Starting phenix.real_space_refine
on Wed Mar  4 03:26:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tyx_26197/03_2026/7tyx_26197.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tyx_26197/03_2026/7tyx_26197.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tyx_26197/03_2026/7tyx_26197.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tyx_26197/03_2026/7tyx_26197.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tyx_26197/03_2026/7tyx_26197.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tyx_26197/03_2026/7tyx_26197.map"
  }
  resolution = 2.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.098
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: 4
    Type Number    sf(0)   Gaussians
     S      71      5.16       5
     C    6565      2.51       5
     N    1739      2.21       5
     O    1844      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10219
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "E"
      Number of atoms: 804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 804
          Classifications: {'peptide': 112}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102}
          Unresolved non-hydrogen bonds: 121
          Unresolved non-hydrogen angles: 152
          Unresolved non-hydrogen dihedrals: 92
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ASN:plan1': 3, 'GLU:plan': 5, 'GLN:plan1': 4, 'ASP:plan': 6, 'ARG:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 79
    Chain: "P"
      Number of atoms: 284
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 37, 273
          Classifications: {'peptide': 37}
          Link IDs: {'PTRANS': 3, 'TRANS': 33}
      Conformer: "B"
        Number of residues, atoms: 37, 273
          Classifications: {'peptide': 37}
          Link IDs: {'PTRANS': 3, 'TRANS': 33}
          bond proxies already assigned to first conformer: 265
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 2962
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 365, 2962
          Classifications: {'peptide': 365}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 16, 'TRANS': 348}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 80
          Unresolved non-hydrogen angles: 102
          Unresolved non-hydrogen dihedrals: 66
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 53
    Chain: "A"
      Number of atoms: 1909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1909
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 6, 'TRANS': 226}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "B"
      Number of atoms: 2606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2606
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 256
          Unusual residues: {'NAG': 3, 'PLM': 8, 'Y01': 2}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG P  18 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG P  18 " occ=0.50
  Time building chain proxies: 1.93, per 1000 atoms: 0.19
  Number of scatterers: 10219
  At special positions: 0
  Unit cell: (125.33, 107.07, 141.93, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      71     16.00
     O    1844      8.00
     N    1739      7.00
     C    6565      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  68 " - pdb=" SG  CYS E  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  84 " - pdb=" SG  CYS E 131 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P   2 " - pdb=" SG  CYS P   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  55 " - pdb=" SG  CYS R  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  72 " - pdb=" SG  CYS R 112 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  95 " - pdb=" SG  CYS R 134 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 219 " - pdb=" SG  CYS R 289 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " 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=1, symmetry=0
  Links applied
    NAG-ASN
      " NAG R 501 " - " ASN R 125 "
      " NAG R 502 " - " ASN R 130 "
      " NAG R 503 " - " ASN R  73 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.71
  Conformation dependent library (CDL) restraints added in 468.0 milliseconds
  

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2404

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 14 sheets defined
      45.5% alpha, 17.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'E' and resid 60 through 77
      removed outlier: 3.583A  pdb=" N   ALA E  64 " --> pdb=" O   ASN E  60 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   CYS E  68 " --> pdb=" O   ALA E  64 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 80 through 84
      removed outlier: 4.342A  pdb=" N   CYS E  84 " --> pdb=" O   LYS E  81 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 107
      removed outlier: 5.670A  pdb=" N   ARG E  91 " --> pdb=" O   ALA E  87 " (cutoff:3.500A)
      Proline residue:  E  92  - end of helix
    Processing helix  chain 'E' and resid 113 through 127
      removed outlier: 3.784A  pdb=" N   ILE E 119 " --> pdb=" O   LEU E 115 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 142 through 167
      removed outlier: 3.791A  pdb=" N   ALA E 148 " --> pdb=" O   ASP E 144 " (cutoff:3.500A)
      Proline residue:  E 153  - end of helix
      removed outlier: 3.580A  pdb=" N   LEU E 156 " --> pdb=" O   ALA E 152 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE E 157 " --> pdb=" O   PRO E 153 " (cutoff:3.500A)
      Proline residue:  E 158  - end of helix
    Processing helix  chain 'P' and resid 7 through 20
    Processing helix  chain 'R' and resid 40 through 61
    Processing helix  chain 'R' and resid 131 through 136
      removed outlier: 4.245A  pdb=" N   ASN R 135 " --> pdb=" O   TYR R 131 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 173
      removed outlier: 3.931A  pdb=" N   VAL R 147 " --> pdb=" O   LYS R 143 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 177
    Processing helix  chain 'R' and resid 178 through 205
      removed outlier: 3.553A  pdb=" N   ASN R 186 " --> pdb=" O   THR R 182 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 215
      removed outlier: 3.851A  pdb=" N   VAL R 212 " --> pdb=" O   ASN R 208 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 216 through 249
      removed outlier: 4.063A  pdb=" N   LYS R 220 " --> pdb=" O   PRO R 216 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU R 238 " --> pdb=" O   TYR R 234 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 259 through 267
    Processing helix  chain 'R' and resid 270 through 284
      removed outlier: 3.510A  pdb=" N   THR R 274 " --> pdb=" O   PRO R 270 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 287 through 291
      removed outlier: 3.652A  pdb=" N   LEU R 291 " --> pdb=" O   ASN R 288 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 295 through 297
      No H-bonds generated for 'chain 'R' and resid 295 through 297'
    Processing helix  chain 'R' and resid 298 through 331
      Proline residue:  R 304  - end of helix
      removed outlier: 3.600A  pdb=" N   ASN R 318 " --> pdb=" O   PHE R 314 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   THR R 330 " --> pdb=" O   LYS R 326 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 333 through 353
      Proline residue:  R 350  - end of helix
    Processing helix  chain 'R' and resid 354 through 359
    Processing helix  chain 'R' and resid 365 through 382
    Processing helix  chain 'R' and resid 382 through 392
    Processing helix  chain 'R' and resid 395 through 405
    Processing helix  chain 'A' and resid 12 through 40
      removed outlier: 3.569A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
      removed outlier: 3.576A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 239
      removed outlier: 3.502A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 3.899A  pdb=" N   ARG A 283 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.573A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.273A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 317
      removed outlier: 3.536A  pdb=" N   ARG A 317 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.785A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 3 through 26
      removed outlier: 3.667A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 3.581A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.540A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.676A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
      removed outlier: 3.527A  pdb=" N   LYS N  65 " --> pdb=" O   GLY N  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 62 through 65'
    Processing helix  chain 'N' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'R' and resid 71 through 72
      removed outlier: 3.713A  pdb=" N   THR R  85 " --> pdb=" O   CYS R  72 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'R' and resid 75 through 76
      removed outlier: 3.769A  pdb=" N   THR R  75 " --> pdb=" O   TRP R  82 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'R' and resid 91 through 94
    Processing sheet with id=AA4, first strand: chain 'R' and resid 120 through 121
      removed outlier: 3.818A  pdb=" N   ARG R 126 " --> pdb=" O   HIS R 121 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.237A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.349A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.083A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.825A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.522A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.663A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.780A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.081A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.907A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.584A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.567A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.544A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB5, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.861A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    518 hydrogen bonds defined for protein.
    1486 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: 1.49

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1637
        1.32 -     1.44: 2928
        1.44 -     1.57: 5793
        1.57 -     1.69: 0
        1.69 -     1.82: 99
  Bond restraints: 10457
  Sorted by residual:
  bond pdb=" N   GLY P  33 "
       pdb=" CA  GLY P  33 "
    ideal  model  delta    sigma   weight residual
    1.446  1.476 -0.030 1.06e-02 8.90e+03 8.03e+00
  bond pdb=" N   VAL P  32 "
       pdb=" CA  VAL P  32 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.98e+00
  bond pdb=" N   THR P  36 "
       pdb=" CA  THR P  36 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.033 1.25e-02 6.40e+03 6.85e+00
  bond pdb=" N   ASN P  35 "
       pdb=" CA  ASN P  35 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.21e-02 6.83e+03 5.40e+00
  bond pdb=" N   SER P  34 "
       pdb=" CA  SER P  34 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.21e-02 6.83e+03 4.86e+00
  ... (remaining 10452 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 13631
        1.20 -     2.40: 436
        2.40 -     3.60: 82
        3.60 -     4.79: 9
        4.79 -     5.99: 10
  Bond angle restraints: 14168
  Sorted by residual:
  angle pdb=" CA  GLY P  33 "
        pdb=" C   GLY P  33 "
        pdb=" O   GLY P  33 "
      ideal   model   delta    sigma   weight residual
     122.28  118.37    3.91 1.00e+00 1.00e+00 1.52e+01
  angle pdb=" CA  THR P  36 "
        pdb=" C   THR P  36 "
        pdb=" O   THR P  36 "
      ideal   model   delta    sigma   weight residual
     121.55  117.78    3.77 1.06e+00 8.90e-01 1.27e+01
  angle pdb=" C   GLU R 255 "
        pdb=" N   LYS R 256 "
        pdb=" CA  LYS R 256 "
      ideal   model   delta    sigma   weight residual
     121.87  127.54   -5.67 2.24e+00 1.99e-01 6.42e+00
  angle pdb=" C   ASN R 124 "
        pdb=" N   ASN R 125 "
        pdb=" CA  ASN R 125 "
      ideal   model   delta    sigma   weight residual
     121.54  126.37   -4.83 1.91e+00 2.74e-01 6.40e+00
  angle pdb=" CA  ASN P  35 "
        pdb=" C   ASN P  35 "
        pdb=" O   ASN P  35 "
      ideal   model   delta    sigma   weight residual
     120.55  117.99    2.56 1.06e+00 8.90e-01 5.82e+00
  ... (remaining 14163 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 5854
       17.83 -    35.67: 386
       35.67 -    53.50: 87
       53.50 -    71.33: 27
       71.33 -    89.16: 9
  Dihedral angle restraints: 6363
    sinusoidal: 2648
      harmonic: 3715
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  177.67  -84.67     1      1.00e+01 1.00e-02 8.71e+01
  dihedral pdb=" CB  CYS E  68 "
           pdb=" SG  CYS E  68 "
           pdb=" SG  CYS E  99 "
           pdb=" CB  CYS E  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -48.61  -37.39     1      1.00e+01 1.00e-02 1.97e+01
  dihedral pdb=" CA  TRP B 169 "
           pdb=" C   TRP B 169 "
           pdb=" N   ASP B 170 "
           pdb=" CA  ASP B 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.70   17.30     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 6360 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1438
       0.069 -    0.137: 128
       0.137 -    0.206: 4
       0.206 -    0.274: 1
       0.274 -    0.343: 1
  Chirality restraints: 1572
  Sorted by residual:
  chirality pdb=" C1  NAG R 501 "
            pdb=" ND2 ASN R 125 "
            pdb=" C2  NAG R 501 "
            pdb=" O5  NAG R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.06   -0.34 2.00e-01 2.50e+01 2.93e+00
  chirality pdb=" CA  TYR P  37 "
            pdb=" N   TYR P  37 "
            pdb=" C   TYR P  37 "
            pdb=" CB  TYR P  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CA  VAL P  32 "
            pdb=" N   VAL P  32 "
            pdb=" C   VAL P  32 "
            pdb=" CB  VAL P  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.88e-01
  ... (remaining 1569 not shown)

  Planarity restraints: 1788
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.026 5.00e-02 4.00e+02   3.94e-02 2.49e+00
        pdb=" N   PRO B 236 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 303 "    0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO R 304 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO R 304 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO R 304 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E  91 "   -0.021 5.00e-02 4.00e+02   3.08e-02 1.52e+00
        pdb=" N   PRO E  92 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO E  92 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO E  92 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1785 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1833
        2.76 -     3.30: 9357
        3.30 -     3.83: 16551
        3.83 -     4.37: 21526
        4.37 -     4.90: 35885
  Nonbonded interactions: 85152
  Sorted by model distance:
  nonbonded pdb=" O   SER N 112 "
            pdb=" NH2 ARG N 118 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   ILE R 347 "
            pdb=" OH  TYR R 391 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   GLU R 397 "
            pdb=" OG1 THR R 401 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   LEU R  62 "
            pdb=" NH2 ARG R  74 "
     model   vdw
     2.269 3.120
  ... (remaining 85147 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.130
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.106  10470  Z= 0.209
  Angle     :  0.531  10.281  14195  Z= 0.301
  Chirality :  0.041   0.343   1572
  Planarity :  0.003   0.039   1785
  Dihedral  : 13.246  89.163   3932
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.62 %
    Favored  : 86.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.16 (0.19), residues: 1252
  helix: -3.28 (0.13), residues: 518
  sheet: -0.41 (0.31), residues: 229
  loop : -1.30 (0.23), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 228 
 TYR   0.009   0.001   TYR R 391 
 PHE   0.011   0.001   PHE A 212 
 TRP   0.011   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (10457)
  covalent geometry    : angle       0.51797 (14168)
  SS BOND              : bond        0.00300 (    9)
  SS BOND              : angle       0.83813 (   18)
  hydrogen bonds       : bond        0.26453 (  518)
  hydrogen bonds       : angle       9.01964 ( 1486)
  Misc. bond           : bond        0.10626 (    1)
  link_NAG-ASN         : bond        0.00937 (    3)
  link_NAG-ASN         : angle       4.63061 (    9)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 199
  time to evaluate  : 0.371 
Fit side-chains
REVERT: R  101 ASP cc_start: 0.5997 (m-30) cc_final: 0.5636 (m-30)
REVERT: R  143 LYS cc_start: 0.7668 (tttt) cc_final: 0.7401 (ttpp)
REVERT: A  311 TYR cc_start: 0.2458 (m-80) cc_final: 0.2258 (m-80)
REVERT: A  368 ASP cc_start: 0.7438 (m-30) cc_final: 0.6859 (m-30)
REVERT: A  386 MET cc_start: 0.6756 (ttm) cc_final: 0.6375 (mtt)
REVERT: A  389 ARG cc_start: 0.7977 (ttt90) cc_final: 0.7355 (ttm110)
REVERT: A  390 GLN cc_start: 0.7358 (mt0) cc_final: 0.7065 (mp10)
REVERT: B   17 GLN cc_start: 0.6387 (tt0) cc_final: 0.6143 (tm-30)
  outliers start: 17
  outliers final: 2
  residues processed: 212
  average time/residue: 0.5549
  time to fit residues: 126.8977
Evaluate side-chains
  138 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 136
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  219 CYS
Chi-restraints excluded: chain A residue  349 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0970
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 117 optimal weight:    1.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
P  14 ASN
P  22 ASN
P  35 ASN
R  52 GLN
R 135 ASN
R 184 HIS
R 186 ASN
R 227 GLN
R 395 ASN
R 399 GLN
A  14 ASN
A 292 ASN
B  17 GLN
N  35 ASN
N  39 GLN
N 120 GLN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.216612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.155061 restraints weight = 24269.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3855 rms_B_bonded: 3.62
r_work: 0.3707 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3778
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3778 r_free = 0.3778    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3778 r_free = 0.3778    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3778
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6353
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10470  Z= 0.144
  Angle     :  0.580   9.424  14195  Z= 0.303
  Chirality :  0.044   0.286   1572
  Planarity :  0.004   0.050   1785
  Dihedral  :  6.437  59.209   1701
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 16.29 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.22), residues: 1252
  helix:  0.02 (0.21), residues: 514
  sheet: -0.15 (0.31), residues: 250
  loop : -0.80 (0.25), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 347 
 TYR   0.022   0.001   TYR N  60 
 PHE   0.017   0.002   PHE A 212 
 TRP   0.020   0.002   TRP B 339 
 HIS   0.005   0.001   HIS R 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (10457)
  covalent geometry    : angle       0.56985 (14168)
  SS BOND              : bond        0.00354 (    9)
  SS BOND              : angle       1.03750 (   18)
  hydrogen bonds       : bond        0.04936 (  518)
  hydrogen bonds       : angle       5.06422 ( 1486)
  Misc. bond           : bond        0.00156 (    1)
  link_NAG-ASN         : bond        0.00967 (    3)
  link_NAG-ASN         : angle       4.05116 (    9)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 149
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: R  101 ASP cc_start: 0.5255 (m-30) cc_final: 0.4988 (m-30)
REVERT: R  140 GLU cc_start: 0.6456 (tp30) cc_final: 0.5958 (tp30)
REVERT: R  143 LYS cc_start: 0.6553 (tttt) cc_final: 0.6296 (ttpp)
REVERT: R  174 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6519 (mtt180)
REVERT: R  186 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.7337 (m-40)
REVERT: R  346 MET cc_start: 0.6715 (mmt) cc_final: 0.6489 (mmp)
REVERT: R  367 MET cc_start: 0.3792 (OUTLIER) cc_final: 0.3306 (tpt)
REVERT: R  405 GLN cc_start: 0.6774 (mp10) cc_final: 0.6464 (mp10)
REVERT: A  386 MET cc_start: 0.6075 (ttm) cc_final: 0.5677 (mtp)
REVERT: A  389 ARG cc_start: 0.7605 (ttt90) cc_final: 0.6324 (ttm110)
REVERT: A  390 GLN cc_start: 0.6300 (mt0) cc_final: 0.5712 (mp10)
REVERT: B   17 GLN cc_start: 0.5794 (tt0) cc_final: 0.5535 (tm-30)
REVERT: B   59 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7248 (t80)
REVERT: B  195 ASP cc_start: 0.7285 (p0) cc_final: 0.6830 (p0)
REVERT: B  217 MET cc_start: 0.7310 (ptt) cc_final: 0.6992 (pmt)
REVERT: N   25 SER cc_start: 0.6037 (OUTLIER) cc_final: 0.5399 (t)
REVERT: N   60 TYR cc_start: 0.7016 (m-80) cc_final: 0.6727 (m-80)
  outliers start: 33
  outliers final: 12
  residues processed: 173
  average time/residue: 0.5421
  time to fit residues: 101.2191
Evaluate side-chains
  147 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  167 ARG
Chi-restraints excluded: chain E residue  168 SER
Chi-restraints excluded: chain P residue    9 THR
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  174 ARG
Chi-restraints excluded: chain R residue  186 ASN
Chi-restraints excluded: chain R residue  367 MET
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   25 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 117 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 66 optimal weight:   40.0000
   chunk 8 optimal weight:    0.9980
   chunk 122 optimal weight:    2.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
R 186 ASN
A 292 ASN
B 220 GLN
N  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.212799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.150250 restraints weight = 26937.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3814 rms_B_bonded: 3.74
r_work: 0.3663 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3755
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3755 r_free = 0.3755    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3755 r_free = 0.3755    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3755
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6442
moved from start:          0.2592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10470  Z= 0.181
  Angle     :  0.587   9.172  14195  Z= 0.307
  Chirality :  0.044   0.290   1572
  Planarity :  0.004   0.055   1785
  Dihedral  :  6.342  59.950   1699
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 16.00 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.23), residues: 1252
  helix:  0.97 (0.23), residues: 514
  sheet: -0.24 (0.31), residues: 250
  loop : -0.75 (0.26), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R  74 
 TYR   0.014   0.002   TYR N  60 
 PHE   0.017   0.002   PHE A 345 
 TRP   0.014   0.002   TRP R 236 
 HIS   0.005   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (10457)
  covalent geometry    : angle       0.57731 (14168)
  SS BOND              : bond        0.00268 (    9)
  SS BOND              : angle       1.09687 (   18)
  hydrogen bonds       : bond        0.05007 (  518)
  hydrogen bonds       : angle       4.88312 ( 1486)
  Misc. bond           : bond        0.00013 (    1)
  link_NAG-ASN         : bond        0.00929 (    3)
  link_NAG-ASN         : angle       3.98011 (    9)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 140
  time to evaluate  : 0.366 
Fit side-chains
REVERT: E   99 CYS cc_start: 0.6643 (OUTLIER) cc_final: 0.6202 (p)
REVERT: R  101 ASP cc_start: 0.5402 (m-30) cc_final: 0.5171 (m-30)
REVERT: R  140 GLU cc_start: 0.6452 (tp30) cc_final: 0.5946 (tp30)
REVERT: R  143 LYS cc_start: 0.6496 (tttt) cc_final: 0.6251 (ttpp)
REVERT: R  174 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6589 (mtt180)
REVERT: R  287 ASP cc_start: 0.5968 (t0) cc_final: 0.5735 (t0)
REVERT: R  405 GLN cc_start: 0.6610 (OUTLIER) cc_final: 0.6288 (mp10)
REVERT: A   60 MET cc_start: 0.5945 (OUTLIER) cc_final: 0.5446 (mpp)
REVERT: A  253 TYR cc_start: 0.5242 (p90) cc_final: 0.4991 (p90)
REVERT: A  356 ARG cc_start: 0.7146 (ptt-90) cc_final: 0.6865 (ptt-90)
REVERT: A  389 ARG cc_start: 0.7596 (ttt90) cc_final: 0.6310 (ttm110)
REVERT: A  390 GLN cc_start: 0.6367 (mt0) cc_final: 0.5730 (mp10)
REVERT: B   13 GLN cc_start: 0.6929 (mm-40) cc_final: 0.6686 (mm-40)
REVERT: B   17 GLN cc_start: 0.5937 (tt0) cc_final: 0.5658 (tm-30)
REVERT: B   59 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7321 (t80)
REVERT: B  154 ASP cc_start: 0.7436 (m-30) cc_final: 0.7205 (m-30)
REVERT: B  215 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7122 (mp0)
REVERT: B  217 MET cc_start: 0.7315 (ptt) cc_final: 0.6810 (pmt)
REVERT: N    1 GLN cc_start: 0.6613 (tp-100) cc_final: 0.6384 (tp40)
REVERT: N    5 GLN cc_start: 0.7114 (tt0) cc_final: 0.6534 (mt0)
REVERT: N   25 SER cc_start: 0.6224 (OUTLIER) cc_final: 0.5664 (t)
REVERT: N   60 TYR cc_start: 0.7078 (m-80) cc_final: 0.6808 (m-80)
  outliers start: 39
  outliers final: 16
  residues processed: 164
  average time/residue: 0.5840
  time to fit residues: 102.9320
Evaluate side-chains
  150 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   99 CYS
Chi-restraints excluded: chain E residue  167 ARG
Chi-restraints excluded: chain E residue  168 SER
Chi-restraints excluded: chain P residue    9 THR
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  174 ARG
Chi-restraints excluded: chain R residue  217 VAL
Chi-restraints excluded: chain R residue  405 GLN
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue  114 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0060
   chunk 55 optimal weight:    2.9990
   chunk 8 optimal weight:    0.3980
   chunk 110 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   chunk 17 optimal weight:   20.0000
   chunk 99 optimal weight:    0.9990
   chunk 93 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.6400

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

Flipped N/Q/H residues before XYZ refinement:
E 124 HIS
P  10 GLN
R 121 HIS
A 357 HIS
B 175 GLN
B 220 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.215347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.153280 restraints weight = 24793.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 3.67
r_work: 0.3702 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3787
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3787 r_free = 0.3787    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3787 r_free = 0.3787    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3787
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6394
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10470  Z= 0.117
  Angle     :  0.517   9.021  14195  Z= 0.270
  Chirality :  0.042   0.290   1572
  Planarity :  0.004   0.056   1785
  Dihedral  :  6.046  59.847   1699
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 16.57 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.23), residues: 1252
  helix:  1.57 (0.23), residues: 515
  sheet: -0.25 (0.31), residues: 248
  loop : -0.63 (0.26), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 347 
 TYR   0.016   0.001   TYR N  60 
 PHE   0.014   0.001   PHE A 212 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.007   0.001   HIS E 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (10457)
  covalent geometry    : angle       0.50733 (14168)
  SS BOND              : bond        0.00636 (    9)
  SS BOND              : angle       0.84907 (   18)
  hydrogen bonds       : bond        0.04012 (  518)
  hydrogen bonds       : angle       4.60848 ( 1486)
  Misc. bond           : bond        0.00021 (    1)
  link_NAG-ASN         : bond        0.00879 (    3)
  link_NAG-ASN         : angle       3.77853 (    9)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 143
  time to evaluate  : 0.430 
Fit side-chains
REVERT: E   99 CYS cc_start: 0.6627 (OUTLIER) cc_final: 0.6181 (p)
REVERT: E  167 ARG cc_start: 0.6231 (OUTLIER) cc_final: 0.5745 (ttm110)
REVERT: P   16 LEU cc_start: 0.5940 (mt) cc_final: 0.5739 (mm)
REVERT: R  101 ASP cc_start: 0.5427 (m-30) cc_final: 0.5208 (m-30)
REVERT: R  140 GLU cc_start: 0.6433 (tp30) cc_final: 0.5989 (tp30)
REVERT: R  174 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6578 (mtt180)
REVERT: R  210 GLU cc_start: 0.6326 (tm-30) cc_final: 0.6112 (tm-30)
REVERT: R  287 ASP cc_start: 0.5854 (t0) cc_final: 0.5621 (t0)
REVERT: R  405 GLN cc_start: 0.6569 (OUTLIER) cc_final: 0.6249 (mp10)
REVERT: A   28 LYS cc_start: 0.6530 (pptt) cc_final: 0.5778 (ptpt)
REVERT: A   35 GLN cc_start: 0.6213 (tt0) cc_final: 0.5438 (mp-120)
REVERT: A   60 MET cc_start: 0.5879 (OUTLIER) cc_final: 0.5438 (mpp)
REVERT: A  389 ARG cc_start: 0.7592 (ttt90) cc_final: 0.6336 (ttm110)
REVERT: A  390 GLN cc_start: 0.6321 (mt0) cc_final: 0.5710 (mp10)
REVERT: B   13 GLN cc_start: 0.6887 (mm-40) cc_final: 0.6352 (tm-30)
REVERT: B  154 ASP cc_start: 0.7414 (m-30) cc_final: 0.7207 (m-30)
REVERT: B  215 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7342 (mm-30)
REVERT: B  217 MET cc_start: 0.7331 (ptt) cc_final: 0.6787 (pmt)
REVERT: N    5 GLN cc_start: 0.7096 (tt0) cc_final: 0.6384 (tm-30)
REVERT: N   25 SER cc_start: 0.6203 (OUTLIER) cc_final: 0.5659 (t)
REVERT: N   60 TYR cc_start: 0.7041 (m-80) cc_final: 0.6771 (m-80)
REVERT: N  105 ARG cc_start: 0.6601 (mtp-110) cc_final: 0.6299 (mtm-85)
REVERT: N  108 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7188 (m-80)
  outliers start: 34
  outliers final: 11
  residues processed: 164
  average time/residue: 0.5862
  time to fit residues: 103.1861
Evaluate side-chains
  152 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   99 CYS
Chi-restraints excluded: chain E residue  163 LEU
Chi-restraints excluded: chain E residue  167 ARG
Chi-restraints excluded: chain P residue    9 THR
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  174 ARG
Chi-restraints excluded: chain R residue  405 GLN
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  114 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 118 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 99 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 17 optimal weight:   20.0000
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
P  10 GLN
** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 201 HIS
B 175 GLN
B 220 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.211119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.149213 restraints weight = 22825.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 3.48
r_work: 0.3660 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3755
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3755 r_free = 0.3755    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3755 r_free = 0.3755    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3755
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6467
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10470  Z= 0.181
  Angle     :  0.589   9.465  14195  Z= 0.305
  Chirality :  0.044   0.294   1572
  Planarity :  0.004   0.060   1785
  Dihedral  :  6.429  59.629   1699
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 16.38 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.23), residues: 1252
  helix:  1.62 (0.23), residues: 517
  sheet: -0.33 (0.32), residues: 243
  loop : -0.60 (0.26), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 347 
 TYR   0.013   0.001   TYR R 391 
 PHE   0.017   0.002   PHE A 212 
 TRP   0.013   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (10457)
  covalent geometry    : angle       0.58065 (14168)
  SS BOND              : bond        0.00239 (    9)
  SS BOND              : angle       1.03150 (   18)
  hydrogen bonds       : bond        0.04599 (  518)
  hydrogen bonds       : angle       4.72396 ( 1486)
  Misc. bond           : bond        0.00018 (    1)
  link_NAG-ASN         : bond        0.00875 (    3)
  link_NAG-ASN         : angle       3.66102 (    9)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 140
  time to evaluate  : 0.375 
Fit side-chains
REVERT: E   99 CYS cc_start: 0.6734 (OUTLIER) cc_final: 0.6309 (p)
REVERT: R  101 ASP cc_start: 0.5568 (m-30) cc_final: 0.5358 (m-30)
REVERT: R  105 SER cc_start: 0.7902 (m) cc_final: 0.7689 (p)
REVERT: R  140 GLU cc_start: 0.6689 (tp30) cc_final: 0.6363 (tp30)
REVERT: R  174 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6693 (mtt180)
REVERT: R  210 GLU cc_start: 0.6350 (tm-30) cc_final: 0.6119 (tm-30)
REVERT: R  257 GLN cc_start: 0.7134 (mt0) cc_final: 0.6850 (mt0)
REVERT: R  287 ASP cc_start: 0.6057 (t70) cc_final: 0.5711 (t0)
REVERT: R  405 GLN cc_start: 0.6597 (OUTLIER) cc_final: 0.6246 (mp10)
REVERT: A   28 LYS cc_start: 0.6690 (pptt) cc_final: 0.5880 (ptpt)
REVERT: A   35 GLN cc_start: 0.6388 (tt0) cc_final: 0.5539 (mp-120)
REVERT: A  389 ARG cc_start: 0.7582 (ttt90) cc_final: 0.6298 (ttm110)
REVERT: A  390 GLN cc_start: 0.6398 (mt0) cc_final: 0.5709 (mp10)
REVERT: B    4 LEU cc_start: 0.3997 (OUTLIER) cc_final: 0.3755 (tp)
REVERT: B   13 GLN cc_start: 0.6973 (mm-40) cc_final: 0.6435 (tm-30)
REVERT: B   17 GLN cc_start: 0.6163 (tm-30) cc_final: 0.5954 (tm130)
REVERT: B   59 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.7462 (t80)
REVERT: B  215 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7392 (mm-30)
REVERT: B  217 MET cc_start: 0.7277 (ptt) cc_final: 0.6660 (pmm)
REVERT: N   25 SER cc_start: 0.6369 (OUTLIER) cc_final: 0.5846 (t)
REVERT: N   34 MET cc_start: 0.7603 (mmm) cc_final: 0.7378 (mmm)
REVERT: N   60 TYR cc_start: 0.7046 (m-80) cc_final: 0.6787 (m-80)
REVERT: N   83 MET cc_start: 0.5569 (mtm) cc_final: 0.4901 (mtm)
REVERT: N  105 ARG cc_start: 0.6645 (mtp-110) cc_final: 0.6214 (mtm-85)
REVERT: N  108 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.7343 (m-80)
  outliers start: 43
  outliers final: 21
  residues processed: 170
  average time/residue: 0.5688
  time to fit residues: 104.5352
Evaluate side-chains
  163 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   99 CYS
Chi-restraints excluded: chain E residue  163 LEU
Chi-restraints excluded: chain E residue  167 ARG
Chi-restraints excluded: chain E residue  168 SER
Chi-restraints excluded: chain P residue    9 THR
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  174 ARG
Chi-restraints excluded: chain R residue  217 VAL
Chi-restraints excluded: chain R residue  339 LEU
Chi-restraints excluded: chain R residue  357 VAL
Chi-restraints excluded: chain R residue  405 GLN
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  114 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 118 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 71 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 0 optimal weight:   60.0000
   chunk 28 optimal weight:    0.9980
   chunk 97 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
P  10 GLN
** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 GLN
B 220 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.214032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.152489 restraints weight = 23850.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3842 rms_B_bonded: 3.54
r_work: 0.3696 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3780
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3780 r_free = 0.3780    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3780 r_free = 0.3780    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3780
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6417
moved from start:          0.3262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  10470  Z= 0.118
  Angle     :  0.513   9.264  14195  Z= 0.267
  Chirality :  0.042   0.292   1572
  Planarity :  0.004   0.057   1785
  Dihedral  :  6.191  59.870   1699
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 17.05 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.24), residues: 1252
  helix:  1.88 (0.23), residues: 517
  sheet: -0.37 (0.32), residues: 250
  loop : -0.48 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 347 
 TYR   0.016   0.001   TYR N  60 
 PHE   0.015   0.001   PHE R  99 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 381 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10457)
  covalent geometry    : angle       0.50434 (14168)
  SS BOND              : bond        0.00298 (    9)
  SS BOND              : angle       0.98597 (   18)
  hydrogen bonds       : bond        0.03875 (  518)
  hydrogen bonds       : angle       4.49143 ( 1486)
  Misc. bond           : bond        0.00010 (    1)
  link_NAG-ASN         : bond        0.00865 (    3)
  link_NAG-ASN         : angle       3.55812 (    9)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 140
  time to evaluate  : 0.448 
Fit side-chains
REVERT: E   99 CYS cc_start: 0.6693 (OUTLIER) cc_final: 0.6276 (p)
REVERT: R  174 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.6682 (mtt180)
REVERT: R  210 GLU cc_start: 0.6333 (tm-30) cc_final: 0.6086 (tm-30)
REVERT: R  257 GLN cc_start: 0.7054 (mt0) cc_final: 0.6808 (mt0)
REVERT: R  287 ASP cc_start: 0.5991 (t70) cc_final: 0.5693 (t0)
REVERT: R  367 MET cc_start: 0.3673 (OUTLIER) cc_final: 0.3420 (ttt)
REVERT: R  405 GLN cc_start: 0.6571 (OUTLIER) cc_final: 0.6229 (mp10)
REVERT: A   28 LYS cc_start: 0.6827 (pptt) cc_final: 0.6093 (ptpt)
REVERT: A   35 GLN cc_start: 0.6308 (tt0) cc_final: 0.5428 (mp-120)
REVERT: A  389 ARG cc_start: 0.7546 (ttt90) cc_final: 0.6305 (ttm110)
REVERT: A  390 GLN cc_start: 0.6293 (mt0) cc_final: 0.5655 (mp10)
REVERT: B    4 LEU cc_start: 0.4079 (OUTLIER) cc_final: 0.3845 (tp)
REVERT: B   13 GLN cc_start: 0.7035 (mm-40) cc_final: 0.6497 (tm-30)
REVERT: B   17 GLN cc_start: 0.6122 (tm-30) cc_final: 0.5898 (tm-30)
REVERT: B   59 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7138 (t80)
REVERT: B  215 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7258 (mp0)
REVERT: B  217 MET cc_start: 0.7281 (ptt) cc_final: 0.6675 (pmm)
REVERT: N    5 GLN cc_start: 0.7189 (tt0) cc_final: 0.6395 (tm-30)
REVERT: N   25 SER cc_start: 0.6442 (OUTLIER) cc_final: 0.5870 (t)
REVERT: N   34 MET cc_start: 0.7585 (mmm) cc_final: 0.7344 (mmm)
REVERT: N   60 TYR cc_start: 0.6989 (m-80) cc_final: 0.6750 (m-80)
REVERT: N  105 ARG cc_start: 0.6650 (mtp-110) cc_final: 0.6309 (mtm-85)
REVERT: N  108 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7100 (m-80)
  outliers start: 35
  outliers final: 19
  residues processed: 163
  average time/residue: 0.5385
  time to fit residues: 95.0289
Evaluate side-chains
  162 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   99 CYS
Chi-restraints excluded: chain E residue  163 LEU
Chi-restraints excluded: chain E residue  167 ARG
Chi-restraints excluded: chain E residue  168 SER
Chi-restraints excluded: chain P residue    9 THR
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  174 ARG
Chi-restraints excluded: chain R residue  217 VAL
Chi-restraints excluded: chain R residue  357 VAL
Chi-restraints excluded: chain R residue  367 MET
Chi-restraints excluded: chain R residue  405 GLN
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  125 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 76 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0050
   chunk 56 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 95 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   chunk 7 optimal weight:    8.9990
   chunk 116 optimal weight:    5.9990
   overall best weight:    0.6996

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

Flipped N/Q/H residues before XYZ refinement:
P  10 GLN
** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.214683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.153174 restraints weight = 24438.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3851 rms_B_bonded: 3.62
r_work: 0.3704 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3788
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3788 r_free = 0.3788    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3788 r_free = 0.3788    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3788
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6399
moved from start:          0.3361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10470  Z= 0.113
  Angle     :  0.508   8.804  14195  Z= 0.263
  Chirality :  0.042   0.293   1572
  Planarity :  0.003   0.058   1785
  Dihedral  :  6.083  59.792   1699
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 17.33 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.24), residues: 1252
  helix:  2.02 (0.23), residues: 517
  sheet: -0.27 (0.32), residues: 251
  loop : -0.41 (0.27), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 347 
 TYR   0.015   0.001   TYR N  60 
 PHE   0.016   0.001   PHE R  99 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 381 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (10457)
  covalent geometry    : angle       0.49978 (14168)
  SS BOND              : bond        0.00217 (    9)
  SS BOND              : angle       0.78755 (   18)
  hydrogen bonds       : bond        0.03730 (  518)
  hydrogen bonds       : angle       4.38924 ( 1486)
  Misc. bond           : bond        0.00001 (    1)
  link_NAG-ASN         : bond        0.00856 (    3)
  link_NAG-ASN         : angle       3.49821 (    9)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 140
  time to evaluate  : 0.410 
Fit side-chains
REVERT: E   99 CYS cc_start: 0.6600 (OUTLIER) cc_final: 0.6197 (p)
REVERT: E  167 ARG cc_start: 0.6409 (OUTLIER) cc_final: 0.5879 (ttm110)
REVERT: R  174 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6693 (mtt180)
REVERT: R  210 GLU cc_start: 0.6367 (tm-30) cc_final: 0.6147 (tm-30)
REVERT: R  257 GLN cc_start: 0.7124 (mt0) cc_final: 0.6915 (mt0)
REVERT: R  287 ASP cc_start: 0.5951 (t70) cc_final: 0.5663 (t0)
REVERT: R  367 MET cc_start: 0.3679 (OUTLIER) cc_final: 0.3422 (ttt)
REVERT: R  405 GLN cc_start: 0.6537 (OUTLIER) cc_final: 0.6165 (mp10)
REVERT: A   28 LYS cc_start: 0.6807 (pptt) cc_final: 0.6102 (ptpt)
REVERT: A   35 GLN cc_start: 0.6302 (tt0) cc_final: 0.5406 (mp-120)
REVERT: A  389 ARG cc_start: 0.7524 (ttt90) cc_final: 0.6274 (ttm110)
REVERT: A  390 GLN cc_start: 0.6374 (mt0) cc_final: 0.5717 (mp10)
REVERT: B    4 LEU cc_start: 0.4049 (OUTLIER) cc_final: 0.3820 (tp)
REVERT: B   13 GLN cc_start: 0.7039 (mm-40) cc_final: 0.6516 (tm-30)
REVERT: B   17 GLN cc_start: 0.6191 (tm-30) cc_final: 0.5929 (tm-30)
REVERT: B   59 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.7114 (t80)
REVERT: B  195 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7000 (p0)
REVERT: B  215 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7308 (mp0)
REVERT: B  217 MET cc_start: 0.7296 (ptt) cc_final: 0.6686 (pmm)
REVERT: N    5 GLN cc_start: 0.7195 (tt0) cc_final: 0.6388 (tm-30)
REVERT: N   25 SER cc_start: 0.6444 (OUTLIER) cc_final: 0.5875 (t)
REVERT: N   60 TYR cc_start: 0.6951 (m-80) cc_final: 0.6750 (m-80)
REVERT: N  105 ARG cc_start: 0.6711 (mtp-110) cc_final: 0.6359 (mtm-85)
REVERT: N  108 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.7036 (m-80)
  outliers start: 36
  outliers final: 19
  residues processed: 166
  average time/residue: 0.5571
  time to fit residues: 100.0914
Evaluate side-chains
  162 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 133
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   99 CYS
Chi-restraints excluded: chain E residue  167 ARG
Chi-restraints excluded: chain E residue  168 SER
Chi-restraints excluded: chain P residue    9 THR
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  174 ARG
Chi-restraints excluded: chain R residue  217 VAL
Chi-restraints excluded: chain R residue  357 VAL
Chi-restraints excluded: chain R residue  367 MET
Chi-restraints excluded: chain R residue  405 GLN
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  114 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 75 optimal weight:    7.9990
   chunk 111 optimal weight:    5.9990
   chunk 5 optimal weight:   20.0000
   chunk 69 optimal weight:    6.9990
   chunk 2 optimal weight:   30.0000
   chunk 103 optimal weight:    0.9990
   chunk 72 optimal weight:    0.6980
   chunk 22 optimal weight:   20.0000
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
P  10 GLN
** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.213176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.152106 restraints weight = 21311.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3838 rms_B_bonded: 3.38
r_work: 0.3697 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3776
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3776 r_free = 0.3776    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3776 r_free = 0.3776    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6424
moved from start:          0.3468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10470  Z= 0.134
  Angle     :  0.529   8.964  14195  Z= 0.274
  Chirality :  0.043   0.295   1572
  Planarity :  0.004   0.058   1785
  Dihedral  :  6.209  59.991   1699
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 17.62 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.24), residues: 1252
  helix:  2.03 (0.23), residues: 517
  sheet: -0.35 (0.32), residues: 253
  loop : -0.41 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 347 
 TYR   0.013   0.001   TYR N  60 
 PHE   0.017   0.002   PHE R  99 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10457)
  covalent geometry    : angle       0.52125 (14168)
  SS BOND              : bond        0.00264 (    9)
  SS BOND              : angle       0.76395 (   18)
  hydrogen bonds       : bond        0.03951 (  518)
  hydrogen bonds       : angle       4.44365 ( 1486)
  Misc. bond           : bond        0.00008 (    1)
  link_NAG-ASN         : bond        0.00850 (    3)
  link_NAG-ASN         : angle       3.45005 (    9)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 137
  time to evaluate  : 0.393 
Fit side-chains
REVERT: E   99 CYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6339 (p)
REVERT: R  174 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6680 (mtt180)
REVERT: R  257 GLN cc_start: 0.7169 (mt0) cc_final: 0.6943 (mt0)
REVERT: R  287 ASP cc_start: 0.5996 (t70) cc_final: 0.5683 (t0)
REVERT: R  367 MET cc_start: 0.3735 (OUTLIER) cc_final: 0.3466 (ttt)
REVERT: R  405 GLN cc_start: 0.6524 (OUTLIER) cc_final: 0.6190 (mp10)
REVERT: A   35 GLN cc_start: 0.6360 (tt0) cc_final: 0.5444 (mp-120)
REVERT: A  389 ARG cc_start: 0.7538 (ttt90) cc_final: 0.6334 (ttm110)
REVERT: A  390 GLN cc_start: 0.6369 (mt0) cc_final: 0.5727 (mp10)
REVERT: B    4 LEU cc_start: 0.4132 (OUTLIER) cc_final: 0.3908 (tp)
REVERT: B   13 GLN cc_start: 0.7097 (mm-40) cc_final: 0.6583 (tm-30)
REVERT: B   17 GLN cc_start: 0.6261 (tm-30) cc_final: 0.5987 (tm-30)
REVERT: B   59 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.7243 (t80)
REVERT: B  195 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7036 (p0)
REVERT: B  215 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7321 (mp0)
REVERT: B  217 MET cc_start: 0.7289 (ptt) cc_final: 0.6652 (pmm)
REVERT: N    5 GLN cc_start: 0.7207 (tt0) cc_final: 0.6475 (mt0)
REVERT: N   25 SER cc_start: 0.6469 (OUTLIER) cc_final: 0.5908 (t)
REVERT: N  105 ARG cc_start: 0.6674 (mtp-110) cc_final: 0.6279 (mtm-85)
REVERT: N  108 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.7129 (m-80)
  outliers start: 35
  outliers final: 20
  residues processed: 164
  average time/residue: 0.5706
  time to fit residues: 100.9528
Evaluate side-chains
  163 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 134
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   99 CYS
Chi-restraints excluded: chain E residue  167 ARG
Chi-restraints excluded: chain E residue  168 SER
Chi-restraints excluded: chain P residue    9 THR
Chi-restraints excluded: chain R residue   55 CYS
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  174 ARG
Chi-restraints excluded: chain R residue  357 VAL
Chi-restraints excluded: chain R residue  367 MET
Chi-restraints excluded: chain R residue  405 GLN
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  114 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 46 optimal weight:    0.7980
   chunk 102 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0010
   chunk 104 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 13 optimal weight:    0.3980
   overall best weight:    0.6388

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

Flipped N/Q/H residues before XYZ refinement:
P  10 GLN
B 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.214959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.155345 restraints weight = 16128.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3870 rms_B_bonded: 2.99
r_work: 0.3741 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3824 r_free = 0.3824    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3824 r_free = 0.3824    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6394
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10470  Z= 0.109
  Angle     :  0.508   8.719  14195  Z= 0.263
  Chirality :  0.041   0.295   1572
  Planarity :  0.003   0.059   1785
  Dihedral  :  6.085  59.620   1699
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 17.90 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.24), residues: 1252
  helix:  2.14 (0.23), residues: 517
  sheet: -0.33 (0.32), residues: 252
  loop : -0.38 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 356 
 TYR   0.026   0.001   TYR N  60 
 PHE   0.017   0.001   PHE R  99 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.003   0.001   HIS R 381 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (10457)
  covalent geometry    : angle       0.49916 (14168)
  SS BOND              : bond        0.00325 (    9)
  SS BOND              : angle       1.25281 (   18)
  hydrogen bonds       : bond        0.03595 (  518)
  hydrogen bonds       : angle       4.31453 ( 1486)
  Misc. bond           : bond        0.00007 (    1)
  link_NAG-ASN         : bond        0.00860 (    3)
  link_NAG-ASN         : angle       3.37207 (    9)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 141
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
REVERT: E   99 CYS cc_start: 0.6735 (OUTLIER) cc_final: 0.6336 (p)
REVERT: E  167 ARG cc_start: 0.6559 (OUTLIER) cc_final: 0.5953 (ttm110)
REVERT: R  101 ASP cc_start: 0.5565 (m-30) cc_final: 0.5274 (t0)
REVERT: R  257 GLN cc_start: 0.7204 (mt0) cc_final: 0.6970 (mt0)
REVERT: R  287 ASP cc_start: 0.5998 (t70) cc_final: 0.5715 (t0)
REVERT: R  367 MET cc_start: 0.3687 (OUTLIER) cc_final: 0.3401 (ttt)
REVERT: R  382 PHE cc_start: 0.6883 (m-80) cc_final: 0.6553 (m-80)
REVERT: R  405 GLN cc_start: 0.6533 (OUTLIER) cc_final: 0.6162 (mp10)
REVERT: A   28 LYS cc_start: 0.6495 (pptt) cc_final: 0.5783 (ptpt)
REVERT: A   35 GLN cc_start: 0.6306 (tt0) cc_final: 0.5419 (mp-120)
REVERT: A  389 ARG cc_start: 0.7562 (ttt90) cc_final: 0.6269 (ttm110)
REVERT: A  390 GLN cc_start: 0.6390 (mt0) cc_final: 0.5694 (mp10)
REVERT: B    4 LEU cc_start: 0.4125 (OUTLIER) cc_final: 0.3903 (tp)
REVERT: B   13 GLN cc_start: 0.7106 (mm-40) cc_final: 0.6585 (tm-30)
REVERT: B   17 GLN cc_start: 0.6360 (tm-30) cc_final: 0.6070 (tm-30)
REVERT: B  215 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7299 (mp0)
REVERT: B  217 MET cc_start: 0.7282 (ptt) cc_final: 0.6676 (pmm)
REVERT: N    5 GLN cc_start: 0.7188 (tt0) cc_final: 0.6374 (tm-30)
REVERT: N   43 LYS cc_start: 0.6612 (mtpt) cc_final: 0.6353 (mttt)
REVERT: N  108 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6898 (m-80)
  outliers start: 32
  outliers final: 19
  residues processed: 166
  average time/residue: 0.5938
  time to fit residues: 105.8268
Evaluate side-chains
  162 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 137
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   99 CYS
Chi-restraints excluded: chain E residue  167 ARG
Chi-restraints excluded: chain E residue  168 SER
Chi-restraints excluded: chain P residue    9 THR
Chi-restraints excluded: chain R residue   55 CYS
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  247 LEU
Chi-restraints excluded: chain R residue  357 VAL
Chi-restraints excluded: chain R residue  367 MET
Chi-restraints excluded: chain R residue  405 GLN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 55 optimal weight:    4.9990
   chunk 118 optimal weight:    0.3980
   chunk 122 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
P  10 GLN
B 175 GLN
B 220 GLN
N  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.213840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.152361 restraints weight = 24361.756|
|-----------------------------------------------------------------------------|
r_work (start): 0.3838 rms_B_bonded: 3.59
r_work: 0.3693 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3783
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3783 r_free = 0.3783    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3783 r_free = 0.3783    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3783
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6415
moved from start:          0.3636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10470  Z= 0.127
  Angle     :  0.526   8.704  14195  Z= 0.273
  Chirality :  0.042   0.297   1572
  Planarity :  0.004   0.059   1785
  Dihedral  :  6.142  59.357   1699
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 18.38 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.24), residues: 1252
  helix:  2.12 (0.23), residues: 517
  sheet: -0.32 (0.32), residues: 251
  loop : -0.38 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 356 
 TYR   0.022   0.001   TYR N  60 
 PHE   0.016   0.001   PHE R  99 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (10457)
  covalent geometry    : angle       0.51849 (14168)
  SS BOND              : bond        0.00256 (    9)
  SS BOND              : angle       1.17654 (   18)
  hydrogen bonds       : bond        0.03798 (  518)
  hydrogen bonds       : angle       4.36153 ( 1486)
  Misc. bond           : bond        0.00011 (    1)
  link_NAG-ASN         : bond        0.00853 (    3)
  link_NAG-ASN         : angle       3.34843 (    9)

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

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

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2504 Ramachandran restraints generated.
    1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 133
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
REVERT: E   99 CYS cc_start: 0.6780 (OUTLIER) cc_final: 0.6363 (p)
REVERT: E  167 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.5926 (ttm110)
REVERT: R  101 ASP cc_start: 0.5542 (m-30) cc_final: 0.5256 (t0)
REVERT: R  210 GLU cc_start: 0.6421 (tm-30) cc_final: 0.6198 (pm20)
REVERT: R  257 GLN cc_start: 0.7173 (mt0) cc_final: 0.6913 (mt0)
REVERT: R  287 ASP cc_start: 0.5995 (t70) cc_final: 0.5714 (t0)
REVERT: R  367 MET cc_start: 0.3660 (OUTLIER) cc_final: 0.3384 (ttt)
REVERT: R  382 PHE cc_start: 0.6945 (m-80) cc_final: 0.6618 (m-80)
REVERT: R  405 GLN cc_start: 0.6528 (OUTLIER) cc_final: 0.6149 (mp10)
REVERT: A   28 LYS cc_start: 0.6489 (pptt) cc_final: 0.5759 (ptpt)
REVERT: A   35 GLN cc_start: 0.6326 (tt0) cc_final: 0.5397 (mp-120)
REVERT: A  389 ARG cc_start: 0.7518 (ttt90) cc_final: 0.6313 (ttm110)
REVERT: A  390 GLN cc_start: 0.6376 (mt0) cc_final: 0.5725 (mp10)
REVERT: B    4 LEU cc_start: 0.4133 (OUTLIER) cc_final: 0.3912 (tp)
REVERT: B   13 GLN cc_start: 0.7046 (mm-40) cc_final: 0.6545 (tm-30)
REVERT: B   17 GLN cc_start: 0.6336 (tm-30) cc_final: 0.6046 (tm-30)
REVERT: B  195 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7044 (p0)
REVERT: B  215 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7315 (mp0)
REVERT: B  217 MET cc_start: 0.7277 (ptt) cc_final: 0.6634 (pmm)
REVERT: N    5 GLN cc_start: 0.7201 (tt0) cc_final: 0.6617 (mt0)
REVERT: N   43 LYS cc_start: 0.6581 (mtpt) cc_final: 0.6326 (mttt)
REVERT: N  105 ARG cc_start: 0.6713 (mtp180) cc_final: 0.6402 (mtp180)
REVERT: N  108 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7049 (m-80)
  outliers start: 29
  outliers final: 21
  residues processed: 156
  average time/residue: 0.5992
  time to fit residues: 100.2603
Evaluate side-chains
  159 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 131
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   99 CYS
Chi-restraints excluded: chain E residue  167 ARG
Chi-restraints excluded: chain E residue  168 SER
Chi-restraints excluded: chain P residue    9 THR
Chi-restraints excluded: chain R residue   55 CYS
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  247 LEU
Chi-restraints excluded: chain R residue  316 LEU
Chi-restraints excluded: chain R residue  357 VAL
Chi-restraints excluded: chain R residue  367 MET
Chi-restraints excluded: chain R residue  405 GLN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  114 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 121 optimal weight:    0.3980
   chunk 38 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 33 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 92 optimal weight:    0.3980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
P  10 GLN
B 175 GLN
B 220 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.215238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.155428 restraints weight = 17486.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3871 rms_B_bonded: 3.10
r_work: 0.3739 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3822
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3822 r_free = 0.3822    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3822 r_free = 0.3822    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3822
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6379
moved from start:          0.3696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  10470  Z= 0.107
  Angle     :  0.517   8.706  14195  Z= 0.268
  Chirality :  0.041   0.297   1572
  Planarity :  0.004   0.058   1785
  Dihedral  :  6.058  59.513   1699
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 18.38 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.24), residues: 1252
  helix:  2.19 (0.23), residues: 518
  sheet: -0.30 (0.32), residues: 250
  loop : -0.36 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 356 
 TYR   0.020   0.001   TYR N  60 
 PHE   0.017   0.001   PHE R  99 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.003   0.001   HIS R 381 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (10457)
  covalent geometry    : angle       0.50917 (14168)
  SS BOND              : bond        0.00238 (    9)
  SS BOND              : angle       1.01476 (   18)
  hydrogen bonds       : bond        0.03654 (  518)
  hydrogen bonds       : angle       4.29735 ( 1486)
  Misc. bond           : bond        0.00006 (    1)
  link_NAG-ASN         : bond        0.00859 (    3)
  link_NAG-ASN         : angle       3.31512 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5488.86 seconds
wall clock time: 93 minutes 47.92 seconds (5627.92 seconds total)