TA1 D 502 "
            pdb=" C02 TA1 D 502 "
            pdb=" C11 TA1 D 502 "
            pdb=" C18 TA1 D 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.54    2.28    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" C02 TA1 D 502 "
            pdb=" C01 TA1 D 502 "
            pdb=" C10 TA1 D 502 "
            pdb=" O02 TA1 D 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.56    2.75   -0.19 2.00e-01 2.50e+01 9.19e-01
  chirality pdb=" CA  ASN A 146 "
            pdb=" N   ASN A 146 "
            pdb=" C   ASN A 146 "
            pdb=" CB  ASN A 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.73e-01
  ... (remaining 1585 not shown)

  Planarity restraints: 1846
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C  31 "    0.092 5.00e-02 4.00e+02   1.25e-01 2.50e+01
        pdb=" N   PRO C  32 "   -0.215 5.00e-02 4.00e+02
        pdb=" CA  PRO C  32 "    0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO C  32 "    0.067 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B  76 "    0.009 2.00e-02 2.50e+03   1.92e-02 3.69e+00
        pdb=" CD  GLU B  76 "   -0.033 2.00e-02 2.50e+03
        pdb=" OE1 GLU B  76 "    0.012 2.00e-02 2.50e+03
        pdb=" OE2 GLU B  76 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B  50 "   -0.009 2.00e-02 2.50e+03   1.87e-02 3.51e+00
        pdb=" CD  GLU B  50 "    0.032 2.00e-02 2.50e+03
        pdb=" OE1 GLU B  50 "   -0.012 2.00e-02 2.50e+03
        pdb=" OE2 GLU B  50 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1843 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 95
        2.56 -     3.15: 8593
        3.15 -     3.73: 16539
        3.73 -     4.32: 21501
        4.32 -     4.90: 35889
  Nonbonded interactions: 82617
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP C  98 "
            pdb="MG    MG C 502 "
     model   vdw
     1.980 2.170
  nonbonded pdb=" O1G GTP C 501 "
            pdb="MG    MG C 502 "
     model   vdw
     2.061 2.170
  nonbonded pdb=" O3G GTP C 501 "
            pdb="MG    MG C 502 "
     model   vdw
     2.152 2.170
  nonbonded pdb=" OG  SER C 178 "
            pdb=" OE1 GLU C 183 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   ALA D  63 "
            pdb=" ND2 ASN D  89 "
     model   vdw
     2.238 3.120
  ... (remaining 82612 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:             1.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     25.860
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6386
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   0.238  10340  Z= 0.277
  Angle     :  0.690  16.538  14079  Z= 0.365
  Chirality :  0.042   0.262   1588
  Planarity :  0.005   0.125   1846
  Dihedral  : 17.836 161.161   3703
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.45 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.50 (0.23), residues: 1333
  helix:  1.34 (0.19), residues: 743
  sheet: -0.49 (0.47), residues: 123
  loop : -1.03 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 388 
 HIS   0.004   0.001   HIS C  88 
 PHE   0.019   0.001   PHE C  49 
 TYR   0.014   0.001   TYR C 282 
 ARG   0.011   0.000   ARG D 306 

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 285
  time to evaluate  : 1.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  154 MET cc_start: 0.5297 (mmm) cc_final: 0.5088 (mmm)
REVERT: C  346 TRP cc_start: 0.6579 (p-90) cc_final: 0.4146 (t60)
REVERT: C  352 LYS cc_start: 0.5687 (mmpt) cc_final: 0.5248 (mmtm)
REVERT: A  225 MET cc_start: 0.8826 (mmp) cc_final: 0.8580 (mmm)
REVERT: B  101 ILE cc_start: 0.6545 (pt) cc_final: 0.6278 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 285
  average time/residue: 0.2177
  time to fit residues: 86.9065
Evaluate side-chains
  178 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:   10.0000
   chunk 100 optimal weight:    8.9990
   chunk 55 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0980
   chunk 53 optimal weight:    5.9990
   chunk 103 optimal weight:   30.0000
   chunk 40 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 77 optimal weight:    7.9990
   chunk 119 optimal weight:   20.0000
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
C 206 ASN
** D   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 105 HIS
D 190 HIS
** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 396 HIS
D 414 ASN
** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 189 GLN
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 ASN
** B  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.106180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.076755 restraints weight = 36018.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.078824 restraints weight = 17230.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.080255 restraints weight = 10523.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10340  Z= 0.234
  Angle     :  0.682   8.150  14079  Z= 0.343
  Chirality :  0.043   0.194   1588
  Planarity :  0.004   0.042   1846
  Dihedral  : 15.217 142.303   1571
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.38 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.37 %
    Favored  : 84.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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:  0.90 (0.23), residues: 1333
  helix:  1.62 (0.19), residues: 752
  sheet: -0.57 (0.48), residues: 111
  loop : -0.75 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D  21 
 HIS   0.006   0.001   HIS C  88 
 PHE   0.019   0.002   PHE B  97 
 TYR   0.029   0.002   TYR B 112 
 ARG   0.006   0.001   ARG D 306 

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 194
  time to evaluate  : 1.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 MET cc_start: 0.9439 (tmm) cc_final: 0.9041 (tmm)
REVERT: C  141 PHE cc_start: 0.9107 (m-10) cc_final: 0.8766 (m-10)
REVERT: C  185 TYR cc_start: 0.9537 (m-80) cc_final: 0.9325 (m-80)
REVERT: C  346 TRP cc_start: 0.8717 (p-90) cc_final: 0.4689 (t60)
REVERT: C  358 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.9070 (tp30)
REVERT: D    1 MET cc_start: 0.8456 (mmm) cc_final: 0.8241 (mmm)
REVERT: D  180 VAL cc_start: 0.9275 (m) cc_final: 0.9047 (p)
REVERT: D  181 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7783 (mt-10)
REVERT: D  257 MET cc_start: 0.8810 (mmm) cc_final: 0.7907 (mmt)
REVERT: D  265 PHE cc_start: 0.9545 (m-80) cc_final: 0.9305 (m-10)
REVERT: D  376 GLU cc_start: 0.9418 (mm-30) cc_final: 0.8946 (mm-30)
REVERT: D  379 LYS cc_start: 0.8891 (ptpt) cc_final: 0.8397 (ptpt)
REVERT: A  177 TYR cc_start: 0.8082 (t80) cc_final: 0.7616 (t80)
REVERT: A  225 MET cc_start: 0.8704 (mmp) cc_final: 0.8146 (mtp)
  outliers start: 19
  outliers final: 11
  residues processed: 208
  average time/residue: 0.2118
  time to fit residues: 64.0592
Evaluate side-chains
  186 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 174
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  119 LEU
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  257 THR
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  316 CYS
Chi-restraints excluded: chain C residue  358 GLU
Chi-restraints excluded: chain C residue  363 VAL
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  354 CYS
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain B residue   39 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 106 optimal weight:   50.0000
   chunk 105 optimal weight:    9.9990
   chunk 94 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 124 optimal weight:   20.0000
   chunk 80 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   chunk 65 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** C  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 347 ASN
** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.106958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.077323 restraints weight = 36438.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.079429 restraints weight = 17552.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.080869 restraints weight = 10704.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10340  Z= 0.194
  Angle     :  0.632  10.317  14079  Z= 0.314
  Chirality :  0.042   0.244   1588
  Planarity :  0.004   0.044   1846
  Dihedral  : 13.509 139.593   1571
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.93 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 15.43 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.23), residues: 1333
  helix:  1.80 (0.19), residues: 756
  sheet: -0.49 (0.48), residues: 111
  loop : -0.65 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP D  21 
 HIS   0.004   0.001   HIS C  88 
 PHE   0.011   0.001   PHE C 267 
 TYR   0.019   0.001   TYR C 172 
 ARG   0.004   0.000   ARG D 306 

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 187
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 MET cc_start: 0.9492 (tmm) cc_final: 0.9025 (tmm)
REVERT: C   77 GLU cc_start: 0.8829 (tp30) cc_final: 0.8593 (tp30)
REVERT: C  141 PHE cc_start: 0.9066 (m-10) cc_final: 0.8733 (m-10)
REVERT: C  346 TRP cc_start: 0.8689 (p-90) cc_final: 0.4789 (t-100)
REVERT: C  377 MET cc_start: 0.8309 (tmm) cc_final: 0.7788 (tmm)
REVERT: C  413 MET cc_start: 0.8630 (tpp) cc_final: 0.8000 (tpp)
REVERT: C  417 GLU cc_start: 0.8628 (tt0) cc_final: 0.8377 (tt0)
REVERT: C  425 MET cc_start: 0.9536 (mmm) cc_final: 0.9149 (tpp)
REVERT: C  429 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8686 (mm-30)
REVERT: D    1 MET cc_start: 0.8382 (mmm) cc_final: 0.8083 (mmm)
REVERT: D   74 ASP cc_start: 0.9245 (m-30) cc_final: 0.8973 (m-30)
REVERT: D  180 VAL cc_start: 0.9312 (m) cc_final: 0.9090 (p)
REVERT: D  181 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7755 (mt-10)
REVERT: D  257 MET cc_start: 0.8761 (mmm) cc_final: 0.7905 (mmt)
REVERT: D  265 PHE cc_start: 0.9508 (m-80) cc_final: 0.9281 (m-10)
REVERT: A  177 TYR cc_start: 0.8328 (t80) cc_final: 0.7914 (t80)
  outliers start: 19
  outliers final: 9
  residues processed: 202
  average time/residue: 0.2022
  time to fit residues: 59.3747
Evaluate side-chains
  179 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 170
  time to evaluate  : 1.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  119 LEU
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  257 THR
Chi-restraints excluded: chain C residue  363 VAL
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  354 CYS
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain B residue   39 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 83 optimal weight:    7.9990
   chunk 85 optimal weight:    0.3980
   chunk 106 optimal weight:   50.0000
   chunk 43 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0470
   overall best weight:    1.0882

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

Flipped N/Q/H residues before XYZ refinement:
C 309 HIS
** D   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 337 ASN
** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.106050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.076685 restraints weight = 36567.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.078762 restraints weight = 17578.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.080177 restraints weight = 10736.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.3262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10340  Z= 0.193
  Angle     :  0.607   8.361  14079  Z= 0.307
  Chirality :  0.043   0.458   1588
  Planarity :  0.004   0.044   1846
  Dihedral  :  9.295 139.303   1571
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.00 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 16.46 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.23), residues: 1333
  helix:  1.95 (0.19), residues: 758
  sheet: -0.55 (0.46), residues: 116
  loop : -0.61 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP D  21 
 HIS   0.004   0.001   HIS C 309 
 PHE   0.018   0.001   PHE A 153 
 TYR   0.022   0.001   TYR C 172 
 ARG   0.005   0.000   ARG B 118 

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 188
  time to evaluate  : 1.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 MET cc_start: 0.9486 (tmm) cc_final: 0.9053 (tmm)
REVERT: C   77 GLU cc_start: 0.8774 (tp30) cc_final: 0.8572 (tp30)
REVERT: C  141 PHE cc_start: 0.8920 (m-10) cc_final: 0.8631 (m-10)
REVERT: C  346 TRP cc_start: 0.8808 (p-90) cc_final: 0.4762 (t-100)
REVERT: C  377 MET cc_start: 0.8412 (tmm) cc_final: 0.7850 (tmm)
REVERT: C  413 MET cc_start: 0.8533 (tpp) cc_final: 0.7908 (tpp)
REVERT: C  417 GLU cc_start: 0.8643 (tt0) cc_final: 0.8392 (tt0)
REVERT: C  425 MET cc_start: 0.9535 (mmm) cc_final: 0.9016 (tpp)
REVERT: C  429 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8672 (mm-30)
REVERT: D    1 MET cc_start: 0.8419 (mmm) cc_final: 0.8109 (mmm)
REVERT: D   74 ASP cc_start: 0.9242 (m-30) cc_final: 0.8959 (m-30)
REVERT: D  147 MET cc_start: 0.9559 (tpp) cc_final: 0.9155 (mmm)
REVERT: D  180 VAL cc_start: 0.9384 (m) cc_final: 0.9087 (p)
REVERT: D  181 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7849 (mt-10)
REVERT: D  257 MET cc_start: 0.8766 (mmm) cc_final: 0.7662 (mmt)
REVERT: D  293 MET cc_start: 0.8692 (mmt) cc_final: 0.8441 (tpt)
REVERT: D  375 GLN cc_start: 0.9406 (pm20) cc_final: 0.9194 (pm20)
REVERT: D  376 GLU cc_start: 0.9300 (mm-30) cc_final: 0.8966 (mm-30)
REVERT: D  379 LYS cc_start: 0.8817 (ptpt) cc_final: 0.8252 (ptpt)
REVERT: A  177 TYR cc_start: 0.8395 (t80) cc_final: 0.8052 (t80)
REVERT: A  185 ASN cc_start: 0.9474 (m-40) cc_final: 0.8956 (p0)
  outliers start: 27
  outliers final: 14
  residues processed: 206
  average time/residue: 0.2223
  time to fit residues: 64.9568
Evaluate side-chains
  181 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 167
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  119 LEU
Chi-restraints excluded: chain C residue  121 ARG
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  257 THR
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  363 VAL
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  432 TYR
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  285 THR
Chi-restraints excluded: chain D residue  354 CYS
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   50 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 103 optimal weight:   40.0000
   chunk 51 optimal weight:    7.9990
   chunk 45 optimal weight:    0.8980
   chunk 1 optimal weight:    6.9990
   chunk 77 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 43 optimal weight:    7.9990
   chunk 23 optimal weight:   10.0000
   chunk 128 optimal weight:    7.9990
   chunk 18 optimal weight:    0.4980
   overall best weight:    1.8182

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

Flipped N/Q/H residues before XYZ refinement:
** D   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.104452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.075452 restraints weight = 36799.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.077489 restraints weight = 17937.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.078874 restraints weight = 11116.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.3601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10340  Z= 0.229
  Angle     :  0.620   7.554  14079  Z= 0.315
  Chirality :  0.043   0.262   1588
  Planarity :  0.004   0.046   1846
  Dihedral  :  8.837 141.801   1571
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.15 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.52 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.24), residues: 1333
  helix:  2.06 (0.19), residues: 758
  sheet: -0.47 (0.47), residues: 116
  loop : -0.50 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP D  21 
 HIS   0.004   0.001   HIS A 223 
 PHE   0.015   0.001   PHE A 162 
 TYR   0.029   0.002   TYR C 210 
 ARG   0.004   0.000   ARG A 114 

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 177
  time to evaluate  : 1.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 MET cc_start: 0.9534 (tmm) cc_final: 0.9075 (tmm)
REVERT: C   77 GLU cc_start: 0.8800 (tp30) cc_final: 0.8600 (tp30)
REVERT: C  116 ASP cc_start: 0.9029 (p0) cc_final: 0.8681 (p0)
REVERT: C  120 ASP cc_start: 0.8777 (m-30) cc_final: 0.8088 (m-30)
REVERT: C  141 PHE cc_start: 0.8922 (m-10) cc_final: 0.8621 (m-10)
REVERT: C  217 LEU cc_start: 0.9488 (tp) cc_final: 0.9283 (tt)
REVERT: C  377 MET cc_start: 0.8394 (tmm) cc_final: 0.8045 (tmm)
REVERT: C  413 MET cc_start: 0.8553 (tpp) cc_final: 0.7881 (tpp)
REVERT: C  417 GLU cc_start: 0.8768 (tt0) cc_final: 0.8484 (tt0)
REVERT: C  425 MET cc_start: 0.9562 (mmm) cc_final: 0.9101 (tpp)
REVERT: C  429 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8605 (mm-30)
REVERT: D    1 MET cc_start: 0.8467 (mmm) cc_final: 0.8193 (mmm)
REVERT: D   74 ASP cc_start: 0.9262 (m-30) cc_final: 0.9014 (m-30)
REVERT: D  147 MET cc_start: 0.9568 (tpp) cc_final: 0.9131 (mmm)
REVERT: D  180 VAL cc_start: 0.9381 (m) cc_final: 0.9059 (p)
REVERT: D  181 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7883 (mt-10)
REVERT: D  375 GLN cc_start: 0.9423 (pm20) cc_final: 0.9177 (pm20)
REVERT: D  376 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8956 (mm-30)
REVERT: D  379 LYS cc_start: 0.8805 (ptpt) cc_final: 0.8297 (ptpt)
REVERT: D  407 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8982 (mp0)
REVERT: A  177 TYR cc_start: 0.8440 (t80) cc_final: 0.8101 (t80)
REVERT: B   58 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8528 (mp0)
  outliers start: 25
  outliers final: 17
  residues processed: 195
  average time/residue: 0.2040
  time to fit residues: 58.3012
Evaluate side-chains
  184 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 167
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  119 LEU
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  257 THR
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  363 VAL
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain D residue  188 SER
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  354 CYS
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  188 TYR
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   39 ASP
Chi-restraints excluded: chain B residue   50 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 85 optimal weight:    8.9990
   chunk 69 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 73 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 116 optimal weight:   10.0000
   chunk 33 optimal weight:    0.2980
   chunk 8 optimal weight:    1.9990
   chunk 128 optimal weight:    6.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** D   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 159 GLN
A 214 ASN
B  86 ASN
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.104269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.074848 restraints weight = 37350.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.076919 restraints weight = 18117.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.078295 restraints weight = 11140.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.3834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10340  Z= 0.202
  Angle     :  0.622  10.817  14079  Z= 0.315
  Chirality :  0.043   0.267   1588
  Planarity :  0.004   0.046   1846
  Dihedral  :  8.790 142.033   1571
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.15 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 19.44 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.24), residues: 1333
  helix:  2.11 (0.19), residues: 756
  sheet: -0.44 (0.47), residues: 116
  loop : -0.49 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP D  21 
 HIS   0.004   0.001   HIS C  88 
 PHE   0.025   0.001   PHE A 153 
 TYR   0.023   0.001   TYR C 210 
 ARG   0.004   0.000   ARG C 123 

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 176
  time to evaluate  : 1.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 MET cc_start: 0.9563 (tmm) cc_final: 0.9053 (tmm)
REVERT: C  116 ASP cc_start: 0.8986 (p0) cc_final: 0.8634 (p0)
REVERT: C  120 ASP cc_start: 0.8741 (m-30) cc_final: 0.8038 (m-30)
REVERT: C  154 MET cc_start: 0.9179 (tpp) cc_final: 0.8841 (mmm)
REVERT: C  172 TYR cc_start: 0.8864 (t80) cc_final: 0.8484 (t80)
REVERT: C  377 MET cc_start: 0.8398 (tmm) cc_final: 0.8033 (tmm)
REVERT: C  388 TRP cc_start: 0.9312 (m100) cc_final: 0.8786 (m100)
REVERT: C  392 ASP cc_start: 0.8880 (m-30) cc_final: 0.8536 (m-30)
REVERT: C  413 MET cc_start: 0.8421 (tpp) cc_final: 0.7736 (tpp)
REVERT: C  417 GLU cc_start: 0.8746 (tt0) cc_final: 0.8435 (tt0)
REVERT: D    1 MET cc_start: 0.8432 (mmm) cc_final: 0.8147 (mmm)
REVERT: D   74 ASP cc_start: 0.9211 (m-30) cc_final: 0.8948 (m-30)
REVERT: D  147 MET cc_start: 0.9578 (tpp) cc_final: 0.9147 (mmm)
REVERT: D  180 VAL cc_start: 0.9376 (m) cc_final: 0.9053 (p)
REVERT: D  181 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7915 (mt-10)
REVERT: D  257 MET cc_start: 0.9087 (mmm) cc_final: 0.8295 (mmt)
REVERT: D  375 GLN cc_start: 0.9373 (pm20) cc_final: 0.9117 (pm20)
REVERT: D  376 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8932 (mm-30)
REVERT: D  379 LYS cc_start: 0.8859 (ptpt) cc_final: 0.8325 (ptpt)
REVERT: D  407 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8959 (mp0)
REVERT: A  134 ASP cc_start: 0.9133 (m-30) cc_final: 0.8679 (p0)
REVERT: A  177 TYR cc_start: 0.8545 (t80) cc_final: 0.8256 (t80)
REVERT: B   58 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8552 (mp0)
  outliers start: 24
  outliers final: 18
  residues processed: 192
  average time/residue: 0.1944
  time to fit residues: 54.9354
Evaluate side-chains
  183 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 165
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  119 LEU
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  363 VAL
Chi-restraints excluded: chain C residue  391 LEU
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  432 TYR
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  354 CYS
Chi-restraints excluded: chain D residue  363 MET
Chi-restraints excluded: chain D residue  374 ILE
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  188 TYR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   39 ASP
Chi-restraints excluded: chain B residue   50 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   chunk 118 optimal weight:   10.0000
   chunk 89 optimal weight:    8.9990
   chunk 109 optimal weight:   30.0000
   chunk 55 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 76 optimal weight:    3.9990
   chunk 85 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:    3.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 372 GLN
** D   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 298 ASN
** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.102400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.072849 restraints weight = 38550.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.074702 restraints weight = 18741.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.076034 restraints weight = 11886.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.4196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  10340  Z= 0.399
  Angle     :  0.760  15.725  14079  Z= 0.384
  Chirality :  0.048   0.310   1588
  Planarity :  0.004   0.045   1846
  Dihedral  :  9.032 150.947   1571
  Min Nonbonded Distance : 1.834

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.90 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 21.09 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.23), residues: 1333
  helix:  1.94 (0.19), residues: 759
  sheet: -0.24 (0.47), residues: 110
  loop : -0.67 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.003   TRP D  21 
 HIS   0.007   0.002   HIS C 139 
 PHE   0.022   0.002   PHE D 167 
 TYR   0.032   0.002   TYR C 210 
 ARG   0.006   0.001   ARG A 114 

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 162
  time to evaluate  : 1.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 MET cc_start: 0.9603 (tmm) cc_final: 0.9245 (tmm)
REVERT: C  116 ASP cc_start: 0.8986 (p0) cc_final: 0.8630 (p0)
REVERT: C  120 ASP cc_start: 0.8705 (m-30) cc_final: 0.8067 (m-30)
REVERT: C  154 MET cc_start: 0.9094 (tpp) cc_final: 0.8786 (mmm)
REVERT: C  377 MET cc_start: 0.8340 (tmm) cc_final: 0.7964 (tmm)
REVERT: C  413 MET cc_start: 0.8408 (tpp) cc_final: 0.7703 (tpp)
REVERT: C  417 GLU cc_start: 0.8740 (tt0) cc_final: 0.8402 (tt0)
REVERT: D    3 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7245 (mp0)
REVERT: D   74 ASP cc_start: 0.9188 (m-30) cc_final: 0.8924 (m-30)
REVERT: D  147 MET cc_start: 0.9597 (tpp) cc_final: 0.8986 (mpp)
REVERT: D  181 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8154 (mt-10)
REVERT: D  184 ASN cc_start: 0.8923 (m-40) cc_final: 0.8715 (m-40)
REVERT: D  233 MET cc_start: 0.9098 (mtt) cc_final: 0.8776 (mtt)
REVERT: D  257 MET cc_start: 0.8978 (mmm) cc_final: 0.8331 (mmt)
REVERT: D  297 LYS cc_start: 0.9131 (tmmt) cc_final: 0.8929 (tttt)
REVERT: A  177 TYR cc_start: 0.8412 (t80) cc_final: 0.8067 (t80)
REVERT: B   58 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8798 (mp0)
  outliers start: 26
  outliers final: 17
  residues processed: 181
  average time/residue: 0.2053
  time to fit residues: 54.3360
Evaluate side-chains
  168 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 150
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  238 ILE
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  363 VAL
Chi-restraints excluded: chain C residue  391 LEU
Chi-restraints excluded: chain C residue  393 HIS
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  432 TYR
Chi-restraints excluded: chain D residue    3 GLU
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  285 THR
Chi-restraints excluded: chain D residue  363 MET
Chi-restraints excluded: chain D residue  374 ILE
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   39 ASP
Chi-restraints excluded: chain B residue   50 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 78 optimal weight:    5.9990
   chunk 120 optimal weight:    7.9990
   chunk 60 optimal weight:    0.0870
   chunk 77 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 109 optimal weight:   30.0000
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.105002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.075609 restraints weight = 37051.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.077655 restraints weight = 17880.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.079076 restraints weight = 11025.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.4288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10340  Z= 0.192
  Angle     :  0.665   9.088  14079  Z= 0.336
  Chirality :  0.044   0.330   1588
  Planarity :  0.004   0.042   1846
  Dihedral  :  8.636 146.709   1571
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.15 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 22.12 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.24), residues: 1333
  helix:  2.09 (0.19), residues: 756
  sheet: -0.28 (0.47), residues: 116
  loop : -0.43 (0.31), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP D  21 
 HIS   0.005   0.001   HIS C  88 
 PHE   0.027   0.001   PHE A 153 
 TYR   0.024   0.001   TYR B  40 
 ARG   0.005   0.001   ARG C 123 

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 173
  time to evaluate  : 1.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 MET cc_start: 0.9562 (tmm) cc_final: 0.9157 (tmm)
REVERT: C  116 ASP cc_start: 0.8979 (p0) cc_final: 0.8627 (p0)
REVERT: C  120 ASP cc_start: 0.8742 (m-30) cc_final: 0.8027 (m-30)
REVERT: C  141 PHE cc_start: 0.8760 (m-80) cc_final: 0.8534 (m-10)
REVERT: C  154 MET cc_start: 0.9174 (tpp) cc_final: 0.8902 (mmm)
REVERT: C  172 TYR cc_start: 0.8795 (t80) cc_final: 0.8590 (t80)
REVERT: C  377 MET cc_start: 0.8393 (tmm) cc_final: 0.8005 (tmm)
REVERT: C  388 TRP cc_start: 0.9403 (m100) cc_final: 0.9166 (m100)
REVERT: C  413 MET cc_start: 0.8352 (tpp) cc_final: 0.7596 (tpp)
REVERT: C  417 GLU cc_start: 0.8741 (tt0) cc_final: 0.8401 (tt0)
REVERT: D   74 ASP cc_start: 0.9198 (m-30) cc_final: 0.8945 (m-30)
REVERT: D  147 MET cc_start: 0.9553 (tpp) cc_final: 0.9128 (mmm)
REVERT: D  180 VAL cc_start: 0.9391 (m) cc_final: 0.9082 (p)
REVERT: D  181 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7843 (mt-10)
REVERT: D  233 MET cc_start: 0.9075 (mtt) cc_final: 0.8618 (mmt)
REVERT: D  257 MET cc_start: 0.9063 (mmm) cc_final: 0.8249 (mmt)
REVERT: D  407 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8963 (mp0)
REVERT: A  134 ASP cc_start: 0.9129 (m-30) cc_final: 0.8648 (p0)
REVERT: A  177 TYR cc_start: 0.8391 (t80) cc_final: 0.8093 (t80)
  outliers start: 20
  outliers final: 15
  residues processed: 185
  average time/residue: 0.2014
  time to fit residues: 54.7543
Evaluate side-chains
  180 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 165
  time to evaluate  : 1.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  363 VAL
Chi-restraints excluded: chain C residue  391 LEU
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  432 TYR
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  363 MET
Chi-restraints excluded: chain D residue  374 ILE
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   39 ASP
Chi-restraints excluded: chain B residue   50 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 124 optimal weight:   50.0000
   chunk 76 optimal weight:    3.9990
   chunk 98 optimal weight:    9.9990
   chunk 114 optimal weight:    9.9990
   chunk 130 optimal weight:   20.0000
   chunk 119 optimal weight:    1.9990
   chunk 126 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 72 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.101221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.071912 restraints weight = 38588.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.073926 restraints weight = 18797.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.075290 restraints weight = 11641.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.4593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  10340  Z= 0.371
  Angle     :  0.754  11.469  14079  Z= 0.382
  Chirality :  0.046   0.268   1588
  Planarity :  0.004   0.040   1846
  Dihedral  :  9.031 153.820   1571
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.68 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 22.43 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.24), residues: 1333
  helix:  1.98 (0.19), residues: 753
  sheet: -0.23 (0.46), residues: 123
  loop : -0.59 (0.31), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.003   TRP D  21 
 HIS   0.007   0.002   HIS C 139 
 PHE   0.020   0.002   PHE D 167 
 TYR   0.032   0.002   TYR A 196 
 ARG   0.006   0.001   ARG D 380 

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 1.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 MET cc_start: 0.9562 (tmm) cc_final: 0.9195 (tmm)
REVERT: C  116 ASP cc_start: 0.9032 (p0) cc_final: 0.8701 (p0)
REVERT: C  120 ASP cc_start: 0.8770 (m-30) cc_final: 0.8123 (m-30)
REVERT: C  172 TYR cc_start: 0.8952 (t80) cc_final: 0.7936 (t80)
REVERT: C  203 MET cc_start: 0.8654 (mmm) cc_final: 0.8330 (mmm)
REVERT: C  210 TYR cc_start: 0.9112 (m-80) cc_final: 0.8888 (m-80)
REVERT: C  377 MET cc_start: 0.8362 (tmm) cc_final: 0.7955 (tmm)
REVERT: C  413 MET cc_start: 0.8433 (tpp) cc_final: 0.7658 (tpp)
REVERT: C  417 GLU cc_start: 0.8793 (tt0) cc_final: 0.8457 (tt0)
REVERT: D    3 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7293 (mp0)
REVERT: D   74 ASP cc_start: 0.9148 (m-30) cc_final: 0.8833 (m-30)
REVERT: D  180 VAL cc_start: 0.9400 (m) cc_final: 0.9093 (p)
REVERT: D  181 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8129 (mt-10)
REVERT: D  233 MET cc_start: 0.9198 (mtt) cc_final: 0.8914 (mtt)
REVERT: D  257 MET cc_start: 0.9028 (mmm) cc_final: 0.8326 (mmt)
REVERT: D  288 GLU cc_start: 0.9061 (tp30) cc_final: 0.8615 (pt0)
REVERT: D  297 LYS cc_start: 0.9121 (tmmt) cc_final: 0.8888 (tttt)
REVERT: D  376 GLU cc_start: 0.9326 (mm-30) cc_final: 0.9002 (pp20)
REVERT: D  408 PHE cc_start: 0.9484 (m-80) cc_final: 0.9270 (m-80)
REVERT: A  177 TYR cc_start: 0.8523 (t80) cc_final: 0.8137 (t80)
  outliers start: 20
  outliers final: 16
  residues processed: 169
  average time/residue: 0.2022
  time to fit residues: 49.8925
Evaluate side-chains
  167 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  238 ILE
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  363 VAL
Chi-restraints excluded: chain C residue  391 LEU
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  432 TYR
Chi-restraints excluded: chain D residue    3 GLU
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  354 CYS
Chi-restraints excluded: chain D residue  363 MET
Chi-restraints excluded: chain D residue  374 ILE
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  160 LYS
Chi-restraints excluded: chain B residue   39 ASP
Chi-restraints excluded: chain B residue   50 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 103 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 109 optimal weight:   40.0000
   chunk 43 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.103099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.074220 restraints weight = 37466.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.076306 restraints weight = 18052.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.077689 restraints weight = 11025.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.4667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10340  Z= 0.210
  Angle     :  0.704  10.294  14079  Z= 0.354
  Chirality :  0.044   0.268   1588
  Planarity :  0.004   0.044   1846
  Dihedral  :  8.781 150.153   1571
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.38 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 23.56 %
    Favored  : 74.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.24), residues: 1333
  helix:  2.01 (0.19), residues: 761
  sheet:  0.09 (0.50), residues: 107
  loop : -0.51 (0.30), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.003   TRP D  21 
 HIS   0.004   0.001   HIS A 223 
 PHE   0.014   0.001   PHE C 351 
 TYR   0.027   0.002   TYR B  40 
 ARG   0.005   0.000   ARG C 121 

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 168
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 MET cc_start: 0.9535 (tmm) cc_final: 0.9171 (tmm)
REVERT: C  116 ASP cc_start: 0.8969 (p0) cc_final: 0.8623 (p0)
REVERT: C  120 ASP cc_start: 0.8751 (m-30) cc_final: 0.8067 (m-30)
REVERT: C  141 PHE cc_start: 0.8861 (m-80) cc_final: 0.8652 (m-10)
REVERT: C  172 TYR cc_start: 0.8684 (t80) cc_final: 0.7500 (t80)
REVERT: C  203 MET cc_start: 0.8721 (mmm) cc_final: 0.8258 (mmm)
REVERT: C  377 MET cc_start: 0.8407 (tmm) cc_final: 0.8003 (tmm)
REVERT: C  413 MET cc_start: 0.8330 (tpp) cc_final: 0.7592 (tpp)
REVERT: C  417 GLU cc_start: 0.8724 (tt0) cc_final: 0.8368 (tt0)
REVERT: D   74 ASP cc_start: 0.9192 (m-30) cc_final: 0.8928 (m-30)
REVERT: D  147 MET cc_start: 0.9541 (tpp) cc_final: 0.9113 (mmm)
REVERT: D  163 ILE cc_start: 0.9076 (tp) cc_final: 0.8864 (tp)
REVERT: D  180 VAL cc_start: 0.9391 (m) cc_final: 0.9098 (p)
REVERT: D  233 MET cc_start: 0.9095 (mtt) cc_final: 0.8845 (mtt)
REVERT: D  257 MET cc_start: 0.9070 (mmm) cc_final: 0.8259 (mmt)
REVERT: D  288 GLU cc_start: 0.8954 (tp30) cc_final: 0.8611 (pt0)
REVERT: D  407 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8963 (mp0)
REVERT: D  414 ASN cc_start: 0.9383 (m-40) cc_final: 0.9086 (m-40)
REVERT: A  134 ASP cc_start: 0.9118 (m-30) cc_final: 0.8622 (p0)
REVERT: A  136 LEU cc_start: 0.8770 (tp) cc_final: 0.8507 (tp)
REVERT: A  177 TYR cc_start: 0.8414 (t80) cc_final: 0.8036 (t80)
  outliers start: 15
  outliers final: 13
  residues processed: 177
  average time/residue: 0.2122
  time to fit residues: 55.2114
Evaluate side-chains
  172 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 159
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  269 LEU
Chi-restraints excluded: chain C residue  363 VAL
Chi-restraints excluded: chain C residue  391 LEU
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain C residue  432 TYR
Chi-restraints excluded: chain D residue  192 LEU
Chi-restraints excluded: chain D residue  250 LEU
Chi-restraints excluded: chain D residue  363 MET
Chi-restraints excluded: chain D residue  374 ILE
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain B residue   39 ASP
Chi-restraints excluded: chain B residue   50 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 5 optimal weight:    0.1980
   chunk 98 optimal weight:   20.0000
   chunk 50 optimal weight:    9.9990
   chunk 48 optimal weight:    0.5980
   chunk 3 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 107 optimal weight:   20.0000
   chunk 103 optimal weight:   20.0000
   chunk 29 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 89 optimal weight:    7.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.103339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.074649 restraints weight = 37013.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.076719 restraints weight = 17994.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.078102 restraints weight = 11034.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.4813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10340  Z= 0.221
  Angle     :  0.691  10.364  14079  Z= 0.349
  Chirality :  0.044   0.272   1588
  Planarity :  0.004   0.044   1846
  Dihedral  :  8.583 150.270   1571
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.30 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 23.87 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.24), residues: 1333
  helix:  2.07 (0.19), residues: 755
  sheet:  0.20 (0.48), residues: 114
  loop : -0.41 (0.31), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.003   TRP D  21 
 HIS   0.003   0.001   HIS A 223 
 PHE   0.013   0.001   PHE D 167 
 TYR   0.026   0.002   TYR B  40 
 ARG   0.006   0.000   ARG C 121 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3537.56 seconds
wall clock time: 64 minutes 10.97 seconds (3850.97 seconds total)