Starting phenix.real_space_refine
on Sat Jun 14 14:21:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cnx_45765/06_2025/9cnx_45765.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cnx_45765/06_2025/9cnx_45765.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cnx_45765/06_2025/9cnx_45765.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cnx_45765/06_2025/9cnx_45765.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cnx_45765/06_2025/9cnx_45765.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cnx_45765/06_2025/9cnx_45765.cif"
  }
  resolution = 3.55
  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=   0.001 sd=   0.030
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5743 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      31      5.16       5
     C    7303      2.51       5
     N    1986      2.21       5
     O    2261      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 11582
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 6025
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 762, 6025
          Classifications: {'peptide': 762}
          Link IDs: {'PTRANS': 28, 'TRANS': 733}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 353, 2657
          Classifications: {'peptide': 353}
          Link IDs: {'PTRANS': 11, 'TRANS': 341}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 385
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 6, 'TRANS': 47}
    Chain: "D"
      Number of atoms: 1703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1703
          Classifications: {'peptide': 211}
          Link IDs: {'PTRANS': 12, 'TRANS': 198}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 691
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 691
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 5, 'TRANS': 82}
    Chain: "G"
      Number of atoms: 119
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 119
          Unusual residues: {'ACY': 1}
          Classifications: {'peptide': 13, 'undetermined': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 12, None: 1}
            Not linked:
              pdbres="ACY G   0 "
              pdbres="PHE G   1 "
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 12
          Planarities with less than four sites: {'ACY:plan-1': 1, 'ALN:plan-2': 1, 'MHS:plan-2': 1, 'ABA:plan-1': 1, 'YNM:plan-2': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "G"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 1, 'NH2': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.95, per 1000 atoms: 0.60
  Number of scatterers: 11582
  At special positions: 0
  Unit cell: (124.8, 126, 151.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      31     16.00
     O    2261      8.00
     N    1986      7.00
     C    7303      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.07
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN G 901 "
        pdb="ZN    ZN G 901 " - pdb=" NE2 MHS G  11 "
        pdb="ZN    ZN G 901 " - pdb=" ND1 HIS G   4 "
        pdb="ZN    ZN G 901 " - pdb=" NE2 HIS G   9 "


  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2702

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 16 sheets defined
      25.3% alpha, 29.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 46
    Processing helix  chain 'A' and resid 55 through 70
      removed outlier: 4.035A  pdb=" N   GLY A  70 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 114
    Processing helix  chain 'A' and resid 115 through 119
      removed outlier: 3.958A  pdb=" N   GLY A 118 " --> pdb=" O   GLU A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 128
      No H-bonds generated for 'chain 'A' and resid 126 through 128'
    Processing helix  chain 'A' and resid 129 through 145
    Processing helix  chain 'A' and resid 189 through 195
      removed outlier: 3.564A  pdb=" N   LEU A 193 " --> pdb=" O   THR A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 232
    Processing helix  chain 'A' and resid 280 through 289
      removed outlier: 3.508A  pdb=" N   LYS A 289 " --> pdb=" O   GLU A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 314
    Processing helix  chain 'A' and resid 361 through 367
      removed outlier: 3.740A  pdb=" N   LEU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 392
      removed outlier: 3.814A  pdb=" N   LEU A 392 " --> pdb=" O   ARG A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 452
    Processing helix  chain 'A' and resid 497 through 500
    Processing helix  chain 'A' and resid 542 through 553
      removed outlier: 3.740A  pdb=" N   TYR A 548 " --> pdb=" O   ALA A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 651
      removed outlier: 3.869A  pdb=" N   ASN A 651 " --> pdb=" O   PHE A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 729 through 733
      removed outlier: 3.547A  pdb=" N   VAL A 733 " --> pdb=" O   ALA A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 754
      removed outlier: 3.668A  pdb=" N   GLN A 753 " --> pdb=" O   ASP A 750 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 39
      removed outlier: 3.749A  pdb=" N   SER C  36 " --> pdb=" O   ARG C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 80
      removed outlier: 3.657A  pdb=" N   ALA C  79 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU C  80 " --> pdb=" O   GLY C  77 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 76 through 80'
    Processing helix  chain 'D' and resid 31 through 42
    Processing helix  chain 'D' and resid 47 through 62
      removed outlier: 3.954A  pdb=" N   ALA D  51 " --> pdb=" O   ASN D  47 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   THR D  53 " --> pdb=" O   ARG D  49 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLN D  54 " --> pdb=" O   GLN D  50 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LEU D  55 " --> pdb=" O   ALA D  51 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 82
    Processing helix  chain 'D' and resid 84 through 99
      removed outlier: 3.942A  pdb=" N   ARG D  97 " --> pdb=" O   ASP D  93 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 118
      removed outlier: 3.672A  pdb=" N   VAL D 108 " --> pdb=" O   ASN D 104 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 121
      No H-bonds generated for 'chain 'D' and resid 119 through 121'
    Processing helix  chain 'D' and resid 137 through 154
    Processing helix  chain 'D' and resid 159 through 189
      removed outlier: 3.829A  pdb=" N   ASP D 172 " --> pdb=" O   VAL D 168 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   TYR D 177 " --> pdb=" O   ARG D 173 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   GLU D 178 " --> pdb=" O   LEU D 174 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLU D 187 " --> pdb=" O   GLU D 183 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 205
      removed outlier: 3.507A  pdb=" N   VAL D 194 " --> pdb=" O   ALA D 190 " (cutoff:3.500A)
    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: 3.834A  pdb=" N   LYS D 233 " --> pdb=" O   ALA D 229 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 39 through 44
    Processing helix  chain 'E' and resid 51 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32
      removed outlier: 6.407A  pdb=" N   HIS A  30 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 7.933A  pdb=" N   VAL A  88 " --> pdb=" O   HIS A  30 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   GLU A  32 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 7.121A  pdb=" N   GLU A  90 " --> pdb=" O   GLU A  32 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ASP A  74 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100
      removed outlier: 7.596A  pdb=" N   LEU A 165 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   ILE A  97 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   LEU A 167 " --> pdb=" O   ILE A  97 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   PHE A  99 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A  99 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183
      removed outlier: 7.564A  pdb=" N   VAL A 256 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   VAL A 258 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   ILE A 260 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   SER A 242 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 5.471A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   SER B 193 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276
      removed outlier: 7.366A  pdb=" N   LEU A 337 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   VAL A 271 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   VAL A 339 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   VAL A 273 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   VAL A 341 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   GLY A 275 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355
      removed outlier: 7.744A  pdb=" N   VAL A 414 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   ILE A 352 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   TYR A 416 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
      removed outlier: 4.879A  pdb=" N   PHE A 354 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   VAL A 418 " --> pdb=" O   PHE A 354 " (cutoff:3.500A)
      removed outlier: 7.780A  pdb=" N   GLN A 411 " --> pdb=" O   ARG A 404 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   ARG A 404 " --> pdb=" O   GLN A 411 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   ASP A 413 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   THR A 402 " --> pdb=" O   ASP A 413 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   VAL A 415 " --> pdb=" O   THR A 400 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   THR A 400 " --> pdb=" O   VAL A 415 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   LYS A 417 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   VAL A 398 " --> pdb=" O   LYS A 417 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   LYS A 419 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 433
      removed outlier: 3.759A  pdb=" N   TYR A 574 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   GLY A 590 " --> pdb=" O   TYR A 618 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   PHE A 738 " --> pdb=" O   GLY A 771 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY A 771 " --> pdb=" O   PHE A 738 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   MET A 768 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   PHE A 791 " --> pdb=" O   MET A 768 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ALA A 770 " --> pdb=" O   GLN A 789 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.872A  pdb=" N   SER B 389 " --> pdb=" O   ALA B  47 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   SER B  49 " --> pdb=" O   VAL B 387 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL B 387 " --> pdb=" O   SER B  49 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 68
      removed outlier: 7.234A  pdb=" N   VAL B  81 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   SER B  94 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   ALA B  83 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 118
      removed outlier: 6.672A  pdb=" N   VAL B 131 " --> pdb=" O   GLN B 144 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   GLN B 144 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   ALA B 133 " --> pdb=" O   ALA B 142 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 156 through 158
      removed outlier: 3.731A  pdb=" N   VAL B 156 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   LEU B 171 " --> pdb=" O   THR B 184 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   THR B 184 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   ALA B 173 " --> pdb=" O   LYS B 182 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 203
      removed outlier: 6.917A  pdb=" N   VAL B 216 " --> pdb=" O   GLN B 229 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   GLN B 229 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   ALA B 218 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 252 through 254
      removed outlier: 6.928A  pdb=" N   LEU B 267 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
      removed outlier: 4.641A  pdb=" N   LYS B 280 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   ALA B 269 " --> pdb=" O   MET B 278 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 290 through 292
      removed outlier: 3.566A  pdb=" N   VAL B 305 " --> pdb=" O   GLN B 319 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   TRP B 317 " --> pdb=" O   ALA B 307 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   THR B 309 " --> pdb=" O   THR B 315 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   THR B 315 " --> pdb=" O   THR B 309 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 331 through 333
      removed outlier: 3.512A  pdb=" N   TRP B 348 " --> pdb=" O   ALA B 358 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ALA B 358 " --> pdb=" O   TRP B 348 " (cutoff:3.500A)
      removed outlier: 5.850A  pdb=" N   ASN B 350 " --> pdb=" O   PHE B 356 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   PHE B 356 " --> pdb=" O   ASN B 350 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 35
      removed outlier: 3.686A  pdb=" N   ILE E  32 " --> pdb=" O   GLN E  80 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   MET E  64 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 35
      removed outlier: 3.686A  pdb=" N   ILE E  32 " --> pdb=" O   GLN E  80 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   THR E  90 " --> pdb=" O   ASN E 106 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   ASN E 106 " --> pdb=" O   THR E  90 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   THR E  92 " --> pdb=" O   ILE E 104 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   ILE E 104 " --> pdb=" O   THR E  92 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   THR E  94 " --> pdb=" O   THR E 102 " (cutoff:3.500A)

    499 hydrogen bonds defined for protein.
    1377 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.51

  Time building geometry restraints manager: 3.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3857
        1.34 -     1.46: 2158
        1.46 -     1.57: 5755
        1.57 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 11831
  Sorted by residual:
  bond pdb=" ND1 MHS G  11 "
       pdb=" CE1 MHS G  11 "
    ideal  model  delta    sigma   weight residual
    1.351  1.399 -0.048 2.00e-02 2.50e+03 5.83e+00
  bond pdb=" CE1 MHS G  11 "
       pdb=" NE2 MHS G  11 "
    ideal  model  delta    sigma   weight residual
    1.307  1.349 -0.042 2.00e-02 2.50e+03 4.34e+00
  bond pdb=" CG  MHS G  11 "
       pdb=" CD2 MHS G  11 "
    ideal  model  delta    sigma   weight residual
    1.370  1.408 -0.038 2.00e-02 2.50e+03 3.66e+00
  bond pdb=" C   ACY G   0 "
       pdb=" O   ACY G   0 "
    ideal  model  delta    sigma   weight residual
    1.248  1.286 -0.038 2.00e-02 2.50e+03 3.60e+00
  bond pdb=" CA  VAL D  27 "
       pdb=" C   VAL D  27 "
    ideal  model  delta    sigma   weight residual
    1.525  1.560 -0.035 2.10e-02 2.27e+03 2.72e+00
  ... (remaining 11826 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 15807
        2.24 -     4.49: 222
        4.49 -     6.73: 30
        6.73 -     8.97: 10
        8.97 -    11.21: 3
  Bond angle restraints: 16072
  Sorted by residual:
  angle pdb=" N   GLU D  56 "
        pdb=" CA  GLU D  56 "
        pdb=" CB  GLU D  56 "
      ideal   model   delta    sigma   weight residual
     110.28  117.40   -7.12 1.55e+00 4.16e-01 2.11e+01
  angle pdb=" N   ARG G   7 "
        pdb=" CA  ARG G   7 "
        pdb=" C   ARG G   7 "
      ideal   model   delta    sigma   weight residual
     111.00  122.21  -11.21 2.80e+00 1.28e-01 1.60e+01
  angle pdb=" C   ASN D  33 "
        pdb=" N   GLU D  34 "
        pdb=" CA  GLU D  34 "
      ideal   model   delta    sigma   weight residual
     122.06  115.15    6.91 1.86e+00 2.89e-01 1.38e+01
  angle pdb=" C   LEU D  55 "
        pdb=" N   GLU D  56 "
        pdb=" CA  GLU D  56 "
      ideal   model   delta    sigma   weight residual
     120.31  114.75    5.56 1.52e+00 4.33e-01 1.34e+01
  angle pdb=" CA  MET D 109 "
        pdb=" CB  MET D 109 "
        pdb=" CG  MET D 109 "
      ideal   model   delta    sigma   weight residual
     114.10  121.15   -7.05 2.00e+00 2.50e-01 1.24e+01
  ... (remaining 16067 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 6481
       17.75 -    35.51: 394
       35.51 -    53.26: 69
       53.26 -    71.01: 17
       71.01 -    88.77: 13
  Dihedral angle restraints: 6974
    sinusoidal: 2726
      harmonic: 4248
  Sorted by residual:
  dihedral pdb=" CA  GLN A 495 "
           pdb=" C   GLN A 495 "
           pdb=" N   ALA A 496 "
           pdb=" CA  ALA A 496 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.29  -17.71     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  HIS B 324 "
           pdb=" C   HIS B 324 "
           pdb=" N   ARG B 325 "
           pdb=" CA  ARG B 325 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.68   17.32     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  TRP A 546 "
           pdb=" C   TRP A 546 "
           pdb=" N   ARG A 547 "
           pdb=" CA  ARG A 547 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.65   16.35     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 6971 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1228
       0.045 -    0.090: 367
       0.090 -    0.135: 140
       0.135 -    0.180: 14
       0.180 -    0.225: 4
  Chirality restraints: 1753
  Sorted by residual:
  chirality pdb=" CB  ILE A  94 "
            pdb=" CA  ILE A  94 "
            pdb=" CG1 ILE A  94 "
            pdb=" CG2 ILE A  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CA  ARG G   7 "
            pdb=" N   ARG G   7 "
            pdb=" C   ARG G   7 "
            pdb=" CB  ARG G   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CB  VAL E  27 "
            pdb=" CA  VAL E  27 "
            pdb=" CG1 VAL E  27 "
            pdb=" CG2 VAL E  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 1750 not shown)

  Planarity restraints: 2111
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  91 "   -0.038 5.00e-02 4.00e+02   5.75e-02 5.29e+00
        pdb=" N   PRO A  92 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A  92 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A  92 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 675 "   -0.035 5.00e-02 4.00e+02   5.35e-02 4.58e+00
        pdb=" N   PRO A 676 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 676 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 676 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 248 "    0.030 5.00e-02 4.00e+02   4.58e-02 3.36e+00
        pdb=" N   PRO A 249 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 249 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 249 "    0.026 5.00e-02 4.00e+02
  ... (remaining 2108 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 3563
        2.83 -     3.35: 10080
        3.35 -     3.86: 17493
        3.86 -     4.38: 19747
        4.38 -     4.90: 36269
  Nonbonded interactions: 87152
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A  79 "
            pdb=" O   ASP A  80 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" ND1 HIS A 533 "
            pdb=" OD1 ASP A 568 "
     model   vdw
     2.331 3.120
  nonbonded pdb=" OG1 THR B 309 "
            pdb=" O   GLY B 312 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" OE1 GLN B 319 "
            pdb=" NH2 ARG B 355 "
     model   vdw
     2.344 3.120
  nonbonded pdb=" NE2 GLN D 230 "
            pdb=" OD1 ASP E  66 "
     model   vdw
     2.352 3.120
  ... (remaining 87147 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             2.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.100
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     30.080
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
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      :  0.008   0.512  11837  Z= 0.290
  Angle     :  0.704  11.214  16072  Z= 0.371
  Chirality :  0.049   0.225   1753
  Planarity :  0.005   0.058   2111
  Dihedral  : 12.672  88.768   4272
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 1.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  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:  0.18 (0.21), residues: 1454
  helix:  0.70 (0.28), residues: 311
  sheet:  0.41 (0.24), residues: 445
  loop : -0.24 (0.23), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  93 
 HIS   0.006   0.001   HIS G   9 
 PHE   0.026   0.002   PHE A 428 
 TYR   0.013   0.001   TYR B 123 
 ARG   0.009   0.001   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20283 (  496)
  hydrogen bonds       : angle       7.17670 ( 1377)
  metal coordination   : bond        0.41581 (    3)
  covalent geometry    : bond        0.00345 (11831)
  covalent geometry    : angle       0.70383 (16072)
  Misc. bond           : bond        0.05802 (    3)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 1.221 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 MET cc_start: 0.9129 (mtp) cc_final: 0.8898 (tpt)
REVERT: A  304 MET cc_start: 0.8080 (ttp) cc_final: 0.7861 (ttm)
REVERT: A  369 MET cc_start: 0.8647 (mmp) cc_final: 0.8328 (mmp)
REVERT: A  459 ASN cc_start: 0.7693 (t0) cc_final: 0.7454 (t0)
REVERT: B   48 TRP cc_start: 0.8592 (p-90) cc_final: 0.7676 (p-90)
REVERT: D   35 ILE cc_start: 0.9057 (mt) cc_final: 0.8707 (mt)
REVERT: D   87 LEU cc_start: 0.9285 (mp) cc_final: 0.9003 (mp)
REVERT: E   44 SER cc_start: 0.8788 (p) cc_final: 0.8432 (p)
REVERT: E   47 ARG cc_start: 0.7416 (mpt180) cc_final: 0.7080 (mmt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.2296
  time to fit residues: 43.5417
Evaluate side-chains
  109 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 1.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 123 optimal weight:    6.9990
   chunk 110 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 114 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 69 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 132 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
D 230 GLN
G   9 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.103652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.075634 restraints weight = 24346.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.074365 restraints weight = 17278.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.075086 restraints weight = 16237.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.1133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.315  11837  Z= 0.167
  Angle     :  0.562   9.997  16072  Z= 0.300
  Chirality :  0.044   0.184   1753
  Planarity :  0.004   0.058   2111
  Dihedral  :  5.059  67.611   1623
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  4.45 %
    Favored  : 94.82 %
  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:  0.43 (0.21), residues: 1454
  helix:  1.10 (0.29), residues: 311
  sheet:  0.62 (0.23), residues: 455
  loop : -0.25 (0.23), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 776 
 HIS   0.003   0.001   HIS A  30 
 PHE   0.014   0.001   PHE A 494 
 TYR   0.013   0.001   TYR D  36 
 ARG   0.007   0.000   ARG E  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04948 (  496)
  hydrogen bonds       : angle       5.22694 ( 1377)
  metal coordination   : bond        0.18189 (    3)
  covalent geometry    : bond        0.00302 (11831)
  covalent geometry    : angle       0.56153 (16072)
  Misc. bond           : bond        0.00014 (    3)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 1.460 
Fit side-chains
REVERT: A  304 MET cc_start: 0.8161 (ttp) cc_final: 0.7928 (ttm)
REVERT: A  369 MET cc_start: 0.8724 (mmp) cc_final: 0.8373 (mmp)
REVERT: A  614 ASP cc_start: 0.8107 (p0) cc_final: 0.7899 (p0)
REVERT: B   48 TRP cc_start: 0.8711 (p-90) cc_final: 0.7681 (p-90)
REVERT: B  278 MET cc_start: 0.7669 (mpp) cc_final: 0.7254 (mpp)
REVERT: D   35 ILE cc_start: 0.8737 (mt) cc_final: 0.8535 (mt)
REVERT: D   42 LYS cc_start: 0.8840 (mtmm) cc_final: 0.8107 (mtmm)
REVERT: D   49 ARG cc_start: 0.7988 (mmm-85) cc_final: 0.7532 (tpp80)
REVERT: D   87 LEU cc_start: 0.9226 (mp) cc_final: 0.8992 (mp)
REVERT: E   44 SER cc_start: 0.8900 (p) cc_final: 0.8599 (p)
REVERT: E   96 ASN cc_start: 0.8449 (t0) cc_final: 0.7828 (p0)
  outliers start: 9
  outliers final: 5
  residues processed: 122
  average time/residue: 0.2396
  time to fit residues: 42.6479
Evaluate side-chains
  114 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 109
  time to evaluate  : 1.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue   97 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 128 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9990
   chunk 112 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 133 optimal weight:    0.5980
   chunk 0 optimal weight:   60.0000
   chunk 98 optimal weight:    3.9990
   chunk 135 optimal weight:    1.9990
   chunk 116 optimal weight:    0.0470
   chunk 91 optimal weight:    3.9990
   chunk 3 optimal weight:    9.9990
   overall best weight:    0.8482

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.103771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.075144 restraints weight = 24604.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.074382 restraints weight = 19746.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.075295 restraints weight = 17199.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11837  Z= 0.138
  Angle     :  0.536   9.349  16072  Z= 0.283
  Chirality :  0.043   0.171   1753
  Planarity :  0.004   0.064   2111
  Dihedral  :  4.891  67.023   1623
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  7.44 %
    Favored  : 91.99 %
  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:  0.57 (0.21), residues: 1454
  helix:  1.48 (0.29), residues: 305
  sheet:  0.58 (0.23), residues: 470
  loop : -0.20 (0.23), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 546 
 HIS   0.005   0.001   HIS G   9 
 PHE   0.021   0.001   PHE A 426 
 TYR   0.015   0.001   TYR B 345 
 ARG   0.003   0.000   ARG E  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04615 (  496)
  hydrogen bonds       : angle       4.85363 ( 1377)
  metal coordination   : bond        0.01128 (    3)
  covalent geometry    : bond        0.00309 (11831)
  covalent geometry    : angle       0.53571 (16072)
  Misc. bond           : bond        0.00020 (    3)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 1.322 
Fit side-chains
REVERT: A  109 MET cc_start: 0.8170 (tpt) cc_final: 0.7937 (tpt)
REVERT: A  304 MET cc_start: 0.8145 (ttp) cc_final: 0.7910 (ttm)
REVERT: A  369 MET cc_start: 0.8713 (mmp) cc_final: 0.8369 (mmp)
REVERT: B   48 TRP cc_start: 0.8696 (p-90) cc_final: 0.7645 (p-90)
REVERT: D   49 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7497 (tpp80)
REVERT: D   87 LEU cc_start: 0.9248 (mp) cc_final: 0.9000 (mp)
REVERT: E   44 SER cc_start: 0.8863 (p) cc_final: 0.8631 (p)
REVERT: E   96 ASN cc_start: 0.8432 (t0) cc_final: 0.7817 (p0)
  outliers start: 7
  outliers final: 4
  residues processed: 115
  average time/residue: 0.2373
  time to fit residues: 40.1481
Evaluate side-chains
  113 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 109
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain E residue  102 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 129 optimal weight:    0.5980
   chunk 1 optimal weight:    8.9990
   chunk 108 optimal weight:    0.9980
   chunk 143 optimal weight:    3.9990
   chunk 8 optimal weight:    0.2980
   chunk 100 optimal weight:    0.6980
   chunk 114 optimal weight:    0.3980
   chunk 141 optimal weight:    0.9990
   chunk 82 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   chunk 122 optimal weight:    4.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  30 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.104309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.076169 restraints weight = 24527.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.074630 restraints weight = 18585.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.075481 restraints weight = 17181.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11837  Z= 0.112
  Angle     :  0.508   8.410  16072  Z= 0.268
  Chirality :  0.042   0.150   1753
  Planarity :  0.004   0.076   2111
  Dihedral  :  4.711  66.167   1623
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  8.58 %
    Favored  : 90.61 %
  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:  0.68 (0.22), residues: 1454
  helix:  1.71 (0.29), residues: 310
  sheet:  0.63 (0.23), residues: 464
  loop : -0.20 (0.23), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 546 
 HIS   0.002   0.000   HIS B 165 
 PHE   0.010   0.001   PHE A 494 
 TYR   0.019   0.001   TYR B 333 
 ARG   0.003   0.000   ARG E  47 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04081 (  496)
  hydrogen bonds       : angle       4.64516 ( 1377)
  metal coordination   : bond        0.00325 (    3)
  covalent geometry    : bond        0.00248 (11831)
  covalent geometry    : angle       0.50771 (16072)
  Misc. bond           : bond        0.00012 (    3)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 1.386 
Fit side-chains
REVERT: A  109 MET cc_start: 0.8169 (tpt) cc_final: 0.7867 (tpt)
REVERT: A  304 MET cc_start: 0.8126 (ttp) cc_final: 0.7902 (ttm)
REVERT: A  369 MET cc_start: 0.8734 (mmp) cc_final: 0.8418 (mmp)
REVERT: B   48 TRP cc_start: 0.8684 (p-90) cc_final: 0.7663 (p-90)
REVERT: B   76 ASP cc_start: 0.7376 (t0) cc_final: 0.7148 (t0)
REVERT: D   42 LYS cc_start: 0.8780 (mtmm) cc_final: 0.8551 (mtmm)
REVERT: D   49 ARG cc_start: 0.7961 (mmm-85) cc_final: 0.7431 (tpp80)
REVERT: D   87 LEU cc_start: 0.9235 (mp) cc_final: 0.8981 (mp)
  outliers start: 10
  outliers final: 5
  residues processed: 121
  average time/residue: 0.2303
  time to fit residues: 41.0122
Evaluate side-chains
  114 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 109
  time to evaluate  : 1.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue  342 SER
Chi-restraints excluded: chain E residue  102 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 116 optimal weight:    0.0170
   chunk 110 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 126 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0270
   chunk 91 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
A 542 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.104549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.076265 restraints weight = 24501.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.074778 restraints weight = 18386.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.075318 restraints weight = 23210.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11837  Z= 0.109
  Angle     :  0.504   7.981  16072  Z= 0.264
  Chirality :  0.042   0.134   1753
  Planarity :  0.004   0.067   2111
  Dihedral  :  4.583  64.864   1623
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  9.79 %
    Favored  : 89.16 %
  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:  0.76 (0.22), residues: 1454
  helix:  1.92 (0.29), residues: 310
  sheet:  0.58 (0.23), residues: 471
  loop : -0.15 (0.24), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 546 
 HIS   0.002   0.000   HIS G   9 
 PHE   0.035   0.001   PHE A 426 
 TYR   0.018   0.001   TYR B 333 
 ARG   0.003   0.000   ARG E  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03902 (  496)
  hydrogen bonds       : angle       4.50669 ( 1377)
  metal coordination   : bond        0.00346 (    3)
  covalent geometry    : bond        0.00242 (11831)
  covalent geometry    : angle       0.50409 (16072)
  Misc. bond           : bond        0.00011 (    3)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 1.146 
Fit side-chains
REVERT: A  109 MET cc_start: 0.8131 (tpt) cc_final: 0.7924 (tpt)
REVERT: A  304 MET cc_start: 0.8103 (ttp) cc_final: 0.7888 (ttm)
REVERT: A  545 MET cc_start: 0.8199 (mtp) cc_final: 0.7867 (mtp)
REVERT: B   32 MET cc_start: 0.7797 (ttm) cc_final: 0.7509 (ttt)
REVERT: B   48 TRP cc_start: 0.8667 (p-90) cc_final: 0.7577 (p-90)
REVERT: D   49 ARG cc_start: 0.7951 (mmm-85) cc_final: 0.7426 (tpp80)
REVERT: D   87 LEU cc_start: 0.9242 (mp) cc_final: 0.8982 (mp)
REVERT: E   47 ARG cc_start: 0.7364 (mpt180) cc_final: 0.7120 (mmt-90)
REVERT: E   96 ASN cc_start: 0.8384 (t0) cc_final: 0.7886 (p0)
  outliers start: 13
  outliers final: 9
  residues processed: 119
  average time/residue: 0.2311
  time to fit residues: 41.4389
Evaluate side-chains
  117 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  567 THR
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  342 SER
Chi-restraints excluded: chain C residue   51 HIS
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue  102 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 120 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 5 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 140 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 136 optimal weight:    0.8980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 542 GLN
D  30 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.102000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.074472 restraints weight = 24688.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.072933 restraints weight = 19809.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.073749 restraints weight = 18163.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  11837  Z= 0.223
  Angle     :  0.576   8.323  16072  Z= 0.305
  Chirality :  0.044   0.153   1753
  Planarity :  0.004   0.067   2111
  Dihedral  :  4.853  67.671   1623
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 10.92 %
    Favored  : 87.70 %
  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:  0.59 (0.22), residues: 1454
  helix:  1.88 (0.30), residues: 306
  sheet:  0.36 (0.23), residues: 475
  loop : -0.20 (0.24), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 546 
 HIS   0.004   0.001   HIS G   9 
 PHE   0.015   0.001   PHE A 517 
 TYR   0.018   0.002   TYR B 333 
 ARG   0.003   0.000   ARG E  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05253 (  496)
  hydrogen bonds       : angle       4.77349 ( 1377)
  metal coordination   : bond        0.00843 (    3)
  covalent geometry    : bond        0.00517 (11831)
  covalent geometry    : angle       0.57628 (16072)
  Misc. bond           : bond        0.00022 (    3)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 1.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 MET cc_start: 0.8146 (ttp) cc_final: 0.7928 (ttm)
REVERT: A  545 MET cc_start: 0.8158 (mtp) cc_final: 0.7879 (mtp)
REVERT: B   48 TRP cc_start: 0.8645 (p-90) cc_final: 0.7576 (p-90)
REVERT: D   49 ARG cc_start: 0.7740 (mmm-85) cc_final: 0.7300 (tpp80)
REVERT: E   47 ARG cc_start: 0.7346 (mpt180) cc_final: 0.7097 (mpt180)
REVERT: E   96 ASN cc_start: 0.8370 (t0) cc_final: 0.7834 (p0)
  outliers start: 17
  outliers final: 12
  residues processed: 116
  average time/residue: 0.2205
  time to fit residues: 38.1764
Evaluate side-chains
  117 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 1.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  718 PHE
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue  342 SER
Chi-restraints excluded: chain C residue   51 HIS
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain D residue  187 GLU
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue  102 THR
Chi-restraints excluded: chain E residue  111 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 114 optimal weight:    0.0770
   chunk 115 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 119 optimal weight:    6.9990
   chunk 106 optimal weight:    4.9990
   chunk 66 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 7 optimal weight:    7.9990
   chunk 108 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   overall best weight:    0.9540

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

Flipped N/Q/H residues before XYZ refinement:
A 542 GLN
** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.103055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.075589 restraints weight = 24784.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.074114 restraints weight = 19268.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.074897 restraints weight = 17479.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11837  Z= 0.149
  Angle     :  0.542   9.032  16072  Z= 0.285
  Chirality :  0.043   0.138   1753
  Planarity :  0.004   0.069   2111
  Dihedral  :  4.719  67.852   1623
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 11.65 %
    Favored  : 87.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.22), residues: 1454
  helix:  1.99 (0.30), residues: 307
  sheet:  0.45 (0.23), residues: 471
  loop : -0.21 (0.24), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 546 
 HIS   0.003   0.000   HIS G   9 
 PHE   0.009   0.001   PHE A 197 
 TYR   0.014   0.001   TYR D  36 
 ARG   0.002   0.000   ARG E  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04450 (  496)
  hydrogen bonds       : angle       4.61362 ( 1377)
  metal coordination   : bond        0.00583 (    3)
  covalent geometry    : bond        0.00341 (11831)
  covalent geometry    : angle       0.54217 (16072)
  Misc. bond           : bond        0.00015 (    3)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 1.323 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 MET cc_start: 0.8095 (ttp) cc_final: 0.7886 (ttm)
REVERT: A  325 MET cc_start: 0.7177 (pmm) cc_final: 0.6964 (pmm)
REVERT: B   48 TRP cc_start: 0.8650 (p-90) cc_final: 0.7612 (p-90)
REVERT: D   42 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8210 (mtmm)
REVERT: D   49 ARG cc_start: 0.7741 (mmm-85) cc_final: 0.7290 (tpp80)
REVERT: D   87 LEU cc_start: 0.9025 (mp) cc_final: 0.8803 (mt)
REVERT: D  227 MET cc_start: 0.8275 (mtp) cc_final: 0.7989 (mtp)
REVERT: E   47 ARG cc_start: 0.7325 (mpt180) cc_final: 0.7057 (mpt180)
REVERT: E   54 GLN cc_start: 0.8353 (mt0) cc_final: 0.8086 (mt0)
REVERT: E   96 ASN cc_start: 0.8319 (t0) cc_final: 0.7828 (p0)
  outliers start: 12
  outliers final: 10
  residues processed: 116
  average time/residue: 0.2235
  time to fit residues: 38.6860
Evaluate side-chains
  117 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 1.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  718 PHE
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  342 SER
Chi-restraints excluded: chain C residue   51 HIS
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue  102 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 97 optimal weight:    0.3980
   chunk 111 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 89 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 93 optimal weight:    0.3980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.103923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.075467 restraints weight = 24598.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.074027 restraints weight = 18624.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.075306 restraints weight = 16939.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11837  Z= 0.120
  Angle     :  0.530   9.423  16072  Z= 0.277
  Chirality :  0.042   0.136   1753
  Planarity :  0.004   0.068   2111
  Dihedral  :  4.547  66.714   1623
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 11.89 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.22), residues: 1454
  helix:  2.12 (0.30), residues: 306
  sheet:  0.54 (0.23), residues: 471
  loop : -0.15 (0.24), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 546 
 HIS   0.004   0.001   HIS B 324 
 PHE   0.009   0.001   PHE A 494 
 TYR   0.012   0.001   TYR B 345 
 ARG   0.002   0.000   ARG E  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03968 (  496)
  hydrogen bonds       : angle       4.48372 ( 1377)
  metal coordination   : bond        0.00411 (    3)
  covalent geometry    : bond        0.00271 (11831)
  covalent geometry    : angle       0.53026 (16072)
  Misc. bond           : bond        0.00012 (    3)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 1.219 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 MET cc_start: 0.8096 (ttp) cc_final: 0.7880 (ttm)
REVERT: B   32 MET cc_start: 0.9252 (tpp) cc_final: 0.9004 (tpp)
REVERT: B   48 TRP cc_start: 0.8730 (p-90) cc_final: 0.7569 (p-90)
REVERT: D   42 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8334 (mtmm)
REVERT: D   49 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.7452 (tpp80)
REVERT: D   87 LEU cc_start: 0.9168 (mp) cc_final: 0.8917 (mp)
REVERT: D  227 MET cc_start: 0.8275 (mtp) cc_final: 0.7959 (mtp)
REVERT: E   54 GLN cc_start: 0.8494 (mt0) cc_final: 0.8082 (mt0)
REVERT: E   96 ASN cc_start: 0.8370 (t0) cc_final: 0.7862 (p0)
  outliers start: 12
  outliers final: 11
  residues processed: 116
  average time/residue: 0.2286
  time to fit residues: 39.0059
Evaluate side-chains
  116 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 1.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  718 PHE
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  342 SER
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue  102 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 125 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 119 optimal weight:    6.9990
   chunk 143 optimal weight:    0.9990
   chunk 38 optimal weight:    0.1980
   chunk 117 optimal weight:   10.0000
   overall best weight:    1.2388

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

Flipped N/Q/H residues before XYZ refinement:
** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.103779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.074519 restraints weight = 24945.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.074106 restraints weight = 18457.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.075059 restraints weight = 15391.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11837  Z= 0.184
  Angle     :  0.560   9.175  16072  Z= 0.295
  Chirality :  0.043   0.144   1753
  Planarity :  0.004   0.067   2111
  Dihedral  :  4.676  67.185   1623
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 11.97 %
    Favored  : 86.89 %
  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:  0.63 (0.22), residues: 1454
  helix:  1.89 (0.30), residues: 310
  sheet:  0.41 (0.23), residues: 475
  loop : -0.21 (0.24), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 546 
 HIS   0.003   0.001   HIS G   9 
 PHE   0.011   0.001   PHE A 517 
 TYR   0.016   0.001   TYR D  36 
 ARG   0.004   0.000   ARG E  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04773 (  496)
  hydrogen bonds       : angle       4.64910 ( 1377)
  metal coordination   : bond        0.00670 (    3)
  covalent geometry    : bond        0.00425 (11831)
  covalent geometry    : angle       0.55981 (16072)
  Misc. bond           : bond        0.00020 (    3)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 1.321 
Fit side-chains
   revert: symmetry clash
REVERT: A  261 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8538 (p)
REVERT: B   32 MET cc_start: 0.9221 (tpp) cc_final: 0.8980 (tpp)
REVERT: B   48 TRP cc_start: 0.8712 (p-90) cc_final: 0.7635 (p-90)
REVERT: D   42 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8385 (mtmm)
REVERT: D   49 ARG cc_start: 0.7987 (mmm-85) cc_final: 0.7443 (tpp80)
REVERT: D   87 LEU cc_start: 0.9184 (mp) cc_final: 0.8955 (mp)
REVERT: D  227 MET cc_start: 0.8401 (mtp) cc_final: 0.8128 (mtp)
REVERT: E   47 ARG cc_start: 0.7419 (mpt180) cc_final: 0.7196 (mmt-90)
REVERT: E   54 GLN cc_start: 0.8496 (mt0) cc_final: 0.8165 (mt0)
REVERT: E   96 ASN cc_start: 0.8372 (t0) cc_final: 0.7878 (p0)
  outliers start: 14
  outliers final: 10
  residues processed: 115
  average time/residue: 0.2334
  time to fit residues: 39.5820
Evaluate side-chains
  115 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  675 PHE
Chi-restraints excluded: chain A residue  718 PHE
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  342 SER
Chi-restraints excluded: chain C residue   62 SER
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue  102 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 138 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 139 optimal weight:    0.0170
   chunk 15 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0060
   chunk 80 optimal weight:    0.0970
   chunk 92 optimal weight:    0.0020
   chunk 91 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 6 optimal weight:   20.0000
   overall best weight:    0.2040

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

Flipped N/Q/H residues before XYZ refinement:
** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.106572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.070928 restraints weight = 24615.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.073725 restraints weight = 13812.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.075471 restraints weight = 9807.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  11837  Z= 0.098
  Angle     :  0.528  11.438  16072  Z= 0.273
  Chirality :  0.042   0.135   1753
  Planarity :  0.004   0.067   2111
  Dihedral  :  4.374  64.699   1623
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 12.54 %
    Favored  : 86.73 %
  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:  0.87 (0.22), residues: 1454
  helix:  2.06 (0.29), residues: 312
  sheet:  0.66 (0.23), residues: 468
  loop : -0.11 (0.24), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 546 
 HIS   0.002   0.000   HIS G   9 
 PHE   0.008   0.001   PHE A 140 
 TYR   0.033   0.001   TYR A 142 
 ARG   0.009   0.000   ARG G  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03414 (  496)
  hydrogen bonds       : angle       4.36507 ( 1377)
  metal coordination   : bond        0.00151 (    3)
  covalent geometry    : bond        0.00211 (11831)
  covalent geometry    : angle       0.52823 (16072)
  Misc. bond           : bond        0.00011 (    3)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 1.321 
Fit side-chains
   revert: symmetry clash
REVERT: A  261 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8501 (p)
REVERT: A  325 MET cc_start: 0.7133 (pmm) cc_final: 0.6914 (pmm)
REVERT: B   48 TRP cc_start: 0.8626 (p-90) cc_final: 0.7613 (p-90)
REVERT: D   42 LYS cc_start: 0.8700 (mtmm) cc_final: 0.8357 (mtmm)
REVERT: D   49 ARG cc_start: 0.8084 (mmm-85) cc_final: 0.7493 (tpp80)
REVERT: D   87 LEU cc_start: 0.9188 (mp) cc_final: 0.8922 (mp)
REVERT: E   37 TYR cc_start: 0.9215 (t80) cc_final: 0.8977 (t80)
REVERT: E   96 ASN cc_start: 0.8145 (t0) cc_final: 0.7829 (p0)
  outliers start: 9
  outliers final: 6
  residues processed: 117
  average time/residue: 0.2545
  time to fit residues: 44.0012
Evaluate side-chains
  112 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  718 PHE
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  342 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 133 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 106 optimal weight:    4.9990
   chunk 102 optimal weight:    2.9990
   chunk 143 optimal weight:    0.9990
   chunk 95 optimal weight:    0.4980
   chunk 44 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 55 optimal weight:    0.3980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.104916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.069067 restraints weight = 24674.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.071789 restraints weight = 13871.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.073494 restraints weight = 9933.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11837  Z= 0.149
  Angle     :  0.559  12.570  16072  Z= 0.291
  Chirality :  0.043   0.135   1753
  Planarity :  0.004   0.066   2111
  Dihedral  :  4.457  65.195   1623
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 12.86 %
    Favored  : 86.49 %
  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:  0.85 (0.22), residues: 1454
  helix:  1.95 (0.30), residues: 315
  sheet:  0.63 (0.23), residues: 453
  loop : -0.07 (0.24), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 546 
 HIS   0.003   0.000   HIS G   9 
 PHE   0.011   0.001   PHE A 648 
 TYR   0.040   0.001   TYR A 142 
 ARG   0.008   0.000   ARG G  10 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04289 (  496)
  hydrogen bonds       : angle       4.48464 ( 1377)
  metal coordination   : bond        0.00561 (    3)
  covalent geometry    : bond        0.00343 (11831)
  covalent geometry    : angle       0.55937 (16072)
  Misc. bond           : bond        0.00014 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 3726.72 seconds
wall clock time: 65 minutes 21.75 seconds (3921.75 seconds total)