Starting phenix.real_space_refine
on Wed Mar  4 10:58:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cag_30330/03_2026/7cag_30330.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cag_30330/03_2026/7cag_30330.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cag_30330/03_2026/7cag_30330.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cag_30330/03_2026/7cag_30330.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cag_30330/03_2026/7cag_30330.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cag_30330/03_2026/7cag_30330.map"
  }
  resolution = 3.78
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      38      5.16       5
     C    8302      2.51       5
     N    2188      2.21       5
     O    2459      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 58 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: 12995
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "E"
      Number of atoms: 3298
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 435, 3298
          Classifications: {'peptide': 435}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 31, 'TRANS': 403}
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "A"
      Number of atoms: 2155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2155
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 14, 'TRANS': 270}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 2051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2051
          Classifications: {'peptide': 273}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 16, 'TRANS': 256}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 6
    Chain: "C"
      Number of atoms: 2704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2704
          Classifications: {'peptide': 362}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 17, 'TRANS': 344}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 81
          Unresolved non-hydrogen angles: 98
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4, 'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 41
    Chain: "D"
      Number of atoms: 2700
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2700
          Classifications: {'peptide': 362}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 17, 'TRANS': 344}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 85
          Unresolved non-hydrogen angles: 105
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 6, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "H"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'GLC': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.70, per 1000 atoms: 0.21
  Number of scatterers: 12995
  At special positions: 0
  Unit cell: (81.18, 95.12, 168.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      38     16.00
     P       6     15.00
     Mg      2     11.99
     O    2459      8.00
     N    2188      7.00
     C    8302      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Links applied
    ALPHA1-1
      " GLC H   1 " - " GLC H   2 "
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 471.9 milliseconds
  

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3192

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 13 sheets defined
      41.9% alpha, 4.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'E' and resid 41 through 53
    Processing helix  chain 'E' and resid 71 through 83
      removed outlier: 3.621A  pdb=" N   GLY E  83 " --> pdb=" O   ARG E  79 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 117 through 122
    Processing helix  chain 'E' and resid 165 through 177
      removed outlier: 4.052A  pdb=" N   ASP E 171 " --> pdb=" O   ASP E 167 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA E 173 " --> pdb=" O   MET E 169 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 192 through 205
      removed outlier: 3.821A  pdb=" N   VAL E 196 " --> pdb=" O   TYR E 192 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   THR E 201 " --> pdb=" O   VAL E 197 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   LEU E 202 " --> pdb=" O   TRP E 198 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 223 through 240
      removed outlier: 4.347A  pdb=" N   ALA E 229 " --> pdb=" O   GLU E 225 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   THR E 230 " --> pdb=" O   HIS E 226 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   VAL E 231 " --> pdb=" O   ARG E 227 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   LYS E 232 " --> pdb=" O   ALA E 228 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL E 240 " --> pdb=" O   ILE E 236 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 254 through 265
      removed outlier: 3.596A  pdb=" N   ALA E 258 " --> pdb=" O   ASP E 254 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   LEU E 262 " --> pdb=" O   ALA E 258 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   GLU E 263 " --> pdb=" O   ARG E 259 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 275 through 284
    Processing helix  chain 'E' and resid 285 through 287
      No H-bonds generated for 'chain 'E' and resid 285 through 287'
    Processing helix  chain 'E' and resid 314 through 324
    Processing helix  chain 'E' and resid 360 through 368
      removed outlier: 4.035A  pdb=" N   ARG E 368 " --> pdb=" O   PHE E 364 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 372 through 382
      removed outlier: 4.388A  pdb=" N   SER E 380 " --> pdb=" O   GLN E 376 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 404 through 409
    Processing helix  chain 'E' and resid 424 through 432
      removed outlier: 4.042A  pdb=" N   THR E 429 " --> pdb=" O   GLN E 425 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ARG E 430 " --> pdb=" O   ALA E 426 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 442 through 460
      removed outlier: 3.656A  pdb=" N   THR E 446 " --> pdb=" O   ASP E 442 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ALA E 447 " --> pdb=" O   PRO E 443 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   ASP E 448 " --> pdb=" O   GLU E 444 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   GLU E 449 " --> pdb=" O   ARG E 445 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLY E 460 " --> pdb=" O   LYS E 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 16 through 38
      removed outlier: 4.178A  pdb=" N   LEU A  23 " --> pdb=" O   SER A  19 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   TRP A  26 " --> pdb=" O   ARG A  22 " (cutoff:3.500A)
      Proline residue:  A  30  - end of helix
      removed outlier: 3.715A  pdb=" N   VAL A  38 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 52
      removed outlier: 3.678A  pdb=" N   SER A  50 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLN A  52 " --> pdb=" O   TRP A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 74
    Processing helix  chain 'A' and resid 79 through 110
      removed outlier: 3.804A  pdb=" N   THR A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLY A  88 " --> pdb=" O   ALA A  84 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   VAL A  92 " --> pdb=" O   GLY A  88 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   ALA A  95 " --> pdb=" O   VAL A  91 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ILE A  96 " --> pdb=" O   VAL A  92 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ALA A  99 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   ALA A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 127
      removed outlier: 3.554A  pdb=" N   TYR A 126 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 141
      removed outlier: 3.947A  pdb=" N   SER A 136 " --> pdb=" O   ALA A 132 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   TRP A 137 " --> pdb=" O   ALA A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 182
      removed outlier: 3.559A  pdb=" N   GLU A 173 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   LYS A 176 " --> pdb=" O   ALA A 172 " (cutoff:3.500A)
      Proline residue:  A 179  - end of helix
    Processing helix  chain 'A' and resid 183 through 188
    Processing helix  chain 'A' and resid 193 through 203
      removed outlier: 3.772A  pdb=" N   LEU A 197 " --> pdb=" O   PRO A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 224
      removed outlier: 3.794A  pdb=" N   LEU A 224 " --> pdb=" O   LYS A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 243
    Processing helix  chain 'A' and resid 253 through 261
      removed outlier: 3.554A  pdb=" N   ASN A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 294
      removed outlier: 4.216A  pdb=" N   ALA A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE A 278 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   SER A 281 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ILE A 285 " --> pdb=" O   SER A 281 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   GLY A 294 " --> pdb=" O   ILE A 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 16
      removed outlier: 3.845A  pdb=" N   TRP B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   TRP B  13 " --> pdb=" O   ARG B   9 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   SER B  14 " --> pdb=" O   ALA B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 36
      removed outlier: 4.159A  pdb=" N   LEU B  32 " --> pdb=" O   VAL B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 61
      removed outlier: 3.589A  pdb=" N   LYS B  58 " --> pdb=" O   PHE B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 75
      removed outlier: 3.924A  pdb=" N   ASN B  72 " --> pdb=" O   SER B  68 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   SER B  73 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 97
      removed outlier: 4.560A  pdb=" N   ILE B  82 " --> pdb=" O   LEU B  78 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ILE B  87 " --> pdb=" O   ILE B  83 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ALA B  91 " --> pdb=" O   ILE B  87 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   ALA B  92 " --> pdb=" O   GLY B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 116
      removed outlier: 3.697A  pdb=" N   LEU B 112 " --> pdb=" O   GLY B 108 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ALA B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   MET B 115 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 133
      removed outlier: 3.679A  pdb=" N   ILE B 125 " --> pdb=" O   LEU B 121 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   GLY B 131 " --> pdb=" O   ASN B 127 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   GLY B 133 " --> pdb=" O   TRP B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 156
      Proline residue:  B 144  - end of helix
      Proline residue:  B 151  - end of helix
    Processing helix  chain 'B' and resid 165 through 175
      removed outlier: 3.585A  pdb=" N   GLU B 169 " --> pdb=" O   PRO B 165 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ASP B 175 " --> pdb=" O   ALA B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 186
      removed outlier: 3.641A  pdb=" N   PHE B 183 " --> pdb=" O   PRO B 179 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ARG B 184 " --> pdb=" O   ALA B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 195
      removed outlier: 3.634A  pdb=" N   ALA B 192 " --> pdb=" O   PRO B 189 " (cutoff:3.500A)
      Proline residue:  B 193  - end of helix
    Processing helix  chain 'B' and resid 200 through 208
      removed outlier: 3.714A  pdb=" N   ASN B 208 " --> pdb=" O   ILE B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 229
    Processing helix  chain 'B' and resid 248 through 253
    Processing helix  chain 'B' and resid 254 through 259
    Processing helix  chain 'B' and resid 259 through 264
    Processing helix  chain 'C' and resid 47 through 56
    Processing helix  chain 'C' and resid 76 through 80
      removed outlier: 3.627A  pdb=" N   ARG C  80 " --> pdb=" O   PRO C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 103
    Processing helix  chain 'C' and resid 104 through 107
      removed outlier: 3.623A  pdb=" N   LEU C 107 " --> pdb=" O   PRO C 104 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 104 through 107'
    Processing helix  chain 'C' and resid 111 through 126
      removed outlier: 4.140A  pdb=" N   ALA C 117 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   GLU C 120 " --> pdb=" O   ALA C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 154
      removed outlier: 4.035A  pdb=" N   ALA C 152 " --> pdb=" O   ALA C 148 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   VAL C 154 " --> pdb=" O   GLY C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 170 through 188
      removed outlier: 3.692A  pdb=" N   GLN C 176 " --> pdb=" O   LYS C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 198 through 202
    Processing helix  chain 'C' and resid 234 through 239
      removed outlier: 3.758A  pdb=" N   ILE C 239 " --> pdb=" O   VAL C 235 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 266 through 277
      removed outlier: 4.144A  pdb=" N   ASP C 271 " --> pdb=" O   PRO C 267 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   LEU C 272 " --> pdb=" O   HIS C 268 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU C 273 " --> pdb=" O   MET C 269 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ALA C 277 " --> pdb=" O   LEU C 273 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 297 through 302
      removed outlier: 3.786A  pdb=" N   ALA C 301 " --> pdb=" O   LEU C 297 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 55
      removed outlier: 3.583A  pdb=" N   LEU D  51 " --> pdb=" O   LYS D  47 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 76 through 81
      removed outlier: 3.696A  pdb=" N   ARG D  80 " --> pdb=" O   PRO D  77 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ASP D  81 " --> pdb=" O   LYS D  78 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 96 through 107
      Proline residue:  D 104  - end of helix
    Processing helix  chain 'D' and resid 111 through 126
      removed outlier: 3.797A  pdb=" N   ILE D 115 " --> pdb=" O   PRO D 111 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ALA D 116 " --> pdb=" O   LYS D 112 " (cutoff:3.500A)
      removed outlier: 5.200A  pdb=" N   ALA D 117 " --> pdb=" O   ALA D 113 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   GLU D 120 " --> pdb=" O   ALA D 116 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ALA D 123 " --> pdb=" O   VAL D 119 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   LEU D 126 " --> pdb=" O   THR D 122 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 154
      removed outlier: 4.083A  pdb=" N   ARG D 146 " --> pdb=" O   GLY D 142 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ALA D 152 " --> pdb=" O   ALA D 148 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 181
      removed outlier: 3.588A  pdb=" N   ALA D 179 " --> pdb=" O   VAL D 175 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 200 through 205
    Processing helix  chain 'D' and resid 224 through 229
    Processing helix  chain 'D' and resid 266 through 268
      No H-bonds generated for 'chain 'D' and resid 266 through 268'
    Processing helix  chain 'D' and resid 269 through 274
      removed outlier: 4.203A  pdb=" N   LEU D 273 " --> pdb=" O   MET D 269 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 291
      removed outlier: 3.541A  pdb=" N   HIS D 290 " --> pdb=" O   ARG D 287 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 90 through 93
      removed outlier: 6.402A  pdb=" N   LEU E 349 " --> pdb=" O   ILE E 145 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 269 through 272
      removed outlier: 3.905A  pdb=" N   ASN E 272 " --> pdb=" O   LEU E 151 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU E 151 " --> pdb=" O   ASN E 272 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA E 331 " --> pdb=" O   LEU E 152 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 6
    Processing sheet with id=AA4, first strand: chain 'C' and resid 38 through 40
      removed outlier: 3.602A  pdb=" N   MET C 212 " --> pdb=" O   VAL C  40 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   VAL C 211 " --> pdb=" O   GLN C 218 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 163
      removed outlier: 7.032A  pdb=" N   MET C 162 " --> pdb=" O   VAL C 195 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 282 through 283
    Processing sheet with id=AA7, first strand: chain 'C' and resid 291 through 292
    Processing sheet with id=AA8, first strand: chain 'C' and resid 314 through 316
      removed outlier: 4.058A  pdb=" N   ILE C 314 " --> pdb=" O   HIS C 325 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 29 through 31
    Processing sheet with id=AB1, first strand: chain 'D' and resid 194 through 195
      removed outlier: 5.664A  pdb=" N   ILE D  38 " --> pdb=" O   VAL D 210 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   MET D 212 " --> pdb=" O   ILE D  38 " (cutoff:3.500A)
      removed outlier: 5.948A  pdb=" N   VAL D  40 " --> pdb=" O   MET D 212 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   VAL D 211 " --> pdb=" O   GLN D 218 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 248 through 249
    Processing sheet with id=AB3, first strand: chain 'D' and resid 292 through 293
    Processing sheet with id=AB4, first strand: chain 'D' and resid 311 through 316
      removed outlier: 5.278A  pdb=" N   ALA D 312 " --> pdb=" O   THR D 327 " (cutoff:3.500A)
      removed outlier: 7.660A  pdb=" N   THR D 327 " --> pdb=" O   ALA D 312 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   ILE D 314 " --> pdb=" O   HIS D 325 " (cutoff:3.500A)

    404 hydrogen bonds defined for protein.
    1146 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: 1.75

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4243
        1.34 -     1.46: 2089
        1.46 -     1.57: 6844
        1.57 -     1.69: 10
        1.69 -     1.81: 73
  Bond restraints: 13259
  Sorted by residual:
  bond pdb=" C1  GLC H   1 "
       pdb=" O5  GLC H   1 "
    ideal  model  delta    sigma   weight residual
    1.402  1.499 -0.097 2.00e-02 2.50e+03 2.33e+01
  bond pdb=" C   ILE A 124 "
       pdb=" N   PRO A 125 "
    ideal  model  delta    sigma   weight residual
    1.334  1.367 -0.033 8.40e-03 1.42e+04 1.57e+01
  bond pdb=" C5  GLC H   2 "
       pdb=" O5  GLC H   2 "
    ideal  model  delta    sigma   weight residual
    1.415  1.487 -0.072 2.00e-02 2.50e+03 1.30e+01
  bond pdb=" C1  GLC H   2 "
       pdb=" O5  GLC H   2 "
    ideal  model  delta    sigma   weight residual
    1.402  1.472 -0.070 2.00e-02 2.50e+03 1.23e+01
  bond pdb=" C3  GLC H   2 "
       pdb=" O3  GLC H   2 "
    ideal  model  delta    sigma   weight residual
    1.412  1.478 -0.066 2.00e-02 2.50e+03 1.08e+01
  ... (remaining 13254 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 17591
        1.97 -     3.93: 410
        3.93 -     5.90: 87
        5.90 -     7.86: 16
        7.86 -     9.83: 2
  Bond angle restraints: 18106
  Sorted by residual:
  angle pdb=" N   GLN C  87 "
        pdb=" CA  GLN C  87 "
        pdb=" C   GLN C  87 "
      ideal   model   delta    sigma   weight residual
     110.97  102.92    8.05 1.09e+00 8.42e-01 5.46e+01
  angle pdb=" PB  ATP C 502 "
        pdb=" O3B ATP C 502 "
        pdb=" PG  ATP C 502 "
      ideal   model   delta    sigma   weight residual
     139.87  132.53    7.34 1.00e+00 1.00e+00 5.39e+01
  angle pdb=" PB  ATP D 502 "
        pdb=" O3B ATP D 502 "
        pdb=" PG  ATP D 502 "
      ideal   model   delta    sigma   weight residual
     139.87  132.63    7.24 1.00e+00 1.00e+00 5.24e+01
  angle pdb=" N   GLN D  87 "
        pdb=" CA  GLN D  87 "
        pdb=" C   GLN D  87 "
      ideal   model   delta    sigma   weight residual
     111.07  104.55    6.52 1.07e+00 8.73e-01 3.72e+01
  angle pdb=" N   THR D 190 "
        pdb=" CA  THR D 190 "
        pdb=" C   THR D 190 "
      ideal   model   delta    sigma   weight residual
     108.52  115.20   -6.68 1.52e+00 4.33e-01 1.93e+01
  ... (remaining 18101 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.57: 7525
       24.57 -    49.15: 416
       49.15 -    73.72: 32
       73.72 -    98.30: 11
       98.30 -   122.87: 2
  Dihedral angle restraints: 7986
    sinusoidal: 3042
      harmonic: 4944
  Sorted by residual:
  dihedral pdb=" CA  THR D 190 "
           pdb=" C   THR D 190 "
           pdb=" N   THR D 191 "
           pdb=" CA  THR D 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.46   25.54     0      5.00e+00 4.00e-02 2.61e+01
  dihedral pdb=" CA  GLY C 240 "
           pdb=" C   GLY C 240 "
           pdb=" N   SER C 241 "
           pdb=" CA  SER C 241 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.22  -23.78     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" CA  GLN C 367 "
           pdb=" C   GLN C 367 "
           pdb=" N   ILE C 368 "
           pdb=" CA  ILE C 368 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.45  -22.55     0      5.00e+00 4.00e-02 2.03e+01
  ... (remaining 7983 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1819
       0.064 -    0.129: 305
       0.129 -    0.193: 19
       0.193 -    0.258: 2
       0.258 -    0.322: 1
  Chirality restraints: 2146
  Sorted by residual:
  chirality pdb=" C1  GLC H   2 "
            pdb=" C2  GLC H   2 "
            pdb=" O1  GLC H   2 "
            pdb=" O5  GLC H   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.04   -2.36    0.32 2.00e-01 2.50e+01 2.59e+00
  chirality pdb=" CA  GLN C  87 "
            pdb=" N   GLN C  87 "
            pdb=" C   GLN C  87 "
            pdb=" CB  GLN C  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CA  GLN D  87 "
            pdb=" N   GLN D  87 "
            pdb=" C   GLN D  87 "
            pdb=" CB  GLN D  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 2143 not shown)

  Planarity restraints: 2322
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 258 "    0.056 5.00e-02 4.00e+02   8.49e-02 1.15e+01
        pdb=" N   PRO C 259 "   -0.147 5.00e-02 4.00e+02
        pdb=" CA  PRO C 259 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO C 259 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY E 181 "   -0.041 5.00e-02 4.00e+02   6.20e-02 6.15e+00
        pdb=" N   PRO E 182 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO E 182 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO E 182 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 220 "    0.037 5.00e-02 4.00e+02   5.62e-02 5.06e+00
        pdb=" N   PRO A 221 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A 221 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 221 "    0.031 5.00e-02 4.00e+02
  ... (remaining 2319 not shown)

  Histogram of nonbonded interaction distances:
        1.85 -     2.46: 84
        2.46 -     3.07: 9118
        3.07 -     3.68: 19391
        3.68 -     4.29: 27180
        4.29 -     4.90: 44946
  Nonbonded interactions: 100719
  Sorted by model distance:
  nonbonded pdb="MG    MG C 501 "
            pdb=" O3G ATP C 502 "
     model   vdw
     1.845 2.170
  nonbonded pdb=" OE1 GLN D  87 "
            pdb="MG    MG D 501 "
     model   vdw
     2.066 2.170
  nonbonded pdb=" OG1 THR C  49 "
            pdb=" O1A ATP C 502 "
     model   vdw
     2.072 3.040
  nonbonded pdb=" OG1 THR A 142 "
            pdb=" O   THR A 145 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OG  SER C  48 "
            pdb="MG    MG C 501 "
     model   vdw
     2.170 2.170
  ... (remaining 100714 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
Found NCS groups:
ncs_group {
  reference = (chain 'C' and (resid 2 through 53 or (resid 54 through 55 and (name N or name C \ 
A or name C or name O or name CB )) or resid 56 through 63 or (resid 64 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 65 through 90 or (resi \ 
d 91 and (name N or name CA or name C or name O or name CB )) or resid 92 throug \ 
h 108 or (resid 109 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 110 through 130 or (resid 131 through 132 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 133 through 187 or (resid 188 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 189 or (resid 190 through 191  \ 
and (name N or name CA or name C or name O or name CB )) or resid 192 through 23 \ 
2 or (resid 233 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 234 through 259 or (resid 260 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 261 through 303 or (resid 304 through 305 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 306 through 362 or (resid 363 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 364 through 387 or \ 
 (resid 388 and (name N or name CA or name C or name O or name CB )) or resid 38 \ 
9 or (resid 390 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 391 through 502))
  selection = (chain 'D' and (resid 2 through 10 or (resid 11 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 12 or (resid 13 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 14 through 44 or (resid 45 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 46 through 52 or (resid 53 thro \ 
ugh 55 and (name N or name CA or name C or name O or name CB )) or resid 56 thro \ 
ugh 65 or (resid 66 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 67 through 69 or (resid 70 and (name N or name CA or name C or name O or n \ 
ame CB )) or resid 71 through 74 or (resid 75 through 76 and (name N or name CA  \ 
or name C or name O or name CB )) or resid 77 through 114 or (resid 115 through  \ 
117 and (name N or name CA or name C or name O or name CB )) or resid 118 throug \ 
h 165 or (resid 166 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 167 through 288 or (resid 289 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 290 through 297 or (resid 298 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 299 through 309 or (resid 310 through 313  \ 
and (name N or name CA or name C or name O or name CB )) or resid 314 through 37 \ 
5 or (resid 376 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 377 through 502))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.320
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
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      :  0.011   0.896  13262  Z= 1.039
  Angle     :  0.767   9.830  18109  Z= 0.430
  Chirality :  0.047   0.322   2146
  Planarity :  0.005   0.085   2322
  Dihedral  : 14.874 122.874   4794
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.60 %
    Favored  : 87.40 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  6.73 %
    Favored  : 93.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.72 (0.16), residues: 1699
  helix: -3.20 (0.15), residues: 674
  sheet: -4.33 (0.31), residues: 118
  loop : -4.36 (0.16), residues: 907

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  80 
 TYR   0.016   0.001   TYR E  34 
 PHE   0.016   0.001   PHE C 326 
 TRP   0.009   0.001   TRP A 141 
 HIS   0.003   0.001   HIS C 290 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (13259)
  covalent geometry    : angle       0.76700 (18106)
  hydrogen bonds       : bond        0.15368 (  404)
  hydrogen bonds       : angle       6.99067 ( 1146)
  glycosidic custom    : bond        0.05174 (    1)
  glycosidic custom    : angle       1.60112 (    3)
  Misc. bond           : bond        0.83151 (    2)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 291
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   73 GLN cc_start: 0.7773 (pt0) cc_final: 0.7261 (tp40)
REVERT: E  252 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8294 (tm-30)
REVERT: E  297 ASP cc_start: 0.5801 (t0) cc_final: 0.5593 (t0)
REVERT: E  405 TYR cc_start: 0.8508 (p90) cc_final: 0.8217 (p90)
REVERT: A   52 GLN cc_start: 0.8316 (pp30) cc_final: 0.7008 (pp30)
REVERT: A   55 ASN cc_start: 0.7877 (t0) cc_final: 0.7366 (t0)
REVERT: A   58 GLU cc_start: 0.8394 (mp0) cc_final: 0.7835 (mp0)
REVERT: A  267 ASN cc_start: 0.8204 (t0) cc_final: 0.7989 (m-40)
REVERT: B   87 ILE cc_start: 0.9236 (pt) cc_final: 0.9010 (pt)
REVERT: B  138 TRP cc_start: 0.8219 (m-10) cc_final: 0.7490 (m-90)
REVERT: B  210 LEU cc_start: 0.8577 (pt) cc_final: 0.8261 (pt)
REVERT: B  221 ARG cc_start: 0.8184 (ttm170) cc_final: 0.7918 (ttm170)
REVERT: C  158 LYS cc_start: 0.8537 (mttt) cc_final: 0.8050 (mtpt)
REVERT: C  244 MET cc_start: 0.7423 (tmm) cc_final: 0.6947 (ttp)
REVERT: C  379 ILE cc_start: 0.8246 (pt) cc_final: 0.7895 (tt)
REVERT: C  390 ARG cc_start: 0.6879 (tpt90) cc_final: 0.5913 (tpt90)
REVERT: D  158 LYS cc_start: 0.7919 (mttt) cc_final: 0.7449 (pttt)
  outliers start: 2
  outliers final: 0
  residues processed: 293
  average time/residue: 0.1190
  time to fit residues: 49.5205
Evaluate side-chains
  213 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    8.9990
   chunk 149 optimal weight:    4.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
** E  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 209 GLN
E 411 GLN
E 414 ASN
E 455 GLN
B  56 ASN
B 127 ASN
C 138 GLN
C 176 GLN
D 138 GLN
D 145 GLN
D 164 GLN
D 197 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.130312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.111868 restraints weight = 25806.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.114721 restraints weight = 14191.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.116685 restraints weight = 9375.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.118038 restraints weight = 7015.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.118887 restraints weight = 5714.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.1284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13262  Z= 0.169
  Angle     :  0.729  10.111  18109  Z= 0.369
  Chirality :  0.047   0.172   2146
  Planarity :  0.006   0.080   2322
  Dihedral  :  8.784 116.503   1942
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.77 %
    Favored  : 87.23 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 15.96 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.82 (0.18), residues: 1699
  helix: -2.39 (0.17), residues: 704
  sheet: -4.03 (0.37), residues: 95
  loop : -3.92 (0.18), residues: 900

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  79 
 TYR   0.014   0.002   TYR E 275 
 PHE   0.015   0.002   PHE B 126 
 TRP   0.015   0.001   TRP B 138 
 HIS   0.004   0.001   HIS C 290 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (13259)
  covalent geometry    : angle       0.72858 (18106)
  hydrogen bonds       : bond        0.03873 (  404)
  hydrogen bonds       : angle       5.42514 ( 1146)
  glycosidic custom    : bond        0.00007 (    1)
  glycosidic custom    : angle       1.14149 (    3)
  Misc. bond           : bond        0.00191 (    2)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 227
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  252 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8236 (tm-30)
REVERT: E  270 GLU cc_start: 0.8617 (pp20) cc_final: 0.7976 (pp20)
REVERT: E  414 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7568 (p0)
REVERT: A   52 GLN cc_start: 0.8395 (pp30) cc_final: 0.7077 (pp30)
REVERT: A   55 ASN cc_start: 0.7702 (t0) cc_final: 0.7485 (t0)
REVERT: A   58 GLU cc_start: 0.8258 (mp0) cc_final: 0.7872 (mp0)
REVERT: A  267 ASN cc_start: 0.8147 (t0) cc_final: 0.7883 (m-40)
REVERT: B   87 ILE cc_start: 0.9405 (pt) cc_final: 0.9173 (pt)
REVERT: B   97 ARG cc_start: 0.8584 (mmm160) cc_final: 0.8242 (mmm160)
REVERT: B  138 TRP cc_start: 0.8472 (m-10) cc_final: 0.7665 (m-90)
REVERT: B  197 THR cc_start: 0.8962 (t) cc_final: 0.8740 (t)
REVERT: B  210 LEU cc_start: 0.8470 (pt) cc_final: 0.8263 (pt)
REVERT: C  168 ASN cc_start: 0.8325 (p0) cc_final: 0.8058 (p0)
REVERT: C  244 MET cc_start: 0.7425 (tmm) cc_final: 0.6974 (ttp)
REVERT: C  390 ARG cc_start: 0.6787 (tpt90) cc_final: 0.5916 (tpt90)
REVERT: D   29 MET cc_start: 0.7796 (ppp) cc_final: 0.7529 (ppp)
REVERT: D  166 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8868 (pp)
  outliers start: 19
  outliers final: 9
  residues processed: 241
  average time/residue: 0.1096
  time to fit residues: 38.5769
Evaluate side-chains
  204 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 193
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  281 LEU
Chi-restraints excluded: chain E residue  375 ASN
Chi-restraints excluded: chain E residue  411 GLN
Chi-restraints excluded: chain E residue  414 ASN
Chi-restraints excluded: chain A residue  264 LYS
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   23 TYR
Chi-restraints excluded: chain C residue  138 GLN
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain D residue  166 LEU
Chi-restraints excluded: chain D residue  201 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 152 optimal weight:    0.0060
   chunk 99 optimal weight:    0.4980
   chunk 111 optimal weight:    0.9990
   chunk 124 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 35 optimal weight:    7.9990
   chunk 72 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 29 optimal weight:    9.9990
   chunk 115 optimal weight:    0.7980
   overall best weight:    0.6600

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

Flipped N/Q/H residues before XYZ refinement:
** E  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 256 ASN
E 411 GLN
E 414 ASN
** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.132729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.114329 restraints weight = 25861.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.117247 restraints weight = 14054.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.119179 restraints weight = 9233.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.120201 restraints weight = 6890.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.121327 restraints weight = 5752.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13262  Z= 0.124
  Angle     :  0.686  10.190  18109  Z= 0.345
  Chirality :  0.046   0.178   2146
  Planarity :  0.005   0.074   2322
  Dihedral  :  8.276 110.710   1942
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.65 %
    Favored  : 89.35 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 18.00 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.35 (0.18), residues: 1699
  helix: -1.97 (0.19), residues: 708
  sheet: -3.60 (0.35), residues: 124
  loop : -3.68 (0.19), residues: 867

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  79 
 TYR   0.013   0.001   TYR E 275 
 PHE   0.013   0.001   PHE B 232 
 TRP   0.010   0.001   TRP B 138 
 HIS   0.002   0.001   HIS C 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (13259)
  covalent geometry    : angle       0.68599 (18106)
  hydrogen bonds       : bond        0.03288 (  404)
  hydrogen bonds       : angle       5.06595 ( 1146)
  glycosidic custom    : bond        0.00497 (    1)
  glycosidic custom    : angle       1.60436 (    3)
  Misc. bond           : bond        0.00091 (    2)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 222
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  252 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7751 (tm-30)
REVERT: A   52 GLN cc_start: 0.8411 (pp30) cc_final: 0.7185 (pp30)
REVERT: A   58 GLU cc_start: 0.8236 (mp0) cc_final: 0.7800 (mp0)
REVERT: A  267 ASN cc_start: 0.8066 (t0) cc_final: 0.7850 (m-40)
REVERT: B  130 ARG cc_start: 0.8362 (tpp-160) cc_final: 0.8018 (tpp80)
REVERT: B  138 TRP cc_start: 0.8397 (m-10) cc_final: 0.7559 (m-90)
REVERT: B  264 GLN cc_start: 0.8564 (pp30) cc_final: 0.8318 (pp30)
REVERT: C  168 ASN cc_start: 0.8230 (p0) cc_final: 0.7926 (p0)
REVERT: C  244 MET cc_start: 0.7364 (tmm) cc_final: 0.6903 (ttp)
REVERT: C  390 ARG cc_start: 0.6710 (tpt90) cc_final: 0.5873 (tpt90)
REVERT: D  158 LYS cc_start: 0.7691 (mttm) cc_final: 0.7392 (pttt)
REVERT: D  166 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8885 (pp)
  outliers start: 30
  outliers final: 14
  residues processed: 245
  average time/residue: 0.0983
  time to fit residues: 36.2103
Evaluate side-chains
  213 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 198
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  253 THR
Chi-restraints excluded: chain E residue  373 VAL
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   23 TYR
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain D residue  166 LEU
Chi-restraints excluded: chain D residue  201 GLU
Chi-restraints excluded: chain D residue  222 THR
Chi-restraints excluded: chain D residue  310 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 146 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 153 optimal weight:    0.6980
   chunk 82 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   chunk 125 optimal weight:    2.9990
   chunk 161 optimal weight:    0.2980
   chunk 156 optimal weight:    0.7980
   chunk 71 optimal weight:    5.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
E  63 GLN
E  76 GLN
** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 256 ASN
** E 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 455 GLN
** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 138 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.133781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.115364 restraints weight = 25713.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.118288 restraints weight = 13989.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.120232 restraints weight = 9150.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.121549 restraints weight = 6814.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.122303 restraints weight = 5540.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13262  Z= 0.122
  Angle     :  0.672   9.740  18109  Z= 0.336
  Chirality :  0.046   0.177   2146
  Planarity :  0.005   0.072   2322
  Dihedral  :  7.957 107.054   1942
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.65 %
    Favored  : 89.35 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 18.46 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.00 (0.19), residues: 1699
  helix: -1.64 (0.19), residues: 708
  sheet: -3.33 (0.35), residues: 138
  loop : -3.53 (0.19), residues: 853

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  79 
 TYR   0.013   0.001   TYR A  45 
 PHE   0.020   0.001   PHE B 232 
 TRP   0.023   0.001   TRP E 166 
 HIS   0.002   0.001   HIS D  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (13259)
  covalent geometry    : angle       0.67165 (18106)
  hydrogen bonds       : bond        0.03004 (  404)
  hydrogen bonds       : angle       4.87224 ( 1146)
  glycosidic custom    : bond        0.00441 (    1)
  glycosidic custom    : angle       1.74631 (    3)
  Misc. bond           : bond        0.00085 (    2)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 222
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   76 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7774 (tm-30)
REVERT: E   93 LEU cc_start: 0.8832 (pp) cc_final: 0.8579 (pp)
REVERT: E  252 GLN cc_start: 0.8466 (tm-30) cc_final: 0.7755 (tm-30)
REVERT: E  442 ASP cc_start: 0.5523 (OUTLIER) cc_final: 0.5131 (t70)
REVERT: A   52 GLN cc_start: 0.8434 (pp30) cc_final: 0.7167 (pp30)
REVERT: A   58 GLU cc_start: 0.8125 (mp0) cc_final: 0.7878 (pm20)
REVERT: A  218 MET cc_start: 0.8668 (mmt) cc_final: 0.8131 (mmt)
REVERT: A  284 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8325 (tp)
REVERT: B  130 ARG cc_start: 0.8367 (tpp-160) cc_final: 0.8084 (tpp80)
REVERT: B  138 TRP cc_start: 0.8426 (m-10) cc_final: 0.7612 (m-90)
REVERT: C  168 ASN cc_start: 0.8184 (p0) cc_final: 0.7889 (p0)
REVERT: C  232 ASN cc_start: 0.7968 (t0) cc_final: 0.7738 (t0)
REVERT: C  244 MET cc_start: 0.7359 (tmm) cc_final: 0.6883 (ttp)
REVERT: C  390 ARG cc_start: 0.6708 (tpt90) cc_final: 0.6021 (tpt90)
REVERT: D  122 THR cc_start: 0.8983 (t) cc_final: 0.8717 (t)
REVERT: D  158 LYS cc_start: 0.7607 (mttm) cc_final: 0.7336 (pttt)
REVERT: D  170 ASP cc_start: 0.7061 (p0) cc_final: 0.6562 (p0)
  outliers start: 44
  outliers final: 24
  residues processed: 255
  average time/residue: 0.1006
  time to fit residues: 38.2470
Evaluate side-chains
  229 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 202
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  253 THR
Chi-restraints excluded: chain E residue  281 LEU
Chi-restraints excluded: chain E residue  373 VAL
Chi-restraints excluded: chain E residue  442 ASP
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   23 TYR
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain D residue   45 CYS
Chi-restraints excluded: chain D residue  201 GLU
Chi-restraints excluded: chain D residue  222 THR
Chi-restraints excluded: chain D residue  310 VAL
Chi-restraints excluded: chain D residue  355 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 102 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 122 optimal weight:    0.3980
   chunk 79 optimal weight:    5.9990
   chunk 85 optimal weight:    6.9990
   chunk 154 optimal weight:    0.7980
   chunk 101 optimal weight:    4.9990
   chunk 129 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 455 GLN
** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 145 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.133461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.115018 restraints weight = 25873.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.117936 restraints weight = 14105.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.119915 restraints weight = 9220.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.121235 restraints weight = 6828.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.122172 restraints weight = 5559.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13262  Z= 0.127
  Angle     :  0.672  10.131  18109  Z= 0.335
  Chirality :  0.045   0.175   2146
  Planarity :  0.005   0.072   2322
  Dihedral  :  7.730 103.068   1942
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.48 %
    Favored  : 89.52 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 19.74 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.80 (0.19), residues: 1699
  helix: -1.46 (0.19), residues: 708
  sheet: -3.11 (0.34), residues: 148
  loop : -3.45 (0.19), residues: 843

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E  79 
 TYR   0.012   0.001   TYR B  23 
 PHE   0.016   0.001   PHE B 232 
 TRP   0.012   0.001   TRP E 166 
 HIS   0.003   0.001   HIS C 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (13259)
  covalent geometry    : angle       0.67202 (18106)
  hydrogen bonds       : bond        0.02905 (  404)
  hydrogen bonds       : angle       4.81432 ( 1146)
  glycosidic custom    : bond        0.00483 (    1)
  glycosidic custom    : angle       1.68862 (    3)
  Misc. bond           : bond        0.00092 (    2)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 203
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   80 ARG cc_start: 0.6173 (tpp80) cc_final: 0.5877 (ttt180)
REVERT: E   93 LEU cc_start: 0.8823 (pp) cc_final: 0.8567 (pp)
REVERT: E  252 GLN cc_start: 0.8450 (tm-30) cc_final: 0.7743 (tm-30)
REVERT: E  271 VAL cc_start: 0.7861 (OUTLIER) cc_final: 0.7636 (m)
REVERT: E  442 ASP cc_start: 0.5421 (OUTLIER) cc_final: 0.5040 (t70)
REVERT: A   52 GLN cc_start: 0.8441 (pp30) cc_final: 0.7188 (pp30)
REVERT: A   58 GLU cc_start: 0.8146 (mp0) cc_final: 0.7879 (pm20)
REVERT: A  218 MET cc_start: 0.8676 (mmt) cc_final: 0.8163 (mmt)
REVERT: A  284 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8347 (tp)
REVERT: B  221 ARG cc_start: 0.8098 (ttm170) cc_final: 0.6865 (tpt170)
REVERT: C  168 ASN cc_start: 0.8212 (p0) cc_final: 0.7779 (p0)
REVERT: C  232 ASN cc_start: 0.7997 (t0) cc_final: 0.7690 (t0)
REVERT: C  244 MET cc_start: 0.7375 (tmm) cc_final: 0.6891 (ttp)
REVERT: C  390 ARG cc_start: 0.6821 (tpt90) cc_final: 0.5974 (tpt90)
REVERT: D  115 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8571 (mt)
REVERT: D  122 THR cc_start: 0.8984 (t) cc_final: 0.8713 (t)
REVERT: D  170 ASP cc_start: 0.7124 (p0) cc_final: 0.6667 (p0)
REVERT: D  201 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7704 (mt-10)
  outliers start: 39
  outliers final: 26
  residues processed: 232
  average time/residue: 0.0939
  time to fit residues: 33.3693
Evaluate side-chains
  225 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 194
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  253 THR
Chi-restraints excluded: chain E residue  271 VAL
Chi-restraints excluded: chain E residue  281 LEU
Chi-restraints excluded: chain E residue  373 VAL
Chi-restraints excluded: chain E residue  442 ASP
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   23 TYR
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain D residue   45 CYS
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  201 GLU
Chi-restraints excluded: chain D residue  222 THR
Chi-restraints excluded: chain D residue  232 ASN
Chi-restraints excluded: chain D residue  310 VAL
Chi-restraints excluded: chain D residue  355 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 148 optimal weight:    0.5980
   chunk 122 optimal weight:    2.9990
   chunk 133 optimal weight:    0.0170
   chunk 62 optimal weight:    3.9990
   chunk 10 optimal weight:    0.1980
   chunk 1 optimal weight:    8.9990
   chunk 57 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 83 optimal weight:    5.9990
   chunk 99 optimal weight:    9.9990
   chunk 108 optimal weight:    0.9990
   overall best weight:    0.9622

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

Flipped N/Q/H residues before XYZ refinement:
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.133939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.115605 restraints weight = 25479.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.118518 restraints weight = 13888.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.120488 restraints weight = 9159.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.121672 restraints weight = 6788.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.122604 restraints weight = 5589.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13262  Z= 0.123
  Angle     :  0.662  11.003  18109  Z= 0.329
  Chirality :  0.045   0.173   2146
  Planarity :  0.005   0.070   2322
  Dihedral  :  7.537 100.328   1942
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.18 %
    Favored  : 89.82 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 19.67 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.59 (0.19), residues: 1699
  helix: -1.30 (0.19), residues: 710
  sheet: -3.08 (0.38), residues: 126
  loop : -3.32 (0.19), residues: 863

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  80 
 TYR   0.017   0.001   TYR E 378 
 PHE   0.024   0.001   PHE B 232 
 TRP   0.018   0.001   TRP E 166 
 HIS   0.004   0.001   HIS C  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (13259)
  covalent geometry    : angle       0.66203 (18106)
  hydrogen bonds       : bond        0.02850 (  404)
  hydrogen bonds       : angle       4.76469 ( 1146)
  glycosidic custom    : bond        0.00729 (    1)
  glycosidic custom    : angle       1.93514 (    3)
  Misc. bond           : bond        0.00083 (    2)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 210
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  111 SER cc_start: 0.8492 (m) cc_final: 0.8249 (t)
REVERT: E  252 GLN cc_start: 0.8421 (tm-30) cc_final: 0.7825 (tm-30)
REVERT: E  442 ASP cc_start: 0.5420 (OUTLIER) cc_final: 0.5051 (t70)
REVERT: A   52 GLN cc_start: 0.8462 (pp30) cc_final: 0.7163 (pp30)
REVERT: A   55 ASN cc_start: 0.7518 (t0) cc_final: 0.7102 (t0)
REVERT: A   58 GLU cc_start: 0.8166 (mp0) cc_final: 0.7625 (mp0)
REVERT: A  284 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8350 (tp)
REVERT: B  221 ARG cc_start: 0.8087 (ttm170) cc_final: 0.6841 (tpt170)
REVERT: C   29 MET cc_start: 0.7793 (ppp) cc_final: 0.7549 (tmm)
REVERT: C  168 ASN cc_start: 0.8183 (p0) cc_final: 0.7765 (p0)
REVERT: C  232 ASN cc_start: 0.7978 (t0) cc_final: 0.7750 (t0)
REVERT: C  244 MET cc_start: 0.7395 (tmm) cc_final: 0.6916 (ttp)
REVERT: C  390 ARG cc_start: 0.6803 (tpt90) cc_final: 0.5926 (tpt90)
REVERT: D  115 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8614 (mt)
REVERT: D  122 THR cc_start: 0.8976 (t) cc_final: 0.8703 (t)
REVERT: D  170 ASP cc_start: 0.7091 (p0) cc_final: 0.6664 (p0)
REVERT: D  201 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7739 (mt-10)
  outliers start: 50
  outliers final: 31
  residues processed: 246
  average time/residue: 0.0920
  time to fit residues: 35.0540
Evaluate side-chains
  237 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 202
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  253 THR
Chi-restraints excluded: chain E residue  281 LEU
Chi-restraints excluded: chain E residue  373 VAL
Chi-restraints excluded: chain E residue  442 ASP
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   23 TYR
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue  115 MET
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  324 VAL
Chi-restraints excluded: chain D residue   37 ILE
Chi-restraints excluded: chain D residue   45 CYS
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  201 GLU
Chi-restraints excluded: chain D residue  222 THR
Chi-restraints excluded: chain D residue  310 VAL
Chi-restraints excluded: chain D residue  355 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 71 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 107 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 148 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 120 optimal weight:    0.0070
   chunk 46 optimal weight:    8.9990
   chunk 136 optimal weight:    2.9990
   overall best weight:    2.8006

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

Flipped N/Q/H residues before XYZ refinement:
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 256 ASN
A 201 GLN
** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.130498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.111903 restraints weight = 26110.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.114810 restraints weight = 14329.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.116751 restraints weight = 9410.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.118015 restraints weight = 7014.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.118923 restraints weight = 5742.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  13262  Z= 0.216
  Angle     :  0.734  10.723  18109  Z= 0.367
  Chirality :  0.048   0.165   2146
  Planarity :  0.005   0.076   2322
  Dihedral  :  7.711 100.596   1942
  Min Nonbonded Distance : 1.789

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.42 %
    Favored  : 87.58 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 21.10 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.65 (0.19), residues: 1699
  helix: -1.38 (0.19), residues: 710
  sheet: -3.02 (0.38), residues: 135
  loop : -3.32 (0.19), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  80 
 TYR   0.017   0.002   TYR A  45 
 PHE   0.020   0.002   PHE D  36 
 TRP   0.022   0.002   TRP A  80 
 HIS   0.005   0.001   HIS C 290 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 (13259)
  covalent geometry    : angle       0.73386 (18106)
  hydrogen bonds       : bond        0.03285 (  404)
  hydrogen bonds       : angle       5.04837 ( 1146)
  glycosidic custom    : bond        0.00566 (    1)
  glycosidic custom    : angle       1.94334 (    3)
  Misc. bond           : bond        0.00112 (    2)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 199
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  252 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7801 (tm-30)
REVERT: E  442 ASP cc_start: 0.5368 (t70) cc_final: 0.5013 (t70)
REVERT: A   55 ASN cc_start: 0.7652 (t0) cc_final: 0.7123 (t0)
REVERT: A   58 GLU cc_start: 0.8251 (mp0) cc_final: 0.7804 (mp0)
REVERT: A  218 MET cc_start: 0.8690 (mmt) cc_final: 0.8106 (mmt)
REVERT: A  284 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8426 (tp)
REVERT: B  221 ARG cc_start: 0.8047 (ttm170) cc_final: 0.6867 (tpt170)
REVERT: B  238 PHE cc_start: 0.6754 (OUTLIER) cc_final: 0.4888 (p90)
REVERT: C   29 MET cc_start: 0.7740 (ppp) cc_final: 0.7492 (tmm)
REVERT: C  168 ASN cc_start: 0.8157 (p0) cc_final: 0.7813 (p0)
REVERT: C  390 ARG cc_start: 0.6714 (tpt90) cc_final: 0.5860 (tpt90)
REVERT: D  115 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8630 (mt)
REVERT: D  170 ASP cc_start: 0.7215 (p0) cc_final: 0.6790 (p0)
REVERT: D  351 GLN cc_start: 0.7996 (mp10) cc_final: 0.7648 (mp10)
  outliers start: 48
  outliers final: 36
  residues processed: 235
  average time/residue: 0.0984
  time to fit residues: 35.1486
Evaluate side-chains
  230 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 191
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  253 THR
Chi-restraints excluded: chain E residue  281 LEU
Chi-restraints excluded: chain E residue  373 VAL
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   23 TYR
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   76 ILE
Chi-restraints excluded: chain B residue  115 MET
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  204 THR
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  379 ILE
Chi-restraints excluded: chain D residue   37 ILE
Chi-restraints excluded: chain D residue   45 CYS
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  154 VAL
Chi-restraints excluded: chain D residue  201 GLU
Chi-restraints excluded: chain D residue  222 THR
Chi-restraints excluded: chain D residue  310 VAL
Chi-restraints excluded: chain D residue  355 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 146 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 113 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 411 GLN
A 201 GLN
** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.132799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.114482 restraints weight = 25313.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.117371 restraints weight = 13906.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.119331 restraints weight = 9136.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.120628 restraints weight = 6802.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.121576 restraints weight = 5564.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.2450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13262  Z= 0.127
  Angle     :  0.683  12.349  18109  Z= 0.339
  Chirality :  0.045   0.169   2146
  Planarity :  0.005   0.071   2322
  Dihedral  :  7.441  97.756   1942
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.95 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 22.39 %
    Favored  : 74.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.47 (0.19), residues: 1699
  helix: -1.24 (0.20), residues: 715
  sheet: -2.93 (0.40), residues: 124
  loop : -3.23 (0.20), residues: 860

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  97 
 TYR   0.012   0.001   TYR B  23 
 PHE   0.020   0.001   PHE B 232 
 TRP   0.025   0.002   TRP A  79 
 HIS   0.003   0.001   HIS C 290 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (13259)
  covalent geometry    : angle       0.68301 (18106)
  hydrogen bonds       : bond        0.02870 (  404)
  hydrogen bonds       : angle       4.85607 ( 1146)
  glycosidic custom    : bond        0.00680 (    1)
  glycosidic custom    : angle       2.08277 (    3)
  Misc. bond           : bond        0.00089 (    2)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 210
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
REVERT: E  111 SER cc_start: 0.8459 (m) cc_final: 0.8237 (t)
REVERT: E  252 GLN cc_start: 0.8412 (tm-30) cc_final: 0.7801 (tm-30)
REVERT: E  442 ASP cc_start: 0.5341 (OUTLIER) cc_final: 0.4980 (t70)
REVERT: A   52 GLN cc_start: 0.8515 (pp30) cc_final: 0.8046 (pt0)
REVERT: A  218 MET cc_start: 0.8717 (mmt) cc_final: 0.8165 (mmt)
REVERT: A  284 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8360 (tp)
REVERT: B   93 TYR cc_start: 0.8371 (t80) cc_final: 0.8127 (t80)
REVERT: B  221 ARG cc_start: 0.8086 (ttm170) cc_final: 0.6807 (tpt170)
REVERT: B  238 PHE cc_start: 0.6690 (OUTLIER) cc_final: 0.4786 (p90)
REVERT: B  250 MET cc_start: 0.7068 (mmp) cc_final: 0.6804 (mmp)
REVERT: C   29 MET cc_start: 0.7723 (ppp) cc_final: 0.7484 (tmm)
REVERT: C  168 ASN cc_start: 0.8102 (p0) cc_final: 0.7752 (p0)
REVERT: C  244 MET cc_start: 0.7395 (tmm) cc_final: 0.7027 (ttp)
REVERT: C  390 ARG cc_start: 0.6624 (tpt90) cc_final: 0.5765 (tpt90)
REVERT: D  115 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8635 (mt)
REVERT: D  170 ASP cc_start: 0.7069 (p0) cc_final: 0.6643 (p0)
REVERT: D  351 GLN cc_start: 0.7980 (mp10) cc_final: 0.7526 (mp10)
  outliers start: 39
  outliers final: 28
  residues processed: 239
  average time/residue: 0.0941
  time to fit residues: 34.6579
Evaluate side-chains
  227 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 195
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  281 LEU
Chi-restraints excluded: chain E residue  373 VAL
Chi-restraints excluded: chain E residue  442 ASP
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   23 TYR
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain D residue   45 CYS
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  201 GLU
Chi-restraints excluded: chain D residue  222 THR
Chi-restraints excluded: chain D residue  310 VAL
Chi-restraints excluded: chain D residue  355 ARG
Chi-restraints excluded: chain D residue  368 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 152 optimal weight:    6.9990
   chunk 113 optimal weight:    0.9990
   chunk 104 optimal weight:   20.0000
   chunk 82 optimal weight:    4.9990
   chunk 142 optimal weight:    4.9990
   chunk 150 optimal weight:    0.8980
   chunk 116 optimal weight:    0.0770
   chunk 114 optimal weight:    0.3980
   chunk 151 optimal weight:    2.9990
   chunk 139 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.6140

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

Flipped N/Q/H residues before XYZ refinement:
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.134556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.116235 restraints weight = 25558.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.119153 restraints weight = 13963.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.121152 restraints weight = 9141.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.122504 restraints weight = 6795.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.123353 restraints weight = 5514.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  13262  Z= 0.123
  Angle     :  0.699  14.396  18109  Z= 0.344
  Chirality :  0.046   0.240   2146
  Planarity :  0.005   0.069   2322
  Dihedral  :  7.259  92.862   1942
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.59 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 23.45 %
    Favored  : 73.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.26 (0.20), residues: 1699
  helix: -1.09 (0.20), residues: 708
  sheet: -2.62 (0.39), residues: 130
  loop : -3.11 (0.20), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C   8 
 TYR   0.012   0.001   TYR E 378 
 PHE   0.019   0.001   PHE B 232 
 TRP   0.027   0.002   TRP A  79 
 HIS   0.002   0.001   HIS C 290 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (13259)
  covalent geometry    : angle       0.69816 (18106)
  hydrogen bonds       : bond        0.02795 (  404)
  hydrogen bonds       : angle       4.78641 ( 1146)
  glycosidic custom    : bond        0.00915 (    1)
  glycosidic custom    : angle       2.01215 (    3)
  Misc. bond           : bond        0.00077 (    2)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 209
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  111 SER cc_start: 0.8508 (m) cc_final: 0.8296 (t)
REVERT: E  238 LYS cc_start: 0.6578 (tttm) cc_final: 0.5722 (tttm)
REVERT: E  252 GLN cc_start: 0.8383 (tm-30) cc_final: 0.7761 (tm-30)
REVERT: E  297 ASP cc_start: 0.6162 (t0) cc_final: 0.5867 (t0)
REVERT: A   26 TRP cc_start: 0.7718 (m100) cc_final: 0.7204 (m-90)
REVERT: A   52 GLN cc_start: 0.8527 (pp30) cc_final: 0.8087 (pt0)
REVERT: A   55 ASN cc_start: 0.7521 (t0) cc_final: 0.7304 (t0)
REVERT: A  218 MET cc_start: 0.8737 (mmt) cc_final: 0.8139 (mmt)
REVERT: A  284 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8350 (tp)
REVERT: B   93 TYR cc_start: 0.8405 (t80) cc_final: 0.8139 (t80)
REVERT: B  221 ARG cc_start: 0.8041 (ttm170) cc_final: 0.6848 (tpt170)
REVERT: B  233 THR cc_start: 0.7563 (OUTLIER) cc_final: 0.7173 (p)
REVERT: B  238 PHE cc_start: 0.6671 (OUTLIER) cc_final: 0.4861 (p90)
REVERT: C   29 MET cc_start: 0.7724 (ppp) cc_final: 0.7479 (tmm)
REVERT: C  168 ASN cc_start: 0.8041 (p0) cc_final: 0.7715 (p0)
REVERT: C  232 ASN cc_start: 0.8121 (t0) cc_final: 0.7709 (t0)
REVERT: C  244 MET cc_start: 0.7385 (tmm) cc_final: 0.7000 (ttp)
REVERT: C  390 ARG cc_start: 0.6624 (tpt90) cc_final: 0.5775 (tpt90)
REVERT: D  115 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8648 (mt)
REVERT: D  122 THR cc_start: 0.8972 (t) cc_final: 0.8695 (t)
REVERT: D  170 ASP cc_start: 0.7038 (p0) cc_final: 0.6609 (p0)
REVERT: D  177 MET cc_start: 0.8947 (mmt) cc_final: 0.8618 (mmm)
REVERT: D  201 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7809 (mt-10)
REVERT: D  351 GLN cc_start: 0.7948 (mp10) cc_final: 0.7491 (mp10)
  outliers start: 37
  outliers final: 28
  residues processed: 235
  average time/residue: 0.0916
  time to fit residues: 33.3951
Evaluate side-chains
  228 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 195
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   93 LEU
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  281 LEU
Chi-restraints excluded: chain E residue  373 VAL
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   23 TYR
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  324 VAL
Chi-restraints excluded: chain D residue   45 CYS
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  201 GLU
Chi-restraints excluded: chain D residue  222 THR
Chi-restraints excluded: chain D residue  244 MET
Chi-restraints excluded: chain D residue  310 VAL
Chi-restraints excluded: chain D residue  355 ARG
Chi-restraints excluded: chain D residue  368 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 76 optimal weight:    9.9990
   chunk 55 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 109 optimal weight:    0.6980
   chunk 148 optimal weight:    0.3980
   chunk 33 optimal weight:    9.9990
   chunk 51 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 95 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
E  76 GLN
** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 201 GLN
** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.135745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.117218 restraints weight = 25863.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.120213 restraints weight = 13893.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.122287 restraints weight = 9022.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.123557 restraints weight = 6594.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.124622 restraints weight = 5351.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13262  Z= 0.129
  Angle     :  0.688  12.579  18109  Z= 0.341
  Chirality :  0.046   0.195   2146
  Planarity :  0.005   0.070   2322
  Dihedral  :  7.084  87.113   1942
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.24 %
    Favored  : 89.76 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 24.36 %
    Favored  : 73.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.14 (0.20), residues: 1699
  helix: -1.02 (0.20), residues: 706
  sheet: -2.56 (0.40), residues: 133
  loop : -3.01 (0.20), residues: 860

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  80 
 TYR   0.012   0.001   TYR B  23 
 PHE   0.019   0.001   PHE A 279 
 TRP   0.029   0.002   TRP A  79 
 HIS   0.002   0.001   HIS C 290 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (13259)
  covalent geometry    : angle       0.68735 (18106)
  hydrogen bonds       : bond        0.02789 (  404)
  hydrogen bonds       : angle       4.78853 ( 1146)
  glycosidic custom    : bond        0.00744 (    1)
  glycosidic custom    : angle       2.29503 (    3)
  Misc. bond           : bond        0.00083 (    2)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 199
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
REVERT: E   76 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7907 (tm-30)
REVERT: E   80 ARG cc_start: 0.6229 (tpp80) cc_final: 0.5830 (ttt180)
REVERT: E  238 LYS cc_start: 0.6621 (tttm) cc_final: 0.5776 (tttm)
REVERT: E  252 GLN cc_start: 0.8397 (tm-30) cc_final: 0.7806 (tm-30)
REVERT: A   26 TRP cc_start: 0.7729 (m100) cc_final: 0.7231 (m-90)
REVERT: A   52 GLN cc_start: 0.8511 (pp30) cc_final: 0.8067 (pt0)
REVERT: A  218 MET cc_start: 0.8735 (mmt) cc_final: 0.8124 (mmt)
REVERT: A  284 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8383 (tp)
REVERT: B   93 TYR cc_start: 0.8391 (t80) cc_final: 0.8153 (t80)
REVERT: B  221 ARG cc_start: 0.8033 (ttm170) cc_final: 0.6792 (tpt170)
REVERT: B  233 THR cc_start: 0.7621 (OUTLIER) cc_final: 0.7281 (p)
REVERT: B  238 PHE cc_start: 0.6742 (OUTLIER) cc_final: 0.4918 (p90)
REVERT: C  168 ASN cc_start: 0.8019 (p0) cc_final: 0.7765 (p0)
REVERT: C  232 ASN cc_start: 0.8120 (t0) cc_final: 0.7704 (t0)
REVERT: C  244 MET cc_start: 0.7395 (tmm) cc_final: 0.7008 (ttp)
REVERT: C  390 ARG cc_start: 0.6588 (tpt90) cc_final: 0.5764 (tpt90)
REVERT: D  115 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8666 (mt)
REVERT: D  122 THR cc_start: 0.8975 (t) cc_final: 0.8702 (t)
REVERT: D  170 ASP cc_start: 0.7038 (p0) cc_final: 0.6627 (p0)
REVERT: D  177 MET cc_start: 0.8943 (mmt) cc_final: 0.8626 (mmm)
REVERT: D  351 GLN cc_start: 0.7921 (mp10) cc_final: 0.7477 (mp10)
  outliers start: 35
  outliers final: 27
  residues processed: 225
  average time/residue: 0.0884
  time to fit residues: 30.6079
Evaluate side-chains
  225 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 193
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   93 LEU
Chi-restraints excluded: chain E residue  108 VAL
Chi-restraints excluded: chain E residue  281 LEU
Chi-restraints excluded: chain E residue  373 VAL
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  249 ASN
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain B residue   23 TYR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  233 THR
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  107 LEU
Chi-restraints excluded: chain C residue  125 ILE
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  324 VAL
Chi-restraints excluded: chain D residue   45 CYS
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  201 GLU
Chi-restraints excluded: chain D residue  244 MET
Chi-restraints excluded: chain D residue  310 VAL
Chi-restraints excluded: chain D residue  355 ARG
Chi-restraints excluded: chain D residue  368 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 94 optimal weight:    0.5980
   chunk 43 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 121 optimal weight:    2.9990
   chunk 139 optimal weight:    0.0980
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0170
   chunk 7 optimal weight:   20.0000
   chunk 4 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 148 optimal weight:    0.0470
   overall best weight:    0.2716

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

Flipped N/Q/H residues before XYZ refinement:
** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.134165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.116000 restraints weight = 25240.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.118837 restraints weight = 13693.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.120910 restraints weight = 8906.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.122185 restraints weight = 6569.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.123154 restraints weight = 5353.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.2738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.276  13262  Z= 0.185
  Angle     :  0.914  59.174  18109  Z= 0.517
  Chirality :  0.049   0.887   2146
  Planarity :  0.005   0.070   2322
  Dihedral  :  7.098  87.367   1942
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.24 %
    Favored  : 89.76 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 24.74 %
    Favored  : 72.84 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.15 (0.20), residues: 1699
  helix: -1.03 (0.20), residues: 706
  sheet: -2.56 (0.40), residues: 133
  loop : -3.01 (0.20), residues: 860

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  80 
 TYR   0.013   0.001   TYR A 139 
 PHE   0.017   0.001   PHE A 279 
 TRP   0.027   0.001   TRP A  79 
 HIS   0.002   0.001   HIS C 290 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 (13259)
  covalent geometry    : angle       0.91402 (18106)
  hydrogen bonds       : bond        0.02798 (  404)
  hydrogen bonds       : angle       4.79584 ( 1146)
  glycosidic custom    : bond        0.00883 (    1)
  glycosidic custom    : angle       2.42254 (    3)
  Misc. bond           : bond        0.00074 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1999.69 seconds
wall clock time: 35 minutes 16.87 seconds (2116.87 seconds total)