Starting phenix.real_space_refine
on Sat May 24 20:28:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pzv_18046/05_2025/8pzv_18046.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pzv_18046/05_2025/8pzv_18046.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pzv_18046/05_2025/8pzv_18046.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pzv_18046/05_2025/8pzv_18046.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pzv_18046/05_2025/8pzv_18046.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pzv_18046/05_2025/8pzv_18046.cif"
  }
  resolution = 2.9
  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
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
     Mg      1      5.21       5
     S      45      5.16       5
     C    8357      2.51       5
     N    2290      2.21       5
     O    2609      1.98       5
     H   12738      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 26040
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 12115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 785, 12115
          Classifications: {'peptide': 785}
          Link IDs: {'PTRANS': 29, 'TRANS': 755}
    Chain: "B"
      Number of atoms: 5375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 369, 5375
          Classifications: {'peptide': 369}
          Link IDs: {'PTRANS': 11, 'TRANS': 357}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "C"
      Number of atoms: 804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 804
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 3485
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 3485
          Classifications: {'peptide': 219}
          Link IDs: {'PTRANS': 12, 'TRANS': 206}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "E"
      Number of atoms: 1291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 1291
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 5, 'TRANS': 78}
    Chain: "F"
      Number of atoms: 2828
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 2828
          Classifications: {'peptide': 175}
          Link IDs: {'PTRANS': 2, 'TRANS': 172}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
    Chain: "I"
      Number of atoms: 139
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 139
          Classifications: {'peptide': 7}
          Modifications used: {'COO': 1, 'NH2NOTPRO': 1}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'UX8:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1, 'water': 2}
          Link IDs: {None: 2}
  Time building chain proxies: 12.16, per 1000 atoms: 0.47
  Number of scatterers: 26040
  At special positions: 0
  Unit cell: (111.93, 133.77, 123.76, 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      45     16.00
     Mg      1     11.99
     O    2609      8.00
     N    2290      7.00
     C    8357      6.00
     H   12738      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 690 " - pdb=" SG  CYS A 700 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 7.03
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3122

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 18 sheets defined
      27.9% alpha, 28.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 46
    Processing helix  chain 'A' and resid 55 through 69
    Processing helix  chain 'A' and resid 106 through 116
      removed outlier: 3.729A  pdb=" N   LEU A 110 " --> pdb=" O   LYS A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 145
    Processing helix  chain 'A' and resid 189 through 195
    Processing helix  chain 'A' and resid 215 through 232
    Processing helix  chain 'A' and resid 280 through 288
    Processing helix  chain 'A' and resid 297 through 314
    Processing helix  chain 'A' and resid 361 through 367
      removed outlier: 3.678A  pdb=" N   LEU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 4.105A  pdb=" N   GLY A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 452
      No H-bonds generated for 'chain 'A' and resid 450 through 452'
    Processing helix  chain 'A' and resid 497 through 500
    Processing helix  chain 'A' and resid 542 through 552
    Processing helix  chain 'A' and resid 647 through 651
    Processing helix  chain 'A' and resid 691 through 695
    Processing helix  chain 'C' and resid 33 through 39
      removed outlier: 3.838A  pdb=" N   GLU C  39 " --> pdb=" O   SER C  36 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 45
    Processing helix  chain 'D' and resid 47 through 62
    Processing helix  chain 'D' and resid 67 through 82
      removed outlier: 3.782A  pdb=" N   VAL D  71 " --> pdb=" O   TYR D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 104 through 121
    Processing helix  chain 'D' and resid 137 through 154
    Processing helix  chain 'D' and resid 159 through 189
    Processing helix  chain 'D' and resid 190 through 205
    Processing helix  chain 'D' and resid 208 through 225
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 227 through 241
      removed outlier: 3.848A  pdb=" N   LYS D 233 " --> pdb=" O   ALA D 229 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 60
    Processing helix  chain 'F' and resid 39 through 45
    Processing helix  chain 'F' and resid 62 through 87
      removed outlier: 4.691A  pdb=" N   HIS F  68 " --> pdb=" O   ALA F  64 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   GLN F  69 " --> pdb=" O   THR F  65 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 92 through 107
      removed outlier: 3.524A  pdb=" N   LEU F  96 " --> pdb=" O   SER F  92 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ASN F 107 " --> pdb=" O   ILE F 103 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 110 through 122
      removed outlier: 4.027A  pdb=" N   TYR F 120 " --> pdb=" O   SER F 116 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 124 through 148
      removed outlier: 3.584A  pdb=" N   ARG F 148 " --> pdb=" O   ASN F 144 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 155 through 164
    Processing helix  chain 'F' and resid 395 through 420
      removed outlier: 3.655A  pdb=" N   ARG F 399 " --> pdb=" O   ASP F 395 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   MET F 400 " --> pdb=" O   ARG F 396 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ALA F 411 " --> pdb=" O   SER F 407 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30
      removed outlier: 6.243A  pdb=" N   HIS A  30 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   VAL A  88 " --> pdb=" O   HIS A  30 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   THR A  83 " --> pdb=" O   ASP A  80 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASP A  80 " --> pdb=" O   THR A  83 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100
      removed outlier: 4.213A  pdb=" N   ILE A  94 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   LEU A 165 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   SER A  96 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   LEU A 167 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   THR A  98 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   PHE A 169 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   SER A 100 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183
      removed outlier: 5.681A  pdb=" N   ILE A 254 " --> pdb=" O   ILE A 177 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLN A 179 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   GLY A 253 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   LEU A 247 " --> pdb=" O   GLY A 253 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   TYR A 255 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   VAL A 245 " --> pdb=" O   TYR A 255 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   THR A 257 " --> pdb=" O   THR A 243 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   THR A 243 " --> pdb=" O   THR A 257 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   ASN A 259 " --> pdb=" O   ASP A 241 " (cutoff:3.500A)
      removed outlier: 8.231A  pdb=" N   SER B 193 " --> pdb=" O   THR A 243 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   VAL A 245 " --> pdb=" O   SER B 193 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295
      removed outlier: 3.808A  pdb=" N   GLU A 294 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   LEU A 268 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   LEU A 337 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   GLY A 270 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   VAL A 339 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   GLU A 272 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   VAL A 341 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   SER A 274 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   ALA A 343 " --> pdb=" O   SER A 274 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   ASN A 276 " --> pdb=" O   ALA A 343 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355
      removed outlier: 4.256A  pdb=" N   VAL A 349 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   VAL A 414 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   LYS A 351 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   TYR A 416 " --> pdb=" O   LYS A 351 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ARG A 353 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   VAL A 418 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      removed outlier: 5.790A  pdb=" N   GLU A 355 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   GLU A 420 " --> pdb=" O   GLU A 355 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   THR A 397 " --> pdb=" O   LYS A 419 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'I' and resid 2 through 5
      removed outlier: 6.414A  pdb=" N   MET A 768 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 4.897A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   TYR A 454 " --> pdb=" O   TRP A 449 " (cutoff:3.500A)
      removed outlier: 5.514A  pdb=" N   VAL A 456 " --> pdb=" O   ASP A 447 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   ASP A 447 " --> pdb=" O   VAL A 456 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   ILE A 458 " --> pdb=" O   GLN A 445 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   GLN A 445 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)
      removed outlier: 7.120A  pdb=" N   GLY A 460 " --> pdb=" O   GLY A 443 " (cutoff:3.500A)
      removed outlier: 5.209A  pdb=" N   GLY A 443 " --> pdb=" O   GLY A 460 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   LYS A 462 " --> pdb=" O   GLN A 441 " (cutoff:3.500A)
      removed outlier: 5.595A  pdb=" N   GLN A 441 " --> pdb=" O   LYS A 462 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 45 through 51
      removed outlier: 6.270A  pdb=" N   THR B  46 " --> pdb=" O   THR B 391 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   THR B 391 " --> pdb=" O   THR B  46 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   TRP B  48 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 75
      removed outlier: 6.531A  pdb=" N   VAL B  81 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   SER B  94 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ALA B  83 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 101
      removed outlier: 3.683A  pdb=" N   GLU B  99 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   GLU B 107 " --> pdb=" O   GLU B  99 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASP B 101 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   SER B 105 " --> pdb=" O   ASP B 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 111 through 117
      removed outlier: 5.542A  pdb=" N   GLY B 114 " --> pdb=" O   GLY B 125 " (cutoff:3.500A)
      removed outlier: 4.954A  pdb=" N   GLY B 125 " --> pdb=" O   GLY B 114 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLN B 130 " --> pdb=" O   SER B 126 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   ASN B 135 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   VAL B 141 " --> pdb=" O   ASN B 135 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158
      removed outlier: 6.164A  pdb=" N   ASN B 175 " --> pdb=" O   VAL B 181 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL B 181 " --> pdb=" O   ASN B 175 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 202
      removed outlier: 5.959A  pdb=" N   VAL B 216 " --> pdb=" O   GLN B 229 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   GLN B 229 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ALA B 218 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254
      removed outlier: 6.404A  pdb=" N   ASP B 271 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   ILE B 277 " --> pdb=" O   ASP B 271 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292
      removed outlier: 6.200A  pdb=" N   THR B 309 " --> pdb=" O   THR B 315 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   THR B 315 " --> pdb=" O   THR B 309 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 332
      removed outlier: 6.068A  pdb=" N   ASN B 350 " --> pdb=" O   PHE B 356 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   PHE B 356 " --> pdb=" O   ASN B 350 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 34
      removed outlier: 3.813A  pdb=" N   MET E  64 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 34
    Processing sheet with id=AB9, first strand: chain 'F' and resid 35 through 38

    627 hydrogen bonds defined for protein.
    1773 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: 9.76

  Time building geometry restraints manager: 8.29 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 12730
        1.03 -     1.23: 19
        1.23 -     1.42: 5809
        1.42 -     1.61: 7661
        1.61 -     1.81: 88
  Bond restraints: 26307
  Sorted by residual:
  bond pdb=" CB  UX8 I   3 "
       pdb=" HB2 UX8 I   3 "
    ideal  model  delta    sigma   weight residual
    0.970  1.244 -0.274 2.00e-02 2.50e+03 1.88e+02
  bond pdb=" CZ3 UX8 I   3 "
       pdb=" HZ3 UX8 I   3 "
    ideal  model  delta    sigma   weight residual
    0.930  1.130 -0.200 2.00e-02 2.50e+03 9.98e+01
  bond pdb=" CA  UX8 I   3 "
       pdb=" C   UX8 I   3 "
    ideal  model  delta    sigma   weight residual
    1.525  1.323  0.202 2.10e-02 2.27e+03 9.21e+01
  bond pdb=" CE3 UX8 I   3 "
       pdb=" HE3 UX8 I   3 "
    ideal  model  delta    sigma   weight residual
    0.930  1.118 -0.188 2.00e-02 2.50e+03 8.80e+01
  bond pdb=" CA  UX8 I   3 "
       pdb=" CB  UX8 I   3 "
    ideal  model  delta    sigma   weight residual
    1.530  1.713 -0.183 2.00e-02 2.50e+03 8.40e+01
  ... (remaining 26302 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.03: 47249
        7.03 -    14.06: 9
       14.06 -    21.09: 1
       21.09 -    28.12: 2
       28.12 -    35.15: 3
  Bond angle restraints: 47264
  Sorted by residual:
  angle pdb=" CA  UX8 I   3 "
        pdb=" C   UX8 I   3 "
        pdb=" O   UX8 I   3 "
      ideal   model   delta    sigma   weight residual
     120.80  142.44  -21.64 1.70e+00 3.46e-01 1.62e+02
  angle pdb=" C   GLN B 234 "
        pdb=" CA  GLN B 234 "
        pdb=" HA  GLN B 234 "
      ideal   model   delta    sigma   weight residual
     109.00   73.85   35.15 3.00e+00 1.11e-01 1.37e+02
  angle pdb=" CB  GLN B 234 "
        pdb=" CA  GLN B 234 "
        pdb=" HA  GLN B 234 "
      ideal   model   delta    sigma   weight residual
     109.00   73.87   35.13 3.00e+00 1.11e-01 1.37e+02
  angle pdb=" N   GLN B 234 "
        pdb=" CA  GLN B 234 "
        pdb=" HA  GLN B 234 "
      ideal   model   delta    sigma   weight residual
     110.00   78.28   31.72 3.00e+00 1.11e-01 1.12e+02
  angle pdb=" H1  TRP I   1 "
        pdb=" N   TRP I   1 "
        pdb=" H2  TRP I   1 "
      ideal   model   delta    sigma   weight residual
     109.47   87.81   21.66 3.00e+00 1.11e-01 5.21e+01
  ... (remaining 47259 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 11289
       17.62 -    35.25: 870
       35.25 -    52.87: 217
       52.87 -    70.50: 63
       70.50 -    88.12: 20
  Dihedral angle restraints: 12459
    sinusoidal: 6734
      harmonic: 5725
  Sorted by residual:
  dihedral pdb=" CB  CYS A 690 "
           pdb=" SG  CYS A 690 "
           pdb=" SG  CYS A 700 "
           pdb=" CB  CYS A 700 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -138.08   52.08     1      1.00e+01 1.00e-02 3.70e+01
  dihedral pdb=" CA  THR A 571 "
           pdb=" C   THR A 571 "
           pdb=" N   PHE A 572 "
           pdb=" CA  PHE A 572 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.59   20.41     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CA  GLN F  55 "
           pdb=" C   GLN F  55 "
           pdb=" N   ALA F  56 "
           pdb=" CA  ALA F  56 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.72  -20.28     0      5.00e+00 4.00e-02 1.65e+01
  ... (remaining 12456 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 1855
       0.083 -    0.167: 159
       0.167 -    0.250: 0
       0.250 -    0.333: 0
       0.333 -    0.417: 2
  Chirality restraints: 2016
  Sorted by residual:
  chirality pdb=" CB  UX8 I   3 "
            pdb=" CA  UX8 I   3 "
            pdb=" CG  UX8 I   3 "
            pdb=" O9  UX8 I   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.38   -2.80    0.42 2.00e-01 2.50e+01 4.34e+00
  chirality pdb=" CA  GLN B 234 "
            pdb=" N   GLN B 234 "
            pdb=" C   GLN B 234 "
            pdb=" CB  GLN B 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.91e+00
  chirality pdb=" CA  UX8 I   3 "
            pdb=" N   UX8 I   3 "
            pdb=" C   UX8 I   3 "
            pdb=" CB  UX8 I   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.77e-01
  ... (remaining 2013 not shown)

  Planarity restraints: 4031
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 546 "    0.023 2.00e-02 2.50e+03   1.45e-02 8.37e+00
        pdb=" CG  TRP A 546 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 546 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 546 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 546 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 546 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 546 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 546 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 546 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 546 "    0.004 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 546 "    0.009 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 546 "    0.002 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 546 "   -0.003 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 546 "    0.000 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 546 "    0.001 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 546 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 107 "   -0.029 5.00e-02 4.00e+02   4.47e-02 3.20e+00
        pdb=" N   PRO B 108 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 108 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 108 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C  45 "   -0.027 5.00e-02 4.00e+02   4.13e-02 2.74e+00
        pdb=" N   PRO C  46 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO C  46 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C  46 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 4028 not shown)

  Histogram of nonbonded interaction distances:
        1.48 -     2.11: 724
        2.11 -     2.73: 47351
        2.73 -     3.35: 78911
        3.35 -     3.98: 103787
        3.98 -     4.60: 161334
  Nonbonded interactions: 392107
  Sorted by model distance:
  nonbonded pdb=" H   HIS C  51 "
            pdb=" OD1 ASN D 241 "
     model   vdw
     1.481 2.450
  nonbonded pdb=" H   LEU B 194 "
            pdb=" OD2 ASP B 246 "
     model   vdw
     1.481 2.450
  nonbonded pdb=" O   HIS A 677 "
            pdb=" H   THR A 692 "
     model   vdw
     1.508 2.450
  nonbonded pdb=" O   PHE A 347 "
            pdb=" H   LEU A 377 "
     model   vdw
     1.538 2.450
  nonbonded pdb=" O   LEU A 247 "
            pdb=" H   ARG B 195 "
     model   vdw
     1.549 2.450
  ... (remaining 392102 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.480
  Extract box with map and model:          1.060
  Check model and map are aligned:         0.200
  Set scattering table:                    0.240
  Process input model:                     54.120
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.070
  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:             0.010
  Load rotamer database and sin/cos tables:10.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   67.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
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      :  0.006   0.202  13572  Z= 0.266
  Angle     :  0.613  21.643  18421  Z= 0.330
  Chirality :  0.046   0.417   2016
  Planarity :  0.004   0.046   2427
  Dihedral  : 13.949  88.120   4956
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.79 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.20), residues: 1678
  helix:  0.88 (0.24), residues: 442
  sheet: -1.71 (0.22), residues: 457
  loop : -1.22 (0.22), residues: 779

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP A 546 
 HIS   0.002   0.001   HIS A 625 
 PHE   0.010   0.001   PHE D 128 
 TYR   0.019   0.001   TYR A 794 
 ARG   0.009   0.001   ARG C  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10101 (  623)
  hydrogen bonds       : angle       6.49994 ( 1773)
  SS BOND              : bond        0.00224 (    1)
  SS BOND              : angle       1.38914 (    2)
  covalent geometry    : bond        0.00556 (13569)
  covalent geometry    : angle       0.61336 (18419)
  Misc. bond           : bond        0.00042 (    2)

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

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

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
Residue LYS    5 is missing expected H atoms. Skipping.
Evaluate side-chains
  224 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 1.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ASP D 121 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   41 GLN cc_start: 0.7149 (mm110) cc_final: 0.6818 (mm110)
REVERT: F   76 MET cc_start: 0.5354 (mmm) cc_final: 0.5064 (tpt)
REVERT: F  136 MET cc_start: 0.6296 (mmt) cc_final: 0.6053 (mmm)
REVERT: F  137 ILE cc_start: 0.4881 (tp) cc_final: 0.4601 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 224
  average time/residue: 2.5743
  time to fit residues: 632.5723
Evaluate side-chains
  179 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 2.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 139 optimal weight:    2.9990
   chunk 125 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 129 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 96 optimal weight:    0.8980
   chunk 149 optimal weight:    6.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 463 ASN
A 538 ASN
B 225 GLN
** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 107 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.154571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.118792 restraints weight = 44107.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 1.39
r_work: 0.3260 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.0999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  13572  Z= 0.196
  Angle     :  0.559   6.011  18421  Z= 0.304
  Chirality :  0.044   0.398   2016
  Planarity :  0.004   0.041   2427
  Dihedral  :  5.076  20.409   1860
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.09 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  7.85 %
    Favored  : 91.03 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.20), residues: 1678
  helix:  0.93 (0.23), residues: 446
  sheet: -1.90 (0.22), residues: 448
  loop : -1.16 (0.22), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 546 
 HIS   0.006   0.001   HIS A 677 
 PHE   0.012   0.001   PHE A 426 
 TYR   0.014   0.001   TYR D 184 
 ARG   0.006   0.001   ARG D 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04152 (  623)
  hydrogen bonds       : angle       5.94594 ( 1773)
  SS BOND              : bond        0.01035 (    1)
  SS BOND              : angle       2.39029 (    2)
  covalent geometry    : bond        0.00410 (13569)
  covalent geometry    : angle       0.55849 (18419)
  Misc. bond           : bond        0.00114 (    2)

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

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

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
Residue LYS    5 is missing expected H atoms. Skipping.
Evaluate side-chains
  203 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 187
  time to evaluate  : 1.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ASP D 121 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  253 VAL cc_start: 0.8758 (t) cc_final: 0.8486 (p)
REVERT: B  303 ASP cc_start: 0.7950 (m-30) cc_final: 0.7738 (m-30)
REVERT: D   41 GLN cc_start: 0.7505 (mm110) cc_final: 0.6992 (mm110)
REVERT: D   84 ASP cc_start: 0.8148 (m-30) cc_final: 0.7896 (m-30)
REVERT: F   76 MET cc_start: 0.5231 (mmm) cc_final: 0.4944 (tpt)
REVERT: F  136 MET cc_start: 0.6415 (mmt) cc_final: 0.6155 (mmm)
REVERT: F  137 ILE cc_start: 0.4823 (tp) cc_final: 0.4584 (tt)
  outliers start: 16
  outliers final: 5
  residues processed: 194
  average time/residue: 2.4157
  time to fit residues: 521.2878
Evaluate side-chains
  178 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 173
  time to evaluate  : 2.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  598 LYS
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain F residue  156 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 162 optimal weight:    6.9990
   chunk 151 optimal weight:   10.0000
   chunk 63 optimal weight:    1.9990
   chunk 161 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 122 optimal weight:    2.9990
   chunk 123 optimal weight:    1.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 463 ASN
A 606 ASN
B 225 GLN
F 107 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.153491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.117318 restraints weight = 44275.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 1.40
r_work: 0.3215 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.1260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  13572  Z= 0.262
  Angle     :  0.584   6.700  18421  Z= 0.317
  Chirality :  0.045   0.386   2016
  Planarity :  0.004   0.041   2427
  Dihedral  :  5.254  20.313   1860
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.75 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  9.53 %
    Favored  : 88.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.20), residues: 1678
  helix:  0.78 (0.23), residues: 447
  sheet: -1.86 (0.22), residues: 419
  loop : -1.30 (0.22), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 745 
 HIS   0.006   0.001   HIS A 677 
 PHE   0.012   0.002   PHE A 791 
 TYR   0.017   0.002   TYR A 794 
 ARG   0.004   0.001   ARG A  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04250 (  623)
  hydrogen bonds       : angle       5.85584 ( 1773)
  SS BOND              : bond        0.00520 (    1)
  SS BOND              : angle       2.62529 (    2)
  covalent geometry    : bond        0.00566 (13569)
  covalent geometry    : angle       0.58362 (18419)
  Misc. bond           : bond        0.00083 (    2)

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

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

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
Residue LYS    5 is missing expected H atoms. Skipping.
Evaluate side-chains
  207 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 182
  time to evaluate  : 2.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7423 (tmtt)
REVERT: D   41 GLN cc_start: 0.7578 (mm110) cc_final: 0.7081 (mm110)
REVERT: D   84 ASP cc_start: 0.8233 (m-30) cc_final: 0.7895 (m-30)
REVERT: F   39 GLU cc_start: 0.5669 (tp30) cc_final: 0.3828 (tt0)
REVERT: F   76 MET cc_start: 0.5261 (mmm) cc_final: 0.5021 (tpt)
REVERT: F  136 MET cc_start: 0.6454 (mmt) cc_final: 0.6202 (mmm)
REVERT: F  137 ILE cc_start: 0.4955 (tp) cc_final: 0.4699 (tt)
REVERT: F  143 ASN cc_start: 0.6705 (OUTLIER) cc_final: 0.5922 (t0)
  outliers start: 25
  outliers final: 15
  residues processed: 199
  average time/residue: 2.1467
  time to fit residues: 477.3086
Evaluate side-chains
  189 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 172
  time to evaluate  : 1.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  217 GLN
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  383 ASP
Chi-restraints excluded: chain A residue  417 LYS
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  497 ASP
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  598 LYS
Chi-restraints excluded: chain A residue  601 ILE
Chi-restraints excluded: chain B residue   58 ASN
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain F residue   86 LYS
Chi-restraints excluded: chain F residue  143 ASN
Chi-restraints excluded: chain F residue  156 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 150 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 131 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 18 optimal weight:    0.4980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 463 ASN
A 538 ASN
E  54 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.153986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.118002 restraints weight = 44501.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 1.39
r_work: 0.3189 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.1423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13572  Z= 0.207
  Angle     :  0.553   5.866  18421  Z= 0.299
  Chirality :  0.044   0.389   2016
  Planarity :  0.004   0.042   2427
  Dihedral  :  5.157  20.224   1860
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.51 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 10.93 %
    Favored  : 86.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.20), residues: 1678
  helix:  0.89 (0.23), residues: 446
  sheet: -1.89 (0.22), residues: 431
  loop : -1.29 (0.22), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 745 
 HIS   0.005   0.001   HIS A 677 
 PHE   0.010   0.001   PHE A 791 
 TYR   0.015   0.001   TYR D 184 
 ARG   0.003   0.000   ARG A 370 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03951 (  623)
  hydrogen bonds       : angle       5.73527 ( 1773)
  SS BOND              : bond        0.00293 (    1)
  SS BOND              : angle       2.34960 (    2)
  covalent geometry    : bond        0.00442 (13569)
  covalent geometry    : angle       0.55243 (18419)
  Misc. bond           : bond        0.00083 (    2)

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

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

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
Residue LYS    5 is missing expected H atoms. Skipping.
Evaluate side-chains
  207 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 177
  time to evaluate  : 2.268 
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: A  417 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7402 (tmtt)
REVERT: D   41 GLN cc_start: 0.7607 (mm110) cc_final: 0.6960 (mm110)
REVERT: F   39 GLU cc_start: 0.5398 (tp30) cc_final: 0.3639 (tt0)
REVERT: F   76 MET cc_start: 0.5177 (mmm) cc_final: 0.4860 (tpt)
REVERT: F  136 MET cc_start: 0.6448 (mmt) cc_final: 0.6202 (mmm)
REVERT: F  137 ILE cc_start: 0.4873 (tp) cc_final: 0.4553 (tt)
REVERT: F  143 ASN cc_start: 0.6531 (OUTLIER) cc_final: 0.5734 (t0)
  outliers start: 30
  outliers final: 16
  residues processed: 200
  average time/residue: 2.2266
  time to fit residues: 496.7631
Evaluate side-chains
  188 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 170
  time to evaluate  : 2.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  383 ASP
Chi-restraints excluded: chain A residue  417 LYS
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  497 ASP
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  598 LYS
Chi-restraints excluded: chain A residue  772 ILE
Chi-restraints excluded: chain B residue   58 ASN
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   53 THR
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain F residue   86 LYS
Chi-restraints excluded: chain F residue  143 ASN
Chi-restraints excluded: chain F residue  156 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 149 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 111 optimal weight:    3.9990
   chunk 130 optimal weight:    0.9980
   chunk 98 optimal weight:    2.9990
   chunk 112 optimal weight:    0.5980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
A 463 ASN
A 538 ASN
** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 606 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.155116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.119526 restraints weight = 43986.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 1.38
r_work: 0.3214 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13572  Z= 0.163
  Angle     :  0.527   5.656  18421  Z= 0.284
  Chirality :  0.044   0.390   2016
  Planarity :  0.004   0.044   2427
  Dihedral  :  4.987  20.196   1860
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.21 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 12.12 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.20), residues: 1678
  helix:  1.07 (0.24), residues: 449
  sheet: -1.84 (0.22), residues: 454
  loop : -1.18 (0.23), residues: 775

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 183 
 HIS   0.005   0.001   HIS A 677 
 PHE   0.008   0.001   PHE A 791 
 TYR   0.015   0.001   TYR D 184 
 ARG   0.003   0.000   ARG A 370 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03709 (  623)
  hydrogen bonds       : angle       5.57638 ( 1773)
  SS BOND              : bond        0.00186 (    1)
  SS BOND              : angle       2.16798 (    2)
  covalent geometry    : bond        0.00343 (13569)
  covalent geometry    : angle       0.52691 (18419)
  Misc. bond           : bond        0.00096 (    2)

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

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

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
Residue LYS    5 is missing expected H atoms. Skipping.
Evaluate side-chains
  211 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 184
  time to evaluate  : 2.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 GLU cc_start: 0.7063 (pt0) cc_final: 0.6744 (pt0)
REVERT: B  253 VAL cc_start: 0.8723 (t) cc_final: 0.8499 (p)
REVERT: D   41 GLN cc_start: 0.7501 (mm110) cc_final: 0.6899 (mm110)
REVERT: F   39 GLU cc_start: 0.5383 (tp30) cc_final: 0.3560 (tt0)
REVERT: F   76 MET cc_start: 0.5231 (mmm) cc_final: 0.4961 (tpt)
REVERT: F  136 MET cc_start: 0.6450 (mmt) cc_final: 0.6214 (mmm)
REVERT: F  137 ILE cc_start: 0.4857 (tp) cc_final: 0.4524 (tt)
REVERT: F  143 ASN cc_start: 0.6545 (OUTLIER) cc_final: 0.5744 (t0)
  outliers start: 27
  outliers final: 14
  residues processed: 201
  average time/residue: 2.2029
  time to fit residues: 493.9057
Evaluate side-chains
  185 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 170
  time to evaluate  : 1.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  772 ILE
Chi-restraints excluded: chain B residue   58 ASN
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   53 THR
Chi-restraints excluded: chain E residue   47 ARG
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain F residue  143 ASN
Chi-restraints excluded: chain F residue  156 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 111 optimal weight:    0.6980
   chunk 68 optimal weight:    0.6980
   chunk 98 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 135 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 163 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
A 463 ASN
** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  54 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.154787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.119088 restraints weight = 44188.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.39
r_work: 0.3208 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.1627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  13572  Z= 0.175
  Angle     :  0.531   5.880  18421  Z= 0.286
  Chirality :  0.044   0.396   2016
  Planarity :  0.004   0.041   2427
  Dihedral  :  4.979  20.136   1860
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.45 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.68 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.20), residues: 1678
  helix:  1.13 (0.24), residues: 449
  sheet: -1.78 (0.23), residues: 433
  loop : -1.21 (0.22), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 745 
 HIS   0.004   0.001   HIS A 677 
 PHE   0.018   0.001   PHE D 128 
 TYR   0.014   0.001   TYR D 184 
 ARG   0.005   0.000   ARG A 634 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03724 (  623)
  hydrogen bonds       : angle       5.52192 ( 1773)
  SS BOND              : bond        0.00201 (    1)
  SS BOND              : angle       2.03220 (    2)
  covalent geometry    : bond        0.00370 (13569)
  covalent geometry    : angle       0.53019 (18419)
  Misc. bond           : bond        0.00088 (    2)

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

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

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
Residue LYS    5 is missing expected H atoms. Skipping.
Evaluate side-chains
  199 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 173
  time to evaluate  : 1.916 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 ASN cc_start: 0.7545 (t0) cc_final: 0.7302 (t0)
REVERT: B  253 VAL cc_start: 0.8714 (t) cc_final: 0.8489 (p)
REVERT: D   41 GLN cc_start: 0.7489 (mm110) cc_final: 0.6867 (mm110)
REVERT: F   39 GLU cc_start: 0.5168 (tp30) cc_final: 0.3593 (tt0)
REVERT: F   76 MET cc_start: 0.5259 (mmm) cc_final: 0.4962 (tpt)
REVERT: F  135 GLU cc_start: 0.5697 (mt-10) cc_final: 0.5459 (mt-10)
REVERT: F  136 MET cc_start: 0.6445 (mmt) cc_final: 0.6209 (mmm)
REVERT: F  137 ILE cc_start: 0.4834 (tp) cc_final: 0.4509 (tt)
REVERT: F  143 ASN cc_start: 0.6469 (OUTLIER) cc_final: 0.5666 (t0)
  outliers start: 26
  outliers final: 21
  residues processed: 190
  average time/residue: 2.1896
  time to fit residues: 466.5004
Evaluate side-chains
  194 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 172
  time to evaluate  : 1.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  383 ASP
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  497 ASP
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  598 LYS
Chi-restraints excluded: chain A residue  772 ILE
Chi-restraints excluded: chain B residue   58 ASN
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  234 GLN
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   53 THR
Chi-restraints excluded: chain E residue   47 ARG
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain F residue   86 LYS
Chi-restraints excluded: chain F residue  140 GLU
Chi-restraints excluded: chain F residue  143 ASN
Chi-restraints excluded: chain F residue  156 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 94 optimal weight:    0.0000
   chunk 128 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 146 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 163 optimal weight:    1.9990
   chunk 134 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 463 ASN
** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 606 ASN
E  54 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.153799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.117880 restraints weight = 44102.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.40
r_work: 0.3183 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  13572  Z= 0.217
  Angle     :  0.553   6.297  18421  Z= 0.299
  Chirality :  0.044   0.390   2016
  Planarity :  0.004   0.056   2427
  Dihedral  :  5.097  20.526   1860
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.75 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.59 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.20), residues: 1678
  helix:  1.03 (0.24), residues: 449
  sheet: -1.72 (0.23), residues: 431
  loop : -1.25 (0.22), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 745 
 HIS   0.004   0.001   HIS A 677 
 PHE   0.011   0.002   PHE A 724 
 TYR   0.014   0.002   TYR A 794 
 ARG   0.004   0.000   ARG A 634 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03882 (  623)
  hydrogen bonds       : angle       5.56313 ( 1773)
  SS BOND              : bond        0.00223 (    1)
  SS BOND              : angle       2.12239 (    2)
  covalent geometry    : bond        0.00464 (13569)
  covalent geometry    : angle       0.55214 (18419)
  Misc. bond           : bond        0.00069 (    2)

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

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

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
Residue LYS    5 is missing expected H atoms. Skipping.
Evaluate side-chains
  197 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 171
  time to evaluate  : 2.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   41 GLN cc_start: 0.7592 (mm110) cc_final: 0.6862 (mm110)
REVERT: F   39 GLU cc_start: 0.5156 (tp30) cc_final: 0.3589 (tt0)
REVERT: F  135 GLU cc_start: 0.5727 (mt-10) cc_final: 0.5435 (mt-10)
REVERT: F  136 MET cc_start: 0.6433 (mmt) cc_final: 0.6199 (mmm)
REVERT: F  137 ILE cc_start: 0.4818 (tp) cc_final: 0.4505 (tt)
REVERT: F  143 ASN cc_start: 0.6479 (OUTLIER) cc_final: 0.5681 (t0)
  outliers start: 26
  outliers final: 20
  residues processed: 188
  average time/residue: 2.1689
  time to fit residues: 455.8666
Evaluate side-chains
  187 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 2.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  217 GLN
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  383 ASP
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  497 ASP
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  598 LYS
Chi-restraints excluded: chain A residue  772 ILE
Chi-restraints excluded: chain B residue   58 ASN
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  234 GLN
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   53 THR
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain F residue   86 LYS
Chi-restraints excluded: chain F residue  140 GLU
Chi-restraints excluded: chain F residue  143 ASN
Chi-restraints excluded: chain F residue  156 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 100 optimal weight:    0.8980
   chunk 127 optimal weight:    1.9990
   chunk 152 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 82 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 90 optimal weight:    0.5980
   chunk 76 optimal weight:    1.9990
   chunk 83 optimal weight:    0.5980
   chunk 136 optimal weight:    0.9980
   chunk 148 optimal weight:    5.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
A 463 ASN
E  54 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.155360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.119914 restraints weight = 44159.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 1.38
r_work: 0.3214 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13572  Z= 0.148
  Angle     :  0.523   5.613  18421  Z= 0.280
  Chirality :  0.043   0.400   2016
  Planarity :  0.004   0.043   2427
  Dihedral  :  4.917  19.958   1860
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.73 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 14.30 %
    Favored  : 84.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.20), residues: 1678
  helix:  1.21 (0.24), residues: 449
  sheet: -1.77 (0.22), residues: 439
  loop : -1.18 (0.23), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 183 
 HIS   0.004   0.001   HIS A 677 
 PHE   0.022   0.001   PHE D 128 
 TYR   0.015   0.001   TYR D 184 
 ARG   0.006   0.000   ARG A 634 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03582 (  623)
  hydrogen bonds       : angle       5.44967 ( 1773)
  SS BOND              : bond        0.00094 (    1)
  SS BOND              : angle       1.98018 (    2)
  covalent geometry    : bond        0.00310 (13569)
  covalent geometry    : angle       0.52250 (18419)
  Misc. bond           : bond        0.00103 (    2)

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

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

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
Residue LYS    5 is missing expected H atoms. Skipping.
Evaluate side-chains
  197 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 175
  time to evaluate  : 1.985 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 ASN cc_start: 0.7473 (t0) cc_final: 0.7266 (t0)
REVERT: B  253 VAL cc_start: 0.8695 (t) cc_final: 0.8472 (p)
REVERT: D   41 GLN cc_start: 0.7653 (mm110) cc_final: 0.6961 (mm110)
REVERT: F   39 GLU cc_start: 0.5265 (tp30) cc_final: 0.3671 (tt0)
REVERT: F  135 GLU cc_start: 0.5747 (mt-10) cc_final: 0.5515 (mt-10)
REVERT: F  136 MET cc_start: 0.6449 (mmt) cc_final: 0.6223 (mmm)
REVERT: F  137 ILE cc_start: 0.4791 (tp) cc_final: 0.4460 (tt)
REVERT: F  143 ASN cc_start: 0.6459 (OUTLIER) cc_final: 0.5648 (t0)
  outliers start: 22
  outliers final: 14
  residues processed: 189
  average time/residue: 2.1838
  time to fit residues: 460.4215
Evaluate side-chains
  183 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 168
  time to evaluate  : 1.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  772 ILE
Chi-restraints excluded: chain B residue   58 ASN
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  234 GLN
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   53 THR
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue  140 GLU
Chi-restraints excluded: chain F residue  143 ASN
Chi-restraints excluded: chain F residue  156 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 161 optimal weight:    0.8980
   chunk 124 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 147 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 151 optimal weight:    0.4980
   chunk 79 optimal weight:    0.4980
   chunk 6 optimal weight:    0.7980
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
A 463 ASN
** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  54 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.155712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.120370 restraints weight = 44164.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 1.39
r_work: 0.3216 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13572  Z= 0.145
  Angle     :  0.520   5.773  18421  Z= 0.278
  Chirality :  0.043   0.408   2016
  Planarity :  0.004   0.046   2427
  Dihedral  :  4.840  19.842   1860
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.09 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.79 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.20), residues: 1678
  helix:  1.29 (0.24), residues: 449
  sheet: -1.76 (0.23), residues: 439
  loop : -1.16 (0.23), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 143 
 HIS   0.004   0.001   HIS A 677 
 PHE   0.009   0.001   PHE A 791 
 TYR   0.014   0.001   TYR D 184 
 ARG   0.007   0.000   ARG A 634 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03529 (  623)
  hydrogen bonds       : angle       5.38659 ( 1773)
  SS BOND              : bond        0.00124 (    1)
  SS BOND              : angle       1.95977 (    2)
  covalent geometry    : bond        0.00306 (13569)
  covalent geometry    : angle       0.51935 (18419)
  Misc. bond           : bond        0.00103 (    2)

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

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

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
Residue LYS    5 is missing expected H atoms. Skipping.
Evaluate side-chains
  193 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 170
  time to evaluate  : 1.993 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  598 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7983 (ptmt)
REVERT: A  798 LYS cc_start: 0.7983 (mmtt) cc_final: 0.7737 (mmmt)
REVERT: B  253 VAL cc_start: 0.8689 (t) cc_final: 0.8465 (p)
REVERT: D   41 GLN cc_start: 0.7695 (mm110) cc_final: 0.6990 (mm110)
REVERT: F   39 GLU cc_start: 0.5263 (tp30) cc_final: 0.3675 (tt0)
REVERT: F  135 GLU cc_start: 0.5715 (mt-10) cc_final: 0.5482 (mt-10)
REVERT: F  137 ILE cc_start: 0.4758 (tp) cc_final: 0.4437 (tt)
REVERT: F  143 ASN cc_start: 0.6448 (OUTLIER) cc_final: 0.5641 (t0)
REVERT: F  400 MET cc_start: 0.5896 (tpp) cc_final: 0.5449 (tpp)
  outliers start: 23
  outliers final: 14
  residues processed: 185
  average time/residue: 2.2256
  time to fit residues: 461.3658
Evaluate side-chains
  184 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 168
  time to evaluate  : 2.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  598 LYS
Chi-restraints excluded: chain A residue  772 ILE
Chi-restraints excluded: chain B residue   58 ASN
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  234 GLN
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   53 THR
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue  140 GLU
Chi-restraints excluded: chain F residue  143 ASN
Chi-restraints excluded: chain F residue  156 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 115 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0980
   chunk 82 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 129 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 463 ASN
** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  85 ASN
E  54 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.155294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.119960 restraints weight = 44099.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 1.38
r_work: 0.3210 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13572  Z= 0.164
  Angle     :  0.528   5.876  18421  Z= 0.282
  Chirality :  0.043   0.403   2016
  Planarity :  0.004   0.046   2427
  Dihedral  :  4.867  19.851   1860
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.51 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 15.00 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.20), residues: 1678
  helix:  1.29 (0.24), residues: 449
  sheet: -1.73 (0.22), residues: 453
  loop : -1.15 (0.23), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 183 
 HIS   0.003   0.001   HIS A 280 
 PHE   0.010   0.001   PHE A 791 
 TYR   0.014   0.001   TYR D 184 
 ARG   0.006   0.000   ARG A 634 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03594 (  623)
  hydrogen bonds       : angle       5.38614 ( 1773)
  SS BOND              : bond        0.00146 (    1)
  SS BOND              : angle       1.96729 (    2)
  covalent geometry    : bond        0.00347 (13569)
  covalent geometry    : angle       0.52727 (18419)
  Misc. bond           : bond        0.00085 (    2)

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

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

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3356 Ramachandran restraints generated.
    1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
Residue LYS    5 is missing expected H atoms. Skipping.
Evaluate side-chains
  192 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 170
  time to evaluate  : 2.089 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  798 LYS cc_start: 0.7978 (mmtt) cc_final: 0.7743 (mmmt)
REVERT: B  253 VAL cc_start: 0.8686 (t) cc_final: 0.8457 (p)
REVERT: D   41 GLN cc_start: 0.7667 (mm110) cc_final: 0.6917 (mm110)
REVERT: E   57 TYR cc_start: 0.7673 (t80) cc_final: 0.7163 (t80)
REVERT: F   39 GLU cc_start: 0.5299 (tp30) cc_final: 0.3708 (tt0)
REVERT: F  135 GLU cc_start: 0.5722 (mt-10) cc_final: 0.5486 (mt-10)
REVERT: F  137 ILE cc_start: 0.4775 (tp) cc_final: 0.4451 (tt)
REVERT: F  143 ASN cc_start: 0.6455 (OUTLIER) cc_final: 0.5637 (t0)
REVERT: F  400 MET cc_start: 0.6020 (tpp) cc_final: 0.5544 (tpp)
  outliers start: 22
  outliers final: 15
  residues processed: 183
  average time/residue: 2.1934
  time to fit residues: 448.6649
Evaluate side-chains
  185 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 169
  time to evaluate  : 2.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 ARG
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  474 THR
Chi-restraints excluded: chain A residue  569 ASP
Chi-restraints excluded: chain A residue  772 ILE
Chi-restraints excluded: chain B residue   58 ASN
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  234 GLN
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain D residue   53 THR
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue  140 GLU
Chi-restraints excluded: chain F residue  143 ASN
Chi-restraints excluded: chain F residue  156 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 150 optimal weight:    7.9990
   chunk 100 optimal weight:    0.8980
   chunk 72 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 161 optimal weight:    0.9980
   chunk 67 optimal weight:    6.9990
   chunk 110 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0770
   chunk 145 optimal weight:    1.9990
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
A 463 ASN
** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 606 ASN
** C  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  54 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.156522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.121328 restraints weight = 44241.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.39
r_work: 0.3232 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13572  Z= 0.133
  Angle     :  0.519   7.841  18421  Z= 0.277
  Chirality :  0.043   0.404   2016
  Planarity :  0.004   0.045   2427
  Dihedral  :  4.753  19.594   1860
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.85 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 15.56 %
    Favored  : 83.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.21), residues: 1678
  helix:  1.39 (0.24), residues: 449
  sheet: -1.71 (0.22), residues: 452
  loop : -1.15 (0.23), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 183 
 HIS   0.004   0.001   HIS A 677 
 PHE   0.027   0.001   PHE D 128 
 TYR   0.015   0.001   TYR D 184 
 ARG   0.006   0.000   ARG A 634 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03431 (  623)
  hydrogen bonds       : angle       5.30842 ( 1773)
  SS BOND              : bond        0.00095 (    1)
  SS BOND              : angle       1.96070 (    2)
  covalent geometry    : bond        0.00282 (13569)
  covalent geometry    : angle       0.51842 (18419)
  Misc. bond           : bond        0.00107 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 17461.03 seconds
wall clock time: 298 minutes 53.99 seconds (17933.99 seconds total)