Starting phenix.real_space_refine
on Sun Jun 22 22:42:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hg9_52131/06_2025/9hg9_52131.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hg9_52131/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hg9_52131/06_2025/9hg9_52131.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hg9_52131/06_2025/9hg9_52131.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hg9_52131/06_2025/9hg9_52131.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hg9_52131/06_2025/9hg9_52131.cif"
  }
  resolution = 2.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.11, per 1000 atoms: 0.50
  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: 7.00
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  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: 2.33
  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: 11.01

  Time building geometry restraints manager: 8.48 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:             4.060
  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:             0.430
  Extract box with map and model:          0.990
  Check model and map are aligned:         0.190
  Set scattering table:                    0.250
  Process input model:                     58.190
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.090
  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:13.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   78.400
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (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
 TRP   0.005   0.001   TRP B 348 
 HIS   0.001   0.000   HIS D 102 
 PHE   0.006   0.001   PHE A  67 
 TYR   0.016   0.001   TYR D 184 
 ARG   0.011   0.000   ARG D  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18298 (  613)
  hydrogen bonds       : angle       6.93174 ( 1755)
  SS BOND              : bond        0.00057 (    1)
  SS BOND              : angle       2.95800 (    2)
  covalent geometry    : bond        0.00288 (13677)
  covalent geometry    : angle       0.50669 (18569)
  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  : 2.228 
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: 0.8379 (tmm-80)
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: 2.9769
  time to fit residues: 489.3355
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  : 2.211 
-------------------------------------------------------------------------------
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 141 optimal weight:    2.9990
   chunk 126 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 130 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 79 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 151 optimal weight:    9.9990
   overall best weight:    1.5188

-------------------------------------------------------------------------------
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 = 0.3487 r_free = 0.3487 target = 0.101603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.069426 restraints weight = 66064.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.2914 rms_B_bonded: 2.73
r_work: 0.2806 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2670 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.0878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  13680  Z= 0.173
  Angle     :  0.507   6.812  18571  Z= 0.271
  Chirality :  0.042   0.150   2031
  Planarity :  0.003   0.035   2448
  Dihedral  :  3.980  44.617   1878
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 13.14 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.21), residues: 1687
  helix:  2.33 (0.24), residues: 461
  sheet:  0.23 (0.25), residues: 466
  loop : -0.46 (0.23), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 776 
 HIS   0.004   0.001   HIS B 347 
 PHE   0.015   0.001   PHE A 517 
 TYR   0.015   0.001   TYR D 184 
 ARG   0.004   0.000   ARG A 526 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05045 (  613)
  hydrogen bonds       : angle       5.13712 ( 1755)
  SS BOND              : bond        0.00377 (    1)
  SS BOND              : angle       2.74026 (    2)
  covalent geometry    : bond        0.00385 (13677)
  covalent geometry    : angle       0.50657 (18569)
  Misc. bond           : bond        0.00156 (    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
  145 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 2.232 
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  192 GLU cc_start: 0.8735 (tp30) cc_final: 0.8368 (tp30)
REVERT: B  311 ASP cc_start: 0.9367 (m-30) cc_final: 0.9038 (t0)
REVERT: E   83 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7310 (p90)
  outliers start: 13
  outliers final: 3
  residues processed: 143
  average time/residue: 2.5259
  time to fit residues: 401.0013
Evaluate side-chains
  123 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 119
  time to evaluate  : 2.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  512 ASP
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 15 optimal weight:    2.9990
   chunk 125 optimal weight:    2.9990
   chunk 141 optimal weight:    2.9990
   chunk 123 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 164 optimal weight:    8.9990
   chunk 35 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    2.1388

-------------------------------------------------------------------------------
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 = 0.3471 r_free = 0.3471 target = 0.101870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.069404 restraints weight = 66728.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 2.78
r_work: 0.2756 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2621 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  13680  Z= 0.221
  Angle     :  0.507   5.794  18571  Z= 0.271
  Chirality :  0.042   0.144   2031
  Planarity :  0.003   0.047   2448
  Dihedral  :  3.880  26.057   1875
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 13.14 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.21), residues: 1687
  helix:  2.24 (0.24), residues: 462
  sheet:  0.05 (0.24), residues: 471
  loop : -0.49 (0.23), residues: 754

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 348 
 HIS   0.002   0.001   HIS D 139 
 PHE   0.015   0.001   PHE A 517 
 TYR   0.014   0.001   TYR D 184 
 ARG   0.008   0.000   ARG A 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04445 (  613)
  hydrogen bonds       : angle       4.86806 ( 1755)
  SS BOND              : bond        0.00421 (    1)
  SS BOND              : angle       2.79715 (    2)
  covalent geometry    : bond        0.00500 (13677)
  covalent geometry    : angle       0.50664 (18569)
  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
  151 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 1.986 
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  120 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7939 (ptm-80)
REVERT: A  441 GLN cc_start: 0.8625 (tt0) cc_final: 0.8328 (tm-30)
REVERT: B  311 ASP cc_start: 0.9378 (m-30) cc_final: 0.9069 (t0)
REVERT: E   83 HIS cc_start: 0.7889 (OUTLIER) cc_final: 0.7210 (p90)
REVERT: F   86 LYS cc_start: 0.9503 (tptp) cc_final: 0.9286 (tptp)
REVERT: F  128 TYR cc_start: 0.6988 (OUTLIER) cc_final: 0.6431 (t80)
  outliers start: 21
  outliers final: 8
  residues processed: 144
  average time/residue: 2.4463
  time to fit residues: 389.7760
Evaluate side-chains
  134 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 1.989 
-------------------------------------------------------------------------------
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 B residue  217 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 50 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0770
   chunk 35 optimal weight:    2.9990
   chunk 133 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 114 optimal weight:    0.9980
   chunk 10 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 102 optimal weight:    3.9990
   overall best weight:    0.9340

-------------------------------------------------------------------------------
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 = 0.3494 r_free = 0.3494 target = 0.103362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.071201 restraints weight = 66547.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.2906 rms_B_bonded: 2.79
r_work: 0.2783 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2648 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.1341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13680  Z= 0.119
  Angle     :  0.473   5.736  18571  Z= 0.249
  Chirality :  0.041   0.146   2031
  Planarity :  0.003   0.044   2448
  Dihedral  :  3.805  24.118   1875
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 13.56 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.21), residues: 1687
  helix:  2.42 (0.24), residues: 462
  sheet:  0.10 (0.24), residues: 463
  loop : -0.43 (0.23), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 348 
 HIS   0.002   0.001   HIS B 347 
 PHE   0.011   0.001   PHE A 517 
 TYR   0.014   0.001   TYR D 184 
 ARG   0.004   0.000   ARG D  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03895 (  613)
  hydrogen bonds       : angle       4.63198 ( 1755)
  SS BOND              : bond        0.00360 (    1)
  SS BOND              : angle       1.77790 (    2)
  covalent geometry    : bond        0.00264 (13677)
  covalent geometry    : angle       0.47304 (18569)
  Misc. bond           : bond        0.00101 (    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
  149 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 2.101 
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  120 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7872 (ptp90)
REVERT: A  192 GLU cc_start: 0.8745 (tp30) cc_final: 0.8332 (tp30)
REVERT: A  441 GLN cc_start: 0.8606 (tt0) cc_final: 0.8266 (tm-30)
REVERT: B  311 ASP cc_start: 0.9375 (m-30) cc_final: 0.9057 (t0)
REVERT: E   83 HIS cc_start: 0.7852 (OUTLIER) cc_final: 0.7235 (p90)
  outliers start: 17
  outliers final: 9
  residues processed: 142
  average time/residue: 2.4004
  time to fit residues: 378.6076
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  : 2.092 
-------------------------------------------------------------------------------
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 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 106 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   chunk 155 optimal weight:    7.9990
   chunk 122 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 120 optimal weight:    1.9990
   chunk 127 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 111 optimal weight:    3.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 107 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.100596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.068201 restraints weight = 66915.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 2.77
r_work: 0.2727 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2594 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043  13680  Z= 0.291
  Angle     :  0.536   6.027  18571  Z= 0.286
  Chirality :  0.043   0.155   2031
  Planarity :  0.004   0.054   2448
  Dihedral  :  4.058  27.193   1875
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.77 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.21), residues: 1687
  helix:  2.19 (0.23), residues: 460
  sheet: -0.09 (0.24), residues: 463
  loop : -0.57 (0.23), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 776 
 HIS   0.003   0.001   HIS D 139 
 PHE   0.015   0.001   PHE A 517 
 TYR   0.014   0.001   TYR D 184 
 ARG   0.007   0.000   ARG D  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04251 (  613)
  hydrogen bonds       : angle       4.76111 ( 1755)
  SS BOND              : bond        0.00177 (    1)
  SS BOND              : angle       1.95016 (    2)
  covalent geometry    : bond        0.00658 (13677)
  covalent geometry    : angle       0.53579 (18569)
  Misc. bond           : bond        0.00050 (    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
  150 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 123
  time to evaluate  : 1.923 
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  120 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7817 (ptp90)
REVERT: A  441 GLN cc_start: 0.8658 (tt0) cc_final: 0.8357 (tm-30)
REVERT: B  311 ASP cc_start: 0.9379 (m-30) cc_final: 0.9075 (t0)
REVERT: E   83 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.7309 (p90)
  outliers start: 27
  outliers final: 12
  residues processed: 142
  average time/residue: 2.4917
  time to fit residues: 391.3031
Evaluate side-chains
  133 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 2.250 
-------------------------------------------------------------------------------
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  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 93 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 83 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9980
   chunk 126 optimal weight:    1.9990
   chunk 111 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
E  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.101789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.069545 restraints weight = 66649.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.2886 rms_B_bonded: 2.80
r_work: 0.2761 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2626 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13680  Z= 0.134
  Angle     :  0.491   7.413  18571  Z= 0.256
  Chirality :  0.042   0.144   2031
  Planarity :  0.003   0.054   2448
  Dihedral  :  3.933  25.547   1875
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 14.67 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.21), residues: 1687
  helix:  2.37 (0.24), residues: 461
  sheet:  0.02 (0.24), residues: 458
  loop : -0.52 (0.23), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 348 
 HIS   0.002   0.001   HIS D 139 
 PHE   0.010   0.001   PHE A 517 
 TYR   0.014   0.001   TYR D 184 
 ARG   0.007   0.000   ARG D  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03820 (  613)
  hydrogen bonds       : angle       4.55943 ( 1755)
  SS BOND              : bond        0.00221 (    1)
  SS BOND              : angle       1.40741 (    2)
  covalent geometry    : bond        0.00305 (13677)
  covalent geometry    : angle       0.49071 (18569)
  Misc. bond           : bond        0.00098 (    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
  146 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 2.263 
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  120 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7803 (ptp-170)
REVERT: A  192 GLU cc_start: 0.8786 (tp30) cc_final: 0.8358 (tp30)
REVERT: A  441 GLN cc_start: 0.8638 (tt0) cc_final: 0.8285 (tm-30)
REVERT: B  311 ASP cc_start: 0.9375 (m-30) cc_final: 0.9065 (t0)
REVERT: E   83 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.7297 (p90)
  outliers start: 20
  outliers final: 10
  residues processed: 139
  average time/residue: 2.5367
  time to fit residues: 390.0173
Evaluate side-chains
  136 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 2.368 
-------------------------------------------------------------------------------
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 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 128 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 146 optimal weight:    0.0980
   chunk 98 optimal weight:    2.9990
   chunk 159 optimal weight:    9.9990
   chunk 88 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 119 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 132 optimal weight:    1.9990
   overall best weight:    2.0188

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

Flipped N/Q/H residues before XYZ refinement:
A 112 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 = 0.3460 r_free = 0.3460 target = 0.100992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.068589 restraints weight = 66484.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 2.77
r_work: 0.2739 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2604 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  13680  Z= 0.215
  Angle     :  0.510   7.821  18571  Z= 0.268
  Chirality :  0.042   0.145   2031
  Planarity :  0.004   0.061   2448
  Dihedral  :  3.987  25.760   1875
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 14.88 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.21), residues: 1687
  helix:  2.30 (0.23), residues: 460
  sheet: -0.07 (0.24), residues: 455
  loop : -0.56 (0.23), residues: 772

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 348 
 HIS   0.002   0.001   HIS D 139 
 PHE   0.012   0.001   PHE A 517 
 TYR   0.015   0.001   TYR D 184 
 ARG   0.009   0.000   ARG D  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03899 (  613)
  hydrogen bonds       : angle       4.58114 ( 1755)
  SS BOND              : bond        0.00161 (    1)
  SS BOND              : angle       1.38067 (    2)
  covalent geometry    : bond        0.00490 (13677)
  covalent geometry    : angle       0.50968 (18569)
  Misc. bond           : bond        0.00064 (    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
  148 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 2.269 
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: 0.8132 (OUTLIER) cc_final: 0.7779 (ptp-170)
REVERT: A  192 GLU cc_start: 0.8805 (tp30) cc_final: 0.8376 (tp30)
REVERT: A  441 GLN cc_start: 0.8677 (tt0) cc_final: 0.8393 (tm-30)
REVERT: B  311 ASP cc_start: 0.9373 (m-30) cc_final: 0.9054 (t0)
REVERT: C   49 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8091 (mm-30)
REVERT: C   78 LYS cc_start: 0.8899 (mttt) cc_final: 0.8671 (mttt)
REVERT: E   83 HIS cc_start: 0.7914 (OUTLIER) cc_final: 0.7313 (p90)
REVERT: F  128 TYR cc_start: 0.7175 (OUTLIER) cc_final: 0.6636 (t80)
  outliers start: 22
  outliers final: 14
  residues processed: 141
  average time/residue: 2.4505
  time to fit residues: 383.1029
Evaluate side-chains
  141 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 1.989 
-------------------------------------------------------------------------------
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 E residue   83 HIS
Chi-restraints excluded: chain E residue   87 THR
Chi-restraints excluded: chain F residue  128 TYR
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 68 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 73 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 100 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 160 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 150 optimal weight:    8.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3487 r_free = 0.3487 target = 0.102712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.070606 restraints weight = 66313.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 2.79
r_work: 0.2777 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2643 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  13680  Z= 0.110
  Angle     :  0.491   8.725  18571  Z= 0.253
  Chirality :  0.041   0.138   2031
  Planarity :  0.003   0.063   2448
  Dihedral  :  3.844  23.388   1875
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 15.44 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.21), residues: 1687
  helix:  2.47 (0.24), residues: 461
  sheet:  0.03 (0.24), residues: 459
  loop : -0.46 (0.23), residues: 767

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 348 
 HIS   0.002   0.000   HIS D 102 
 PHE   0.010   0.001   PHE A  31 
 TYR   0.016   0.001   TYR D 184 
 ARG   0.010   0.000   ARG D  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03554 (  613)
  hydrogen bonds       : angle       4.40137 ( 1755)
  SS BOND              : bond        0.00252 (    1)
  SS BOND              : angle       1.11789 (    2)
  covalent geometry    : bond        0.00249 (13677)
  covalent geometry    : angle       0.49059 (18569)
  Misc. bond           : bond        0.00112 (    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
  155 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 2.299 
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   89 LYS cc_start: 0.8380 (tppt) cc_final: 0.8157 (tptm)
REVERT: A  120 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7806 (ptp-170)
REVERT: A  192 GLU cc_start: 0.8806 (tp30) cc_final: 0.8365 (tp30)
REVERT: A  294 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7733 (pt0)
REVERT: A  441 GLN cc_start: 0.8641 (tt0) cc_final: 0.8300 (tm-30)
REVERT: A  741 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7631 (mpp)
REVERT: B  311 ASP cc_start: 0.9378 (m-30) cc_final: 0.9071 (t0)
REVERT: E   83 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7315 (p90)
  outliers start: 21
  outliers final: 10
  residues processed: 149
  average time/residue: 2.8401
  time to fit residues: 472.0980
Evaluate side-chains
  141 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 2.137 
-------------------------------------------------------------------------------
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  294 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 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 131 optimal weight:    1.9990
   chunk 99 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 160 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 118 optimal weight:    0.2980
   chunk 30 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    1.6588

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 540 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.101959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.069693 restraints weight = 66606.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 2.78
r_work: 0.2770 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2633 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13680  Z= 0.178
  Angle     :  0.507  10.256  18571  Z= 0.263
  Chirality :  0.041   0.141   2031
  Planarity :  0.003   0.063   2448
  Dihedral  :  3.872  24.225   1875
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 15.86 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.21), residues: 1687
  helix:  2.38 (0.24), residues: 461
  sheet: -0.05 (0.24), residues: 457
  loop : -0.46 (0.23), residues: 769

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03665 (  613)
  hydrogen bonds       : angle       4.46558 ( 1755)
  SS BOND              : bond        0.00133 (    1)
  SS BOND              : angle       1.14168 (    2)
  covalent geometry    : bond        0.00409 (13677)
  covalent geometry    : angle       0.50687 (18569)
  Misc. bond           : bond        0.00078 (    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
  144 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 1.918 
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  120 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7803 (ptp-170)
REVERT: A  192 GLU cc_start: 0.8843 (tp30) cc_final: 0.8404 (tp30)
REVERT: A  294 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7843 (pt0)
REVERT: A  441 GLN cc_start: 0.8690 (tt0) cc_final: 0.8404 (tm-30)
REVERT: A  741 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7738 (mpp)
REVERT: B  311 ASP cc_start: 0.9370 (m-30) cc_final: 0.9074 (t0)
REVERT: C   49 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8131 (mm-30)
REVERT: C   78 LYS cc_start: 0.8923 (mttt) cc_final: 0.8710 (mttt)
REVERT: E   83 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7335 (p90)
  outliers start: 18
  outliers final: 11
  residues processed: 137
  average time/residue: 2.4687
  time to fit residues: 375.2981
Evaluate side-chains
  137 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 1.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  294 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 E residue   87 THR
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 26 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 79 optimal weight:    0.7980
   chunk 114 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 42 optimal weight:    0.3980
   chunk 131 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 95 optimal weight:    1.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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 = 0.3472 r_free = 0.3472 target = 0.101490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.069367 restraints weight = 66643.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.2886 rms_B_bonded: 2.78
r_work: 0.2760 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2626 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13680  Z= 0.155
  Angle     :  0.517  11.950  18571  Z= 0.266
  Chirality :  0.042   0.143   2031
  Planarity :  0.004   0.068   2448
  Dihedral  :  3.877  24.060   1875
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 15.65 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.21), residues: 1687
  helix:  2.40 (0.24), residues: 461
  sheet: -0.04 (0.24), residues: 457
  loop : -0.43 (0.23), residues: 769

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 348 
 HIS   0.024   0.001   HIS A 677 
 PHE   0.011   0.001   PHE A  31 
 TYR   0.016   0.001   TYR D 184 
 ARG   0.011   0.000   ARG D  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03623 (  613)
  hydrogen bonds       : angle       4.41605 ( 1755)
  SS BOND              : bond        0.00156 (    1)
  SS BOND              : angle       1.13640 (    2)
  covalent geometry    : bond        0.00356 (13677)
  covalent geometry    : angle       0.51646 (18569)
  Misc. bond           : bond        0.00088 (    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
  147 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 1.928 
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  120 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7797 (ptp-170)
REVERT: A  192 GLU cc_start: 0.8839 (tp30) cc_final: 0.8406 (tp30)
REVERT: A  294 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7852 (pt0)
REVERT: A  441 GLN cc_start: 0.8674 (tt0) cc_final: 0.8338 (tm-30)
REVERT: A  741 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7701 (mpp)
REVERT: B  311 ASP cc_start: 0.9377 (m-30) cc_final: 0.9074 (t0)
REVERT: C   49 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8141 (mm-30)
REVERT: C   78 LYS cc_start: 0.8921 (mttt) cc_final: 0.8713 (mttt)
REVERT: E   83 HIS cc_start: 0.7892 (OUTLIER) cc_final: 0.7323 (p90)
REVERT: F  128 TYR cc_start: 0.7180 (OUTLIER) cc_final: 0.6620 (t80)
  outliers start: 21
  outliers final: 10
  residues processed: 141
  average time/residue: 2.3847
  time to fit residues: 373.2630
Evaluate side-chains
  137 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 1.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 ARG
Chi-restraints excluded: chain A residue  285 GLU
Chi-restraints excluded: chain A residue  294 GLU
Chi-restraints excluded: chain A residue  512 ASP
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 E residue   87 THR
Chi-restraints excluded: chain F residue  128 TYR
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 31 optimal weight:    3.9990
   chunk 146 optimal weight:    0.9980
   chunk 124 optimal weight:    2.9990
   chunk 94 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 112 optimal weight:    0.2980
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 540 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.102748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.070543 restraints weight = 66074.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.2906 rms_B_bonded: 2.77
r_work: 0.2780 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2645 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.1962

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= 0.109
  Angle     :  0.506  12.530  18571  Z= 0.257
  Chirality :  0.042   0.144   2031
  Planarity :  0.003   0.069   2448
  Dihedral  :  3.798  22.504   1875
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 16.20 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.21), residues: 1687
  helix:  2.55 (0.24), residues: 461
  sheet: -0.01 (0.24), residues: 457
  loop : -0.36 (0.23), residues: 769

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 348 
 HIS   0.003   0.001   HIS A 677 
 PHE   0.013   0.001   PHE A  31 
 TYR   0.017   0.001   TYR D 184 
 ARG   0.011   0.000   ARG D  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03446 (  613)
  hydrogen bonds       : angle       4.31138 ( 1755)
  SS BOND              : bond        0.00204 (    1)
  SS BOND              : angle       1.07192 (    2)
  covalent geometry    : bond        0.00249 (13677)
  covalent geometry    : angle       0.50566 (18569)
  Misc. bond           : bond        0.00110 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 18699.83 seconds
wall clock time: 319 minutes 47.32 seconds (19187.32 seconds total)