Starting phenix.real_space_refine
on Mon Aug 25 08:04:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hg9_52131/08_2025/9hg9_52131.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hg9_52131/08_2025/9hg9_52131.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hg9_52131/08_2025/9hg9_52131.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hg9_52131/08_2025/9hg9_52131.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hg9_52131/08_2025/9hg9_52131.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hg9_52131/08_2025/9hg9_52131.map"
  }
  resolution = 2.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      43      5.16       5
     C    8417      2.51       5
     N    2313      2.21       5
     O    2632      1.98       5
     H   12929      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 26335
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 12165
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 787, 12165
          Classifications: {'peptide': 787}
          Link IDs: {'PTRANS': 29, 'TRANS': 757}
    Chain: "B"
      Number of atoms: 5519
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 370, 5519
          Classifications: {'peptide': 370}
          Link IDs: {'PTRANS': 11, 'TRANS': 358}
    Chain: "C"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 845
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 6, 'TRANS': 51}
    Chain: "D"
      Number of atoms: 3348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 3348
          Classifications: {'peptide': 209}
          Link IDs: {'PTRANS': 12, 'TRANS': 196}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 1345
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 5, 'TRANS': 85}
    Chain: "F"
      Number of atoms: 2986
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 186, 2986
          Classifications: {'peptide': 186}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 182}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 126
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 126
          Classifications: {'peptide': 7}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'UX8:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.19, per 1000 atoms: 0.16
  Number of scatterers: 26335
  At special positions: 0
  Unit cell: (102.93, 126.29, 140.89, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      43     16.00
     Mg      1     11.99
     O    2632      8.00
     N    2313      7.00
     C    8417      6.00
     H   12929      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.49
  Conformation dependent library (CDL) restraints added in 683.8 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3146

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 20 sheets defined
      29.6% alpha, 28.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 46
    Processing helix  chain 'A' and resid 55 through 69
    Processing helix  chain 'A' and resid 106 through 118
    Processing helix  chain 'A' and resid 129 through 145
    Processing helix  chain 'A' and resid 189 through 195
    Processing helix  chain 'A' and resid 215 through 232
    Processing helix  chain 'A' and resid 280 through 286
      removed outlier: 3.810A  pdb=" N   GLN A 286 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 315
    Processing helix  chain 'A' and resid 361 through 367
      removed outlier: 3.663A  pdb=" N   LEU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 3.891A  pdb=" N   GLY A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 452
      removed outlier: 3.822A  pdb=" N   GLY A 451 " --> pdb=" O   ASN A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 500
    Processing helix  chain 'A' and resid 542 through 552
    Processing helix  chain 'A' and resid 647 through 651
      removed outlier: 3.551A  pdb=" N   ASN A 651 " --> pdb=" O   PHE A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 691 through 695
    Processing helix  chain 'A' and resid 729 through 731
      No H-bonds generated for 'chain 'A' and resid 729 through 731'
    Processing helix  chain 'C' and resid 31 through 38
      removed outlier: 3.811A  pdb=" N   VAL C  35 " --> pdb=" O   TYR C  31 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   SER C  36 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 46
      removed outlier: 3.546A  pdb=" N   GLY D  46 " --> pdb=" O   LYS D  42 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 62
      removed outlier: 3.712A  pdb=" N   ALA D  51 " --> pdb=" O   ASN D  47 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 82
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 102 through 104
      No H-bonds generated for 'chain 'D' and resid 102 through 104'
    Processing helix  chain 'D' and resid 105 through 121
    Processing helix  chain 'D' and resid 137 through 154
    Processing helix  chain 'D' and resid 159 through 189
    Processing helix  chain 'D' and resid 190 through 205
      removed outlier: 3.617A  pdb=" N   VAL D 195 " --> pdb=" O   TRP D 191 " (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 242
      removed outlier: 3.656A  pdb=" N   ASN D 241 " --> pdb=" O   ILE D 237 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 22 through 27
      removed outlier: 3.837A  pdb=" N   VAL E  26 " --> pdb=" O   THR E  22 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 60
    Processing helix  chain 'F' and resid 39 through 56
      removed outlier: 3.779A  pdb=" N   GLN F  55 " --> pdb=" O   LEU F  51 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ALA F  56 " --> pdb=" O   ASN F  52 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 57 through 60
    Processing helix  chain 'F' and resid 63 through 88
    Processing helix  chain 'F' and resid 92 through 101
      removed outlier: 3.644A  pdb=" N   ALA F 101 " --> pdb=" O   ASP F  97 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 111 through 118
      removed outlier: 3.645A  pdb=" N   ARG F 115 " --> pdb=" O   LEU F 111 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU F 118 " --> pdb=" O   MET F 114 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 124 through 149
      removed outlier: 4.272A  pdb=" N   TYR F 128 " --> pdb=" O   ASN F 124 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ARG F 129 " --> pdb=" O   TYR F 125 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 153 through 167
      removed outlier: 3.859A  pdb=" N   VAL F 157 " --> pdb=" O   LEU F 153 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 391 through 421
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 90
      removed outlier: 7.058A  pdb=" N   GLN A  87 " --> pdb=" O   VAL A  75 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   VAL A  75 " --> pdb=" O   GLN A  87 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   LYS A  89 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ARG A  79 " --> pdb=" O   GLN F  23 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLN F  23 " --> pdb=" O   ARG A  79 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100
      removed outlier: 4.179A  pdb=" N   ILE A  94 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   LEU A 165 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   SER A  96 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   LEU A 167 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   THR A  98 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.692A  pdb=" N   PHE A 169 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   SER A 100 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183
      removed outlier: 7.506A  pdb=" N   VAL A 256 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   VAL A 258 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   ILE A 260 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER A 242 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
      removed outlier: 8.767A  pdb=" N   SER B 193 " --> pdb=" O   THR A 243 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   VAL A 245 " --> pdb=" O   SER B 193 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295
      removed outlier: 4.012A  pdb=" N   GLU A 294 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   LEU A 268 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   LEU A 337 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   GLY A 270 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 7.717A  pdb=" N   VAL A 339 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   GLU A 272 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 7.405A  pdb=" N   VAL A 341 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   SER A 274 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 294 through 295
      removed outlier: 4.012A  pdb=" N   GLU A 294 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   LEU A 268 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   LEU A 337 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   GLY A 270 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 7.717A  pdb=" N   VAL A 339 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   GLU A 272 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 7.405A  pdb=" N   VAL A 341 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   SER A 274 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 355
      removed outlier: 7.518A  pdb=" N   VAL A 414 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   ILE A 352 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   TYR A 416 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   PHE A 354 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   VAL A 418 " --> pdb=" O   PHE A 354 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   GLN A 411 " --> pdb=" O   ARG A 404 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   ARG A 404 " --> pdb=" O   GLN A 411 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   ASP A 413 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   THR A 402 " --> pdb=" O   ASP A 413 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   VAL A 415 " --> pdb=" O   THR A 400 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   THR A 400 " --> pdb=" O   VAL A 415 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   LYS A 417 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   VAL A 398 " --> pdb=" O   LYS A 417 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   LYS A 419 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 484 through 485
    Processing sheet with id=AA8, first strand: chain 'A' and resid 484 through 485
      removed outlier: 3.507A  pdb=" N   VAL A 599 " --> pdb=" O   PHE A 572 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   TYR A 574 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLY A 590 " --> pdb=" O   TYR A 618 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   MET A 768 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ALA A 770 " --> pdb=" O   GLN A 789 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 671 through 674
      removed outlier: 5.424A  pdb=" N   ASP A 704 " --> pdb=" O   ALA A 672 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   TYR A 674 " --> pdb=" O   SER A 702 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   SER A 702 " --> pdb=" O   TYR A 674 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 44 through 50
      removed outlier: 5.135A  pdb=" N   THR B  46 " --> pdb=" O   THR B 391 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   THR B 391 " --> pdb=" O   THR B  46 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   TRP B  48 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 67
      removed outlier: 6.749A  pdb=" N   VAL B  81 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   SER B  94 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ALA B  83 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 117
      removed outlier: 6.590A  pdb=" N   VAL B 131 " --> pdb=" O   GLN B 144 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   GLN B 144 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   ALA B 133 " --> pdb=" O   ALA B 142 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 156 through 158
      removed outlier: 3.906A  pdb=" N   TRP B 183 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   ASN B 175 " --> pdb=" O   VAL B 181 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   VAL B 181 " --> pdb=" O   ASN B 175 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 201 through 202
      removed outlier: 3.610A  pdb=" N   TRP B 228 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   LEU B 220 " --> pdb=" O   MET B 226 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   MET B 226 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 252 through 254
      removed outlier: 6.578A  pdb=" N   LEU B 267 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   LYS B 280 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   ALA B 269 " --> pdb=" O   MET B 278 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 290 through 292
      removed outlier: 4.082A  pdb=" N   TRP B 317 " --> pdb=" O   ALA B 307 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   THR B 309 " --> pdb=" O   THR B 315 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   THR B 315 " --> pdb=" O   THR B 309 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 331 through 333
      removed outlier: 5.612A  pdb=" N   ASN B 350 " --> pdb=" O   PHE B 356 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   PHE B 356 " --> pdb=" O   ASN B 350 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 35
      removed outlier: 4.162A  pdb=" N   MET E  64 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 32 through 35
    Processing sheet with id=AC2, first strand: chain 'F' and resid 35 through 38

    624 hydrogen bonds defined for protein.
    1755 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: 6.03

  Time building geometry restraints manager: 3.39 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 12929
        1.03 -     1.23: 5
        1.23 -     1.42: 5868
        1.42 -     1.62: 7720
        1.62 -     1.81: 84
  Bond restraints: 26606
  Sorted by residual:
  bond pdb=" CA  UX8 G   3 "
       pdb=" C   UX8 G   3 "
    ideal  model  delta    sigma   weight residual
    1.525  1.351  0.174 2.10e-02 2.27e+03 6.88e+01
  bond pdb=" N   UX8 G   3 "
       pdb=" H   UX8 G   3 "
    ideal  model  delta    sigma   weight residual
    0.860  1.000 -0.140 2.00e-02 2.50e+03 4.87e+01
  bond pdb=" NE1 UX8 G   3 "
       pdb=" HE1 UX8 G   3 "
    ideal  model  delta    sigma   weight residual
    0.860  1.000 -0.140 2.00e-02 2.50e+03 4.87e+01
  bond pdb=" CE3 UX8 G   3 "
       pdb=" HE3 UX8 G   3 "
    ideal  model  delta    sigma   weight residual
    0.930  1.000 -0.070 2.00e-02 2.50e+03 1.24e+01
  bond pdb=" CZ2 UX8 G   3 "
       pdb=" HZ2 UX8 G   3 "
    ideal  model  delta    sigma   weight residual
    0.930  1.000 -0.070 2.00e-02 2.50e+03 1.24e+01
  ... (remaining 26601 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 47628
        2.24 -     4.47: 189
        4.47 -     6.71: 17
        6.71 -     8.94: 3
        8.94 -    11.18: 3
  Bond angle restraints: 47840
  Sorted by residual:
  angle pdb=" CA  UX8 G   3 "
        pdb=" C   UX8 G   3 "
        pdb=" O   UX8 G   3 "
      ideal   model   delta    sigma   weight residual
     120.80  129.85   -9.05 1.70e+00 3.46e-01 2.83e+01
  angle pdb=" CA  ASP A 512 "
        pdb=" CB  ASP A 512 "
        pdb=" CG  ASP A 512 "
      ideal   model   delta    sigma   weight residual
     112.60  117.09   -4.49 1.00e+00 1.00e+00 2.01e+01
  angle pdb=" CB  MET A 109 "
        pdb=" CG  MET A 109 "
        pdb=" SD  MET A 109 "
      ideal   model   delta    sigma   weight residual
     112.70  123.88  -11.18 3.00e+00 1.11e-01 1.39e+01
  angle pdb=" CB  MET F  46 "
        pdb=" CG  MET F  46 "
        pdb=" SD  MET F  46 "
      ideal   model   delta    sigma   weight residual
     112.70  122.21   -9.51 3.00e+00 1.11e-01 1.01e+01
  angle pdb=" CB  LYS F  50 "
        pdb=" CG  LYS F  50 "
        pdb=" CD  LYS F  50 "
      ideal   model   delta    sigma   weight residual
     111.30  117.95   -6.65 2.30e+00 1.89e-01 8.37e+00
  ... (remaining 47835 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 11439
       17.31 -    34.63: 772
       34.63 -    51.94: 280
       51.94 -    69.26: 81
       69.26 -    86.57: 10
  Dihedral angle restraints: 12582
    sinusoidal: 6824
      harmonic: 5758
  Sorted by residual:
  dihedral pdb=" CB  CYS A 690 "
           pdb=" SG  CYS A 690 "
           pdb=" SG  CYS A 700 "
           pdb=" CB  CYS A 700 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -125.57   39.57     1      1.00e+01 1.00e-02 2.20e+01
  dihedral pdb=" CA  GLU A 689 "
           pdb=" C   GLU A 689 "
           pdb=" N   CYS A 690 "
           pdb=" CA  CYS A 690 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.94   20.06     0      5.00e+00 4.00e-02 1.61e+01
  dihedral pdb=" CG  ARG D  94 "
           pdb=" CD  ARG D  94 "
           pdb=" NE  ARG D  94 "
           pdb=" CZ  ARG D  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -40.27  -49.73     2      1.50e+01 4.44e-03 1.24e+01
  ... (remaining 12579 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1803
       0.062 -    0.125: 222
       0.125 -    0.187: 5
       0.187 -    0.249: 0
       0.249 -    0.311: 1
  Chirality restraints: 2031
  Sorted by residual:
  chirality pdb=" CA  UX8 G   3 "
            pdb=" N   UX8 G   3 "
            pdb=" C   UX8 G   3 "
            pdb=" CB  UX8 G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.42e+00
  chirality pdb=" CA  LYS E 107 "
            pdb=" N   LYS E 107 "
            pdb=" C   LYS E 107 "
            pdb=" CB  LYS E 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.84e-01
  chirality pdb=" CA  VAL A 673 "
            pdb=" N   VAL A 673 "
            pdb=" C   VAL A 673 "
            pdb=" CB  VAL A 673 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.19e-01
  ... (remaining 2028 not shown)

  Planarity restraints: 4074
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 512 "    0.011 2.00e-02 2.50e+03   2.02e-02 4.07e+00
        pdb=" N   VAL A 513 "   -0.035 2.00e-02 2.50e+03
        pdb=" CA  VAL A 513 "    0.009 2.00e-02 2.50e+03
        pdb=" H   VAL A 513 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D  94 "    0.159 9.50e-02 1.11e+02   5.34e-02 3.49e+00
        pdb=" NE  ARG D  94 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG D  94 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG D  94 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG D  94 "   -0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG D  94 "   -0.003 2.00e-02 2.50e+03
        pdb="HH12 ARG D  94 "    0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG D  94 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG D  94 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 154 "    0.021 5.00e-02 4.00e+02   3.12e-02 1.56e+00
        pdb=" N   PRO B 155 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B 155 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 155 "    0.018 5.00e-02 4.00e+02
  ... (remaining 4071 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 1087
        2.18 -     2.78: 51751
        2.78 -     3.39: 70809
        3.39 -     3.99: 93559
        3.99 -     4.60: 145530
  Nonbonded interactions: 362736
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU C  39 "
            pdb=" H   GLU C  39 "
     model   vdw
     1.574 2.450
  nonbonded pdb=" OE1 GLU B  27 "
            pdb=" H   GLU B  27 "
     model   vdw
     1.604 2.450
  nonbonded pdb=" O   LEU A  66 "
            pdb=" HG1 THR A  69 "
     model   vdw
     1.616 2.450
  nonbonded pdb=" HD1 HIS A 533 "
            pdb=" OD1 ASP A 568 "
     model   vdw
     1.617 2.450
  nonbonded pdb=" O   VAL D  27 "
            pdb="HH22 ARG D  61 "
     model   vdw
     1.625 2.450
  ... (remaining 362731 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.170
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.080
  Set scattering table:                    0.060
  Process input model:                     24.580
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:9.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
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      :  0.003   0.174  13680  Z= 0.142
  Angle     :  0.508  11.180  18571  Z= 0.266
  Chirality :  0.041   0.311   2031
  Planarity :  0.003   0.070   2448
  Dihedral  : 13.877  86.572   4997
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 13.77 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.21), residues: 1687
  helix:  2.47 (0.24), residues: 454
  sheet:  0.27 (0.25), residues: 462
  loop : -0.40 (0.23), residues: 771

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D  94 
 TYR   0.016   0.001   TYR D 184 
 PHE   0.006   0.001   PHE A  67 
 TRP   0.005   0.001   TRP B 348 
 HIS   0.001   0.000   HIS D 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (13677)
  covalent geometry    : angle       0.50669 (18569)
  SS BOND              : bond        0.00057 (    1)
  SS BOND              : angle       2.95800 (    2)
  hydrogen bonds       : bond        0.18298 (  613)
  hydrogen bonds       : angle       6.93174 ( 1755)
  Misc. bond           : bond        0.02984 (    2)

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

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

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 146
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 ARG cc_start: 0.8715 (ttp-170) cc_final: 0.7977 (ptp90)
REVERT: E   46 ILE cc_start: 0.7466 (pp) cc_final: 0.7165 (pp)
REVERT: F  416 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8426 (tm-30)
  outliers start: 4
  outliers final: 2
  residues processed: 150
  average time/residue: 1.2687
  time to fit residues: 206.4226
Evaluate side-chains
  122 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 120
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain D residue  134 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    0.5980
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 427 ASN
A 441 GLN
B  58 ASN
B 276 GLN
F 393 GLN
G   2 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.101317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.069317 restraints weight = 66567.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.2909 rms_B_bonded: 2.67
r_work: 0.2803 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2667 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.0950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  13680  Z= 0.188
  Angle     :  0.513   6.552  18571  Z= 0.275
  Chirality :  0.042   0.153   2031
  Planarity :  0.003   0.034   2448
  Dihedral  :  4.033  44.885   1878
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 13.14 %
    Favored  : 85.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.21), residues: 1687
  helix:  2.31 (0.24), residues: 461
  sheet:  0.17 (0.24), residues: 468
  loop : -0.49 (0.23), residues: 758

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 526 
 TYR   0.015   0.001   TYR D 184 
 PHE   0.016   0.001   PHE A 517 
 TRP   0.012   0.001   TRP A 776 
 HIS   0.004   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (13677)
  covalent geometry    : angle       0.51241 (18569)
  SS BOND              : bond        0.00384 (    1)
  SS BOND              : angle       2.82441 (    2)
  hydrogen bonds       : bond        0.04694 (  613)
  hydrogen bonds       : angle       5.07207 ( 1755)
  Misc. bond           : bond        0.00092 (    2)

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

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

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 MET cc_start: 0.8951 (tmm) cc_final: 0.8682 (tmm)
REVERT: A  192 GLU cc_start: 0.8739 (tp30) cc_final: 0.8365 (tp30)
REVERT: B  276 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7524 (mm110)
REVERT: B  311 ASP cc_start: 0.9358 (m-30) cc_final: 0.9035 (t0)
REVERT: E   83 HIS cc_start: 0.7895 (OUTLIER) cc_final: 0.7260 (p90)
  outliers start: 16
  outliers final: 5
  residues processed: 144
  average time/residue: 1.0742
  time to fit residues: 170.9228
Evaluate side-chains
  124 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  276 GLN
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue   83 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 128 optimal weight:    1.9990
   chunk 142 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 159 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 121 optimal weight:    4.9990
   chunk 161 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN
A 217 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.101944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.069453 restraints weight = 67100.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.2874 rms_B_bonded: 2.79
r_work: 0.2765 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2628 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038  13680  Z= 0.244
  Angle     :  0.518   6.420  18571  Z= 0.277
  Chirality :  0.043   0.145   2031
  Planarity :  0.003   0.045   2448
  Dihedral  :  3.945  26.522   1875
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 13.77 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.21), residues: 1687
  helix:  2.18 (0.24), residues: 461
  sheet:  0.03 (0.24), residues: 471
  loop : -0.53 (0.23), residues: 755

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 120 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.015   0.001   PHE A 517 
 TRP   0.012   0.001   TRP B 348 
 HIS   0.006   0.001   HIS A  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 (13677)
  covalent geometry    : angle       0.51669 (18569)
  SS BOND              : bond        0.00422 (    1)
  SS BOND              : angle       2.85963 (    2)
  hydrogen bonds       : bond        0.04534 (  613)
  hydrogen bonds       : angle       4.90110 ( 1755)
  Misc. bond           : bond        0.00073 (    2)

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

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

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  441 GLN cc_start: 0.8651 (tt0) cc_final: 0.8362 (tm-30)
REVERT: B  311 ASP cc_start: 0.9365 (m-30) cc_final: 0.9057 (t0)
REVERT: E   83 HIS cc_start: 0.7942 (OUTLIER) cc_final: 0.7257 (p90)
REVERT: F  128 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.6477 (t80)
  outliers start: 19
  outliers final: 8
  residues processed: 139
  average time/residue: 1.0108
  time to fit residues: 155.3027
Evaluate side-chains
  128 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue   83 HIS
Chi-restraints excluded: chain F residue  128 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 102 optimal weight:    3.9990
   chunk 132 optimal weight:    0.7980
   chunk 67 optimal weight:    6.9990
   chunk 94 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 147 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 112 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A  30 HIS
A 217 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.102678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.070410 restraints weight = 66329.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 2.78
r_work: 0.2771 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2636 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13680  Z= 0.143
  Angle     :  0.482   5.908  18571  Z= 0.254
  Chirality :  0.042   0.146   2031
  Planarity :  0.003   0.049   2448
  Dihedral  :  3.880  25.005   1875
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 13.42 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.21), residues: 1687
  helix:  2.33 (0.24), residues: 461
  sheet:  0.07 (0.24), residues: 463
  loop : -0.50 (0.23), residues: 763

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  94 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.012   0.001   PHE A 517 
 TRP   0.013   0.001   TRP B 348 
 HIS   0.002   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (13677)
  covalent geometry    : angle       0.48191 (18569)
  SS BOND              : bond        0.00327 (    1)
  SS BOND              : angle       2.25554 (    2)
  hydrogen bonds       : bond        0.03946 (  613)
  hydrogen bonds       : angle       4.64958 ( 1755)
  Misc. bond           : bond        0.00089 (    2)

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

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

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  192 GLU cc_start: 0.8755 (tp30) cc_final: 0.8348 (tp30)
REVERT: A  441 GLN cc_start: 0.8614 (tt0) cc_final: 0.8293 (tm-30)
REVERT: B  311 ASP cc_start: 0.9371 (m-30) cc_final: 0.9060 (t0)
REVERT: E   83 HIS cc_start: 0.7890 (OUTLIER) cc_final: 0.7280 (p90)
  outliers start: 19
  outliers final: 10
  residues processed: 143
  average time/residue: 1.0657
  time to fit residues: 168.0847
Evaluate side-chains
  133 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue   83 HIS
Chi-restraints excluded: chain F residue  137 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 10 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 121 optimal weight:    0.6980
   chunk 99 optimal weight:    6.9990
   chunk 79 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 106 optimal weight:    0.7980
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.103256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.071092 restraints weight = 66228.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.2906 rms_B_bonded: 2.78
r_work: 0.2795 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2658 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13680  Z= 0.122
  Angle     :  0.480   7.779  18571  Z= 0.250
  Chirality :  0.041   0.160   2031
  Planarity :  0.003   0.048   2448
  Dihedral  :  3.824  23.820   1875
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 13.91 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.21), residues: 1687
  helix:  2.42 (0.24), residues: 461
  sheet:  0.03 (0.24), residues: 462
  loop : -0.45 (0.23), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  94 
 TYR   0.015   0.001   TYR D 184 
 PHE   0.010   0.001   PHE A 517 
 TRP   0.012   0.001   TRP B 348 
 HIS   0.002   0.000   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (13677)
  covalent geometry    : angle       0.47956 (18569)
  SS BOND              : bond        0.00663 (    1)
  SS BOND              : angle       1.33902 (    2)
  hydrogen bonds       : bond        0.03745 (  613)
  hydrogen bonds       : angle       4.53467 ( 1755)
  Misc. bond           : bond        0.00100 (    2)

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

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

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7852 (ptp-170)
REVERT: A  192 GLU cc_start: 0.8794 (tp30) cc_final: 0.8369 (tp30)
REVERT: A  441 GLN cc_start: 0.8632 (tt0) cc_final: 0.8259 (tm-30)
REVERT: B  311 ASP cc_start: 0.9362 (m-30) cc_final: 0.9056 (t0)
REVERT: E   83 HIS cc_start: 0.7908 (OUTLIER) cc_final: 0.7269 (p90)
  outliers start: 22
  outliers final: 12
  residues processed: 140
  average time/residue: 1.0672
  time to fit residues: 164.9997
Evaluate side-chains
  135 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue   83 HIS
Chi-restraints excluded: chain F residue  137 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 133 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 145 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 80 optimal weight:    0.6980
   chunk 84 optimal weight:    0.6980
   chunk 105 optimal weight:    2.9990
   chunk 126 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.102060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.069811 restraints weight = 66452.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 2.78
r_work: 0.2791 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2654 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13680  Z= 0.144
  Angle     :  0.484   7.233  18571  Z= 0.252
  Chirality :  0.041   0.140   2031
  Planarity :  0.003   0.053   2448
  Dihedral  :  3.813  23.587   1875
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 14.39 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.21), residues: 1687
  helix:  2.44 (0.24), residues: 461
  sheet: -0.00 (0.24), residues: 459
  loop : -0.44 (0.23), residues: 767

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  94 
 TYR   0.015   0.001   TYR D 184 
 PHE   0.010   0.001   PHE A 517 
 TRP   0.011   0.001   TRP B 348 
 HIS   0.002   0.000   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (13677)
  covalent geometry    : angle       0.48366 (18569)
  SS BOND              : bond        0.00261 (    1)
  SS BOND              : angle       1.53658 (    2)
  hydrogen bonds       : bond        0.03684 (  613)
  hydrogen bonds       : angle       4.48395 ( 1755)
  Misc. bond           : bond        0.00090 (    2)

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

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

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7833 (ptp-170)
REVERT: A  192 GLU cc_start: 0.8801 (tp30) cc_final: 0.8364 (tp30)
REVERT: A  441 GLN cc_start: 0.8643 (tt0) cc_final: 0.8334 (tm-30)
REVERT: B  311 ASP cc_start: 0.9361 (m-30) cc_final: 0.9062 (t0)
REVERT: E   83 HIS cc_start: 0.7886 (OUTLIER) cc_final: 0.7299 (p90)
  outliers start: 22
  outliers final: 14
  residues processed: 141
  average time/residue: 1.1158
  time to fit residues: 173.9445
Evaluate side-chains
  138 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  466 GLN
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain E residue   83 HIS
Chi-restraints excluded: chain F residue  137 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 153 optimal weight:    0.7980
   chunk 106 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 127 optimal weight:    2.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.102886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.070608 restraints weight = 66052.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 2.79
r_work: 0.2779 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2645 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13680  Z= 0.128
  Angle     :  0.479   7.786  18571  Z= 0.249
  Chirality :  0.041   0.141   2031
  Planarity :  0.003   0.060   2448
  Dihedral  :  3.778  22.910   1875
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 15.02 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.21), residues: 1687
  helix:  2.46 (0.24), residues: 461
  sheet:  0.03 (0.24), residues: 459
  loop : -0.41 (0.23), residues: 767

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  94 
 TYR   0.016   0.001   TYR D 184 
 PHE   0.009   0.001   PHE A 517 
 TRP   0.011   0.001   TRP B 348 
 HIS   0.002   0.000   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (13677)
  covalent geometry    : angle       0.47873 (18569)
  SS BOND              : bond        0.00260 (    1)
  SS BOND              : angle       1.34867 (    2)
  hydrogen bonds       : bond        0.03569 (  613)
  hydrogen bonds       : angle       4.40182 ( 1755)
  Misc. bond           : bond        0.00096 (    2)

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

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

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7824 (ptp-170)
REVERT: A  192 GLU cc_start: 0.8794 (tp30) cc_final: 0.8355 (tp30)
REVERT: A  441 GLN cc_start: 0.8634 (tt0) cc_final: 0.8271 (tm-30)
REVERT: B  311 ASP cc_start: 0.9379 (m-30) cc_final: 0.9082 (t0)
REVERT: E   83 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.7255 (p90)
  outliers start: 21
  outliers final: 11
  residues processed: 140
  average time/residue: 1.2447
  time to fit residues: 192.1236
Evaluate side-chains
  136 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain E residue   83 HIS
Chi-restraints excluded: chain F residue  137 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 133 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 162 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 73 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 142 optimal weight:    2.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
F 107 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.100630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.068618 restraints weight = 66939.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 2.75
r_work: 0.2743 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2609 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039  13680  Z= 0.246
  Angle     :  0.524   8.064  18571  Z= 0.276
  Chirality :  0.042   0.142   2031
  Planarity :  0.004   0.065   2448
  Dihedral  :  3.960  26.179   1875
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 15.51 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.21), residues: 1687
  helix:  2.29 (0.23), residues: 460
  sheet: -0.06 (0.24), residues: 463
  loop : -0.49 (0.23), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  94 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.012   0.001   PHE A 517 
 TRP   0.009   0.001   TRP A 776 
 HIS   0.003   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 (13677)
  covalent geometry    : angle       0.52380 (18569)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       1.47821 (    2)
  hydrogen bonds       : bond        0.03919 (  613)
  hydrogen bonds       : angle       4.55280 ( 1755)
  Misc. bond           : bond        0.00054 (    2)

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

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

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7822 (ptp-170)
REVERT: A  192 GLU cc_start: 0.8818 (tp30) cc_final: 0.8378 (tp30)
REVERT: A  441 GLN cc_start: 0.8673 (tt0) cc_final: 0.8382 (tm-30)
REVERT: B  311 ASP cc_start: 0.9381 (m-30) cc_final: 0.9088 (t0)
REVERT: E   83 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.7265 (p90)
REVERT: F  128 TYR cc_start: 0.7138 (OUTLIER) cc_final: 0.6569 (t80)
  outliers start: 20
  outliers final: 12
  residues processed: 141
  average time/residue: 1.1042
  time to fit residues: 171.8950
Evaluate side-chains
  134 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  466 GLN
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue   83 HIS
Chi-restraints excluded: chain F residue  128 TYR
Chi-restraints excluded: chain F residue  137 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 99 optimal weight:    6.9990
   chunk 102 optimal weight:    0.9990
   chunk 105 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.101988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.069949 restraints weight = 66993.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 2.79
r_work: 0.2763 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2628 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13680  Z= 0.140
  Angle     :  0.506   9.964  18571  Z= 0.261
  Chirality :  0.042   0.138   2031
  Planarity :  0.003   0.066   2448
  Dihedral  :  3.891  24.730   1875
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 15.99 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.21), residues: 1687
  helix:  2.40 (0.24), residues: 461
  sheet: -0.04 (0.24), residues: 459
  loop : -0.44 (0.23), residues: 767

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  94 
 TYR   0.015   0.001   TYR D 184 
 PHE   0.010   0.001   PHE A  31 
 TRP   0.011   0.001   TRP B 348 
 HIS   0.002   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (13677)
  covalent geometry    : angle       0.50556 (18569)
  SS BOND              : bond        0.00216 (    1)
  SS BOND              : angle       1.37265 (    2)
  hydrogen bonds       : bond        0.03655 (  613)
  hydrogen bonds       : angle       4.42968 ( 1755)
  Misc. bond           : bond        0.00092 (    2)

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

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

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7802 (ptp-170)
REVERT: A  192 GLU cc_start: 0.8818 (tp30) cc_final: 0.8381 (tp30)
REVERT: A  441 GLN cc_start: 0.8631 (tt0) cc_final: 0.8287 (tm-30)
REVERT: A  741 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7652 (mpp)
REVERT: B  311 ASP cc_start: 0.9380 (m-30) cc_final: 0.9079 (t0)
REVERT: C   49 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8139 (mm-30)
REVERT: E   83 HIS cc_start: 0.7868 (OUTLIER) cc_final: 0.7310 (p90)
  outliers start: 16
  outliers final: 12
  residues processed: 133
  average time/residue: 1.1516
  time to fit residues: 169.4850
Evaluate side-chains
  134 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain D residue  172 ASP
Chi-restraints excluded: chain E residue   83 HIS
Chi-restraints excluded: chain F residue  137 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 140 optimal weight:    4.9990
   chunk 128 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 164 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   chunk 106 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 161 optimal weight:    4.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 563 ASN
B 229 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.100892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.068817 restraints weight = 66449.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.2862 rms_B_bonded: 2.75
r_work: 0.2737 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2602 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039  13680  Z= 0.246
  Angle     :  0.538   9.417  18571  Z= 0.282
  Chirality :  0.042   0.144   2031
  Planarity :  0.004   0.070   2448
  Dihedral  :  4.032  26.532   1875
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 15.92 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.21), residues: 1687
  helix:  2.21 (0.23), residues: 460
  sheet: -0.12 (0.24), residues: 463
  loop : -0.52 (0.23), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D  94 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.012   0.001   PHE A 517 
 TRP   0.009   0.001   TRP A 776 
 HIS   0.003   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 (13677)
  covalent geometry    : angle       0.53818 (18569)
  SS BOND              : bond        0.00175 (    1)
  SS BOND              : angle       1.52838 (    2)
  hydrogen bonds       : bond        0.03940 (  613)
  hydrogen bonds       : angle       4.55814 ( 1755)
  Misc. bond           : bond        0.00058 (    2)

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

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

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3374 Ramachandran restraints generated.
    1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7814 (ptp-170)
REVERT: A  192 GLU cc_start: 0.8831 (tp30) cc_final: 0.8396 (tp30)
REVERT: A  441 GLN cc_start: 0.8668 (tt0) cc_final: 0.8380 (tm-30)
REVERT: A  741 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7688 (mpp)
REVERT: B  311 ASP cc_start: 0.9379 (m-30) cc_final: 0.9089 (t0)
REVERT: C   49 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8131 (mm-30)
REVERT: E   83 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.7379 (p90)
  outliers start: 17
  outliers final: 11
  residues processed: 136
  average time/residue: 1.0853
  time to fit residues: 163.9429
Evaluate side-chains
  130 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  512 ASP
Chi-restraints excluded: chain A residue  540 GLN
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain B residue  217 SER
Chi-restraints excluded: chain B residue  346 LEU
Chi-restraints excluded: chain D residue  120 ASP
Chi-restraints excluded: chain D residue  134 ASP
Chi-restraints excluded: chain E residue   83 HIS
Chi-restraints excluded: chain F residue  137 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 119 optimal weight:    0.6980
   chunk 113 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 158 optimal weight:   10.0000
   chunk 29 optimal weight:    0.0870
   chunk 132 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 155 optimal weight:    4.9990
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.102380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.070455 restraints weight = 66046.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.2898 rms_B_bonded: 2.78
r_work: 0.2773 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2638 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  13680  Z= 0.107
  Angle     :  0.501  11.018  18571  Z= 0.257
  Chirality :  0.042   0.137   2031
  Planarity :  0.003   0.068   2448
  Dihedral  :  3.890  23.968   1875
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 16.41 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.21), residues: 1687
  helix:  2.40 (0.24), residues: 461
  sheet: -0.01 (0.24), residues: 462
  loop : -0.44 (0.23), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D  94 
 TYR   0.016   0.001   TYR D 184 
 PHE   0.013   0.001   PHE A  31 
 TRP   0.013   0.001   TRP B 348 
 HIS   0.003   0.001   HIS B 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (13677)
  covalent geometry    : angle       0.50109 (18569)
  SS BOND              : bond        0.00246 (    1)
  SS BOND              : angle       1.33497 (    2)
  hydrogen bonds       : bond        0.03529 (  613)
  hydrogen bonds       : angle       4.39399 ( 1755)
  Misc. bond           : bond        0.00112 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8434.53 seconds
wall clock time: 143 minutes 5.04 seconds (8585.04 seconds total)