Starting phenix.real_space_refine
on Wed Aug  5 09:10:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9tby_55775/08_2026/9tby_55775.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9tby_55775/08_2026/9tby_55775.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9tby_55775/08_2026/9tby_55775.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9tby_55775/08_2026/9tby_55775.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9tby_55775/08_2026/9tby_55775.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9tby_55775/08_2026/9tby_55775.cif"
  }
  resolution = 3.71
  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=   0.004 sd=   0.061
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      29      5.16       5
     C    5709      2.51       5
     N    1568      2.21       5
     O    1603      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 71 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8909
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 4425
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4425
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 18, 'TRANS': 553}
    Chain: "D"
      Number of atoms: 4484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 577, 4484
          Classifications: {'peptide': 577}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 27, 'TRANS': 549}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
  Time building chain proxies: 1.42, per 1000 atoms: 0.16
  Number of scatterers: 8909
  At special positions: 0
  Unit cell: (83.6, 99, 145.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      29     16.00
     O    1603      8.00
     N    1568      7.00
     C    5709      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=0, symmetry=0
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 457.0 milliseconds
  

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2124

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 5 sheets defined
      56.0% alpha, 2.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'C' and resid 4 through 9
    Processing helix  chain 'C' and resid 10 through 15
      removed outlier: 3.920A  pdb=" N   HIS C  14 " --> pdb=" O   TYR C  11 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   LYS C  15 " --> pdb=" O   LYS C  12 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 19 through 24
      removed outlier: 4.218A  pdb=" N   VAL C  23 " --> pdb=" O   SER C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 49
      removed outlier: 3.517A  pdb=" N   ALA C  31 " --> pdb=" O   VAL C  27 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU C  36 " --> pdb=" O   SER C  32 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   SER C  39 " --> pdb=" O   LEU C  35 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LEU C  43 " --> pdb=" O   SER C  39 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER C  44 " --> pdb=" O   GLY C  40 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   VAL C  48 " --> pdb=" O   SER C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 92
      removed outlier: 3.677A  pdb=" N   ARG C  67 " --> pdb=" O   ALA C  63 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   THR C  74 " --> pdb=" O   ALA C  70 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLY C  76 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ARG C  77 " --> pdb=" O   ARG C  73 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   TYR C  78 " --> pdb=" O   THR C  74 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   PHE C  79 " --> pdb=" O   ALA C  75 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ARG C  81 " --> pdb=" O   ARG C  77 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LEU C  82 " --> pdb=" O   TYR C  78 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   SER C  84 " --> pdb=" O   GLU C  80 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   HIS C  85 " --> pdb=" O   ARG C  81 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ASP C  86 " --> pdb=" O   LEU C  82 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA C  87 " --> pdb=" O   VAL C  83 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   THR C  88 " --> pdb=" O   SER C  84 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   PHE C  89 " --> pdb=" O   HIS C  85 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ARG C  90 " --> pdb=" O   ASP C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 103
      removed outlier: 3.816A  pdb=" N   ILE C  97 " --> pdb=" O   GLN C  93 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   THR C  99 " --> pdb=" O   LEU C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 130
      removed outlier: 4.005A  pdb=" N   LEU C 120 " --> pdb=" O   GLN C 116 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   ASN C 121 " --> pdb=" O   GLY C 117 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   VAL C 124 " --> pdb=" O   LEU C 120 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ALA C 125 " --> pdb=" O   ASN C 121 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ASP C 128 " --> pdb=" O   VAL C 124 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   THR C 129 " --> pdb=" O   ALA C 125 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 137
    Processing helix  chain 'C' and resid 138 through 155
      removed outlier: 3.626A  pdb=" N   ALA C 144 " --> pdb=" O   PRO C 140 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   PHE C 145 " --> pdb=" O   LEU C 141 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   VAL C 146 " --> pdb=" O   VAL C 142 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   VAL C 147 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   ILE C 148 " --> pdb=" O   ALA C 144 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   MET C 149 " --> pdb=" O   PHE C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 156 through 158
      No H-bonds generated for 'chain 'C' and resid 156 through 158'
    Processing helix  chain 'C' and resid 164 through 175
      removed outlier: 3.706A  pdb=" N   MET C 170 " --> pdb=" O   LEU C 166 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   THR C 173 " --> pdb=" O   ILE C 169 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 208
      removed outlier: 4.122A  pdb=" N   ARG C 183 " --> pdb=" O   PRO C 179 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   ALA C 184 " --> pdb=" O   LEU C 180 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLY C 185 " --> pdb=" O   PHE C 181 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LYS C 186 " --> pdb=" O   TYR C 182 " (cutoff:3.500A)
      removed outlier: 5.283A  pdb=" N   SER C 187 " --> pdb=" O   ARG C 183 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   THR C 188 " --> pdb=" O   ALA C 184 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   GLN C 190 " --> pdb=" O   LYS C 186 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   ASN C 191 " --> pdb=" O   SER C 187 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ARG C 196 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   GLY C 197 " --> pdb=" O   THR C 193 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   GLN C 198 " --> pdb=" O   HIS C 194 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   TYR C 199 " --> pdb=" O   LEU C 195 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   TRP C 206 " --> pdb=" O   GLN C 202 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 214
    Processing helix  chain 'C' and resid 222 through 227
      removed outlier: 3.921A  pdb=" N   LEU C 226 " --> pdb=" O   TYR C 222 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLU C 227 " --> pdb=" O   ARG C 223 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 222 through 227'
    Processing helix  chain 'C' and resid 227 through 242
      removed outlier: 3.717A  pdb=" N   ILE C 231 " --> pdb=" O   GLU C 227 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   GLN C 232 " --> pdb=" O   ASN C 228 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   TRP C 233 " --> pdb=" O   THR C 229 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ARG C 238 " --> pdb=" O   LEU C 234 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ARG C 239 " --> pdb=" O   GLU C 235 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLN C 240 " --> pdb=" O   ALA C 236 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   SER C 241 " --> pdb=" O   GLN C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 242 through 266
      removed outlier: 3.684A  pdb=" N   LEU C 246 " --> pdb=" O   GLU C 242 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLN C 248 " --> pdb=" O   THR C 244 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA C 249 " --> pdb=" O   ALA C 245 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   MET C 251 " --> pdb=" O   SER C 247 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   LEU C 252 " --> pdb=" O   GLN C 248 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LEU C 253 " --> pdb=" O   ALA C 249 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ILE C 254 " --> pdb=" O   ILE C 250 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   GLY C 255 " --> pdb=" O   MET C 251 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   MET C 262 " --> pdb=" O   ALA C 258 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LEU C 263 " --> pdb=" O   VAL C 259 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   TRP C 264 " --> pdb=" O   ILE C 260 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 290
      removed outlier: 4.085A  pdb=" N   LEU C 282 " --> pdb=" O   ALA C 278 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   PHE C 283 " --> pdb=" O   LEU C 279 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   VAL C 284 " --> pdb=" O   ILE C 280 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 298
      removed outlier: 3.649A  pdb=" N   THR C 298 " --> pdb=" O   ALA C 295 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 318
      removed outlier: 3.729A  pdb=" N   ARG C 313 " --> pdb=" O   ALA C 309 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 382 through 387
    Processing helix  chain 'C' and resid 408 through 413
      removed outlier: 3.713A  pdb=" N   LEU C 412 " --> pdb=" O   ASN C 408 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 434
      removed outlier: 3.845A  pdb=" N   LEU C 434 " --> pdb=" O   LEU C 430 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 444 through 454
      removed outlier: 3.858A  pdb=" N   LEU C 450 " --> pdb=" O   LEU C 446 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL C 453 " --> pdb=" O   ILE C 449 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLY C 454 " --> pdb=" O   LEU C 450 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 476 through 492
    Processing helix  chain 'C' and resid 506 through 521
    Processing helix  chain 'C' and resid 555 through 562
    Processing helix  chain 'C' and resid 565 through 571
      removed outlier: 4.369A  pdb=" N   GLN C 571 " --> pdb=" O   TYR C 567 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 8 through 17
    Processing helix  chain 'D' and resid 28 through 53
      removed outlier: 3.961A  pdb=" N   PHE D  32 " --> pdb=" O   ARG D  28 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ALA D  42 " --> pdb=" O   ILE D  38 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   TRP D  43 " --> pdb=" O   ILE D  39 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   PHE D  44 " --> pdb=" O   ALA D  40 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   MET D  45 " --> pdb=" O   GLN D  41 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA D  46 " --> pdb=" O   ALA D  42 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU D  49 " --> pdb=" O   MET D  45 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 62
      removed outlier: 3.553A  pdb=" N   ALA D  61 " --> pdb=" O   PRO D  58 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   LEU D  62 " --> pdb=" O   ARG D  59 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 58 through 62'
    Processing helix  chain 'D' and resid 63 through 77
      removed outlier: 3.544A  pdb=" N   LEU D  68 " --> pdb=" O   LEU D  64 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   LEU D  69 " --> pdb=" O   PRO D  65 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   VAL D  70 " --> pdb=" O   PHE D  66 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU D  75 " --> pdb=" O   LEU D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 85
      removed outlier: 3.837A  pdb=" N   ARG D  85 " --> pdb=" O   TRP D  81 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 88 through 109
      removed outlier: 4.767A  pdb=" N   ILE D  94 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ARG D  95 " --> pdb=" O   GLY D  91 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   PHE D  96 " --> pdb=" O   GLN D  92 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ALA D  97 " --> pdb=" O   HIS D  93 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ASP D 104 " --> pdb=" O   ARG D 100 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLN D 107 " --> pdb=" O   LEU D 103 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ALA D 109 " --> pdb=" O   ARG D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 126
      removed outlier: 4.421A  pdb=" N   THR D 124 " --> pdb=" O   GLY D 120 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   LEU D 125 " --> pdb=" O   SER D 121 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   VAL D 126 " --> pdb=" O   TRP D 122 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 132 through 140
      removed outlier: 4.180A  pdb=" N   TYR D 136 " --> pdb=" O   ASP D 132 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   TYR D 140 " --> pdb=" O   TYR D 136 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 147
      removed outlier: 3.657A  pdb=" N   ALA D 147 " --> pdb=" O   GLN D 143 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 150 through 158
      removed outlier: 4.514A  pdb=" N   VAL D 156 " --> pdb=" O   LEU D 152 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ALA D 157 " --> pdb=" O   LEU D 153 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ILE D 158 " --> pdb=" O   ILE D 154 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 162
    Processing helix  chain 'D' and resid 164 through 172
      removed outlier: 3.890A  pdb=" N   LEU D 169 " --> pdb=" O   ALA D 165 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   THR D 172 " --> pdb=" O   ILE D 168 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 175 through 184
      removed outlier: 3.664A  pdb=" N   ALA D 181 " --> pdb=" O   PRO D 177 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   VAL D 183 " --> pdb=" O   PHE D 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 185 through 190
      removed outlier: 3.525A  pdb=" N   ALA D 190 " --> pdb=" O   GLY D 186 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 191 through 195
      removed outlier: 3.571A  pdb=" N   PHE D 195 " --> pdb=" O   ARG D 192 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 203 through 210
    Processing helix  chain 'D' and resid 211 through 218
      removed outlier: 3.987A  pdb=" N   LEU D 215 " --> pdb=" O   GLY D 211 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   PHE D 218 " --> pdb=" O   THR D 214 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 238
      removed outlier: 4.021A  pdb=" N   GLU D 226 " --> pdb=" O   GLU D 222 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ALA D 231 " --> pdb=" O   SER D 227 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER D 232 " --> pdb=" O   ILE D 228 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLU D 233 " --> pdb=" O   ARG D 229 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   ASP D 234 " --> pdb=" O   SER D 230 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLN D 237 " --> pdb=" O   GLU D 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 239 through 244
    Processing helix  chain 'D' and resid 247 through 271
      removed outlier: 4.163A  pdb=" N   LEU D 253 " --> pdb=" O   SER D 249 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLU D 254 " --> pdb=" O   SER D 250 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   SER D 260 " --> pdb=" O   PHE D 256 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   ILE D 261 " --> pdb=" O   THR D 257 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA D 262 " --> pdb=" O   SER D 258 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 297
      removed outlier: 4.081A  pdb=" N   ALA D 293 " --> pdb=" O   ALA D 289 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 301 through 304
    Processing helix  chain 'D' and resid 305 through 310
      removed outlier: 3.696A  pdb=" N   THR D 309 " --> pdb=" O   ARG D 305 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 310 through 316
      removed outlier: 4.138A  pdb=" N   LYS D 314 " --> pdb=" O   PHE D 310 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 320 through 330
      removed outlier: 4.391A  pdb=" N   LEU D 324 " --> pdb=" O   ALA D 320 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   THR D 326 " --> pdb=" O   ASP D 322 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 390 through 398
    Processing helix  chain 'D' and resid 454 through 462
      removed outlier: 4.323A  pdb=" N   ASP D 460 " --> pdb=" O   GLN D 456 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 487 through 499
      removed outlier: 4.341A  pdb=" N   ARG D 493 " --> pdb=" O   GLY D 489 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL D 496 " --> pdb=" O   GLN D 492 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ALA D 497 " --> pdb=" O   ARG D 493 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ARG D 498 " --> pdb=" O   VAL D 494 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 517 through 531
      removed outlier: 4.494A  pdb=" N   ARG D 523 " --> pdb=" O   HIS D 519 " (cutoff:3.500A)
      removed outlier: 5.172A  pdb=" N   VAL D 524 " --> pdb=" O   SER D 520 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   MET D 525 " --> pdb=" O   GLU D 521 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA D 530 " --> pdb=" O   GLU D 526 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 370 through 373
      removed outlier: 6.282A  pdb=" N   ALA C 370 " --> pdb=" O   ILE C 543 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   MET C 545 " --> pdb=" O   ALA C 370 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   LEU C 372 " --> pdb=" O   MET C 545 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'D' and resid 372 through 373
      removed outlier: 3.716A  pdb=" N   ILE D 350 " --> pdb=" O   LEU D 373 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ARG D 407 " --> pdb=" O   GLU D 351 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ILE D 411 " --> pdb=" O   ILE D 408 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 364 through 365
      removed outlier: 3.729A  pdb=" N   LEU D 365 " --> pdb=" O   ILE D 357 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   PHE D 356 " --> pdb=" O   GLN D 403 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   THR D 358 " --> pdb=" O   SER D 401 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   SER D 401 " --> pdb=" O   THR D 358 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 425 through 426
      removed outlier: 3.666A  pdb=" N   SER D 426 " --> pdb=" O   LEU D 506 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'D' and resid 554 through 556
      removed outlier: 3.501A  pdb=" N   VAL D 555 " --> pdb=" O   ILE D 562 " (cutoff:3.500A)

    285 hydrogen bonds defined for protein.
    840 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: 1.33

  Time building geometry restraints manager: 0.75 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: 2971
        1.34 -     1.46: 1888
        1.46 -     1.58: 4170
        1.58 -     1.69: 0
        1.69 -     1.81: 55
  Bond restraints: 9084
  Sorted by residual:
  bond pdb=" C   GLN D 302 "
       pdb=" N   PRO D 303 "
    ideal  model  delta    sigma   weight residual
    1.337  1.356 -0.020 1.11e-02 8.12e+03 3.16e+00
  bond pdb=" N   PRO D 448 "
       pdb=" CA  PRO D 448 "
    ideal  model  delta    sigma   weight residual
    1.469  1.481 -0.012 7.40e-03 1.83e+04 2.56e+00
  bond pdb=" N   ILE D 562 "
       pdb=" CA  ILE D 562 "
    ideal  model  delta    sigma   weight residual
    1.459  1.473 -0.014 1.25e-02 6.40e+03 1.17e+00
  bond pdb=" C   SER C 107 "
       pdb=" N   PRO C 108 "
    ideal  model  delta    sigma   weight residual
    1.334  1.358 -0.024 2.34e-02 1.83e+03 1.09e+00
  bond pdb=" C   LEU D 468 "
       pdb=" N   PRO D 469 "
    ideal  model  delta    sigma   weight residual
    1.334  1.357 -0.023 2.34e-02 1.83e+03 9.46e-01
  ... (remaining 9079 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 12013
        1.58 -     3.16: 259
        3.16 -     4.74: 48
        4.74 -     6.32: 18
        6.32 -     7.90: 3
  Bond angle restraints: 12341
  Sorted by residual:
  angle pdb=" N   VAL D 148 "
        pdb=" CA  VAL D 148 "
        pdb=" C   VAL D 148 "
      ideal   model   delta    sigma   weight residual
     113.10  106.95    6.15 9.70e-01 1.06e+00 4.02e+01
  angle pdb=" N   ILE D  26 "
        pdb=" CA  ILE D  26 "
        pdb=" C   ILE D  26 "
      ideal   model   delta    sigma   weight residual
     113.53  107.90    5.63 9.80e-01 1.04e+00 3.30e+01
  angle pdb=" N   ILE D 130 "
        pdb=" CA  ILE D 130 "
        pdb=" C   ILE D 130 "
      ideal   model   delta    sigma   weight residual
     113.47  108.63    4.84 1.01e+00 9.80e-01 2.30e+01
  angle pdb=" N   VAL C 137 "
        pdb=" CA  VAL C 137 "
        pdb=" C   VAL C 137 "
      ideal   model   delta    sigma   weight residual
     113.71  110.27    3.44 9.50e-01 1.11e+00 1.31e+01
  angle pdb=" N   ARG C 565 "
        pdb=" CA  ARG C 565 "
        pdb=" C   ARG C 565 "
      ideal   model   delta    sigma   weight residual
     114.56  109.98    4.58 1.27e+00 6.20e-01 1.30e+01
  ... (remaining 12336 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 4908
       17.87 -    35.74: 409
       35.74 -    53.61: 81
       53.61 -    71.47: 18
       71.47 -    89.34: 8
  Dihedral angle restraints: 5424
    sinusoidal: 2129
      harmonic: 3295
  Sorted by residual:
  dihedral pdb=" CA  ASN C 547 "
           pdb=" C   ASN C 547 "
           pdb=" N   GLY C 548 "
           pdb=" CA  GLY C 548 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.46  -18.54     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CB  GLU D 241 "
           pdb=" CG  GLU D 241 "
           pdb=" CD  GLU D 241 "
           pdb=" OE1 GLU D 241 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.30   89.30     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CB  GLU D 275 "
           pdb=" CG  GLU D 275 "
           pdb=" CD  GLU D 275 "
           pdb=" OE1 GLU D 275 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.04   89.04     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 5421 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 846
       0.030 -    0.060: 436
       0.060 -    0.091: 108
       0.091 -    0.121: 41
       0.121 -    0.151: 5
  Chirality restraints: 1436
  Sorted by residual:
  chirality pdb=" CA  VAL D 464 "
            pdb=" N   VAL D 464 "
            pdb=" C   VAL D 464 "
            pdb=" CB  VAL D 464 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.72e-01
  chirality pdb=" CA  VAL D 148 "
            pdb=" N   VAL D 148 "
            pdb=" C   VAL D 148 "
            pdb=" CB  VAL D 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.70e-01
  chirality pdb=" CA  ILE C 542 "
            pdb=" N   ILE C 542 "
            pdb=" C   ILE C 542 "
            pdb=" CB  ILE C 542 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.16e-01
  ... (remaining 1433 not shown)

  Planarity restraints: 1582
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 346 "    0.030 5.00e-02 4.00e+02   4.55e-02 3.32e+00
        pdb=" N   PRO D 347 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO D 347 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 347 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 468 "    0.027 5.00e-02 4.00e+02   4.14e-02 2.75e+00
        pdb=" N   PRO D 469 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO D 469 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO D 469 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET C 177 "   -0.025 5.00e-02 4.00e+02   3.72e-02 2.22e+00
        pdb=" N   PRO C 178 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO C 178 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C 178 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1579 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2829
        2.83 -     3.35: 8113
        3.35 -     3.86: 12997
        3.86 -     4.38: 14794
        4.38 -     4.90: 25322
  Nonbonded interactions: 64055
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN C 362 "
            pdb=" OD1 ASN C 364 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" O   SER D 417 "
            pdb=" OG  SER D 417 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" OG  SER D 426 "
            pdb=" O   ALA D 499 "
     model   vdw
     2.331 3.040
  nonbonded pdb=" O   PRO C 403 "
            pdb=" OG  SER C 406 "
     model   vdw
     2.340 3.040
  nonbonded pdb=" O   SER D 387 "
            pdb=" OG  SER D 387 "
     model   vdw
     2.345 3.040
  ... (remaining 64050 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.470
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.820
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
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      :  0.002   0.036   9084  Z= 0.128
  Angle     :  0.630   7.902  12341  Z= 0.377
  Chirality :  0.039   0.151   1436
  Planarity :  0.003   0.046   1582
  Dihedral  : 14.126  89.343   3300
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  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: -5.36 (0.19), residues: 1145
  helix: -3.16 (0.16), residues: 610
  sheet: -3.37 (0.86), residues: 27
  loop : -4.06 (0.21), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 342 
 TYR   0.009   0.001   TYR C   7 
 PHE   0.005   0.000   PHE C 301 
 TRP   0.008   0.000   TRP C 390 
 HIS   0.002   0.000   HIS D 424 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00213 /  0.13 ( 9084)
  covalent geometry    : angle       0.63031 /  0.38 (12341)
  hydrogen bonds       : bond        0.19420 / 12.85 (  285)
  hydrogen bonds       : angle       6.06999 /  4.13 (  840)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  121 ASN cc_start: 0.8802 (t0) cc_final: 0.8593 (t0)
REVERT: C  467 TRP cc_start: 0.8571 (t-100) cc_final: 0.8134 (t-100)
REVERT: C  539 PHE cc_start: 0.6845 (t80) cc_final: 0.6409 (t80)
REVERT: C  545 MET cc_start: 0.7679 (mtt) cc_final: 0.7173 (mtm)
REVERT: C  563 GLN cc_start: 0.7635 (tp40) cc_final: 0.7046 (tp40)
REVERT: D  302 GLN cc_start: 0.8669 (tp40) cc_final: 0.8372 (tp40)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.1231
  time to fit residues: 31.0919
Evaluate side-chains
  102 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    0.3980
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    5.9990
   overall best weight:    2.2186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 121 ASN
C 190 GLN
C 368 HIS
** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  16 GLN
D 107 GLN
D 143 GLN
D 191 ASN
D 394 ASN
D 424 HIS
D 433 GLN
D 453 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.124192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.090110 restraints weight = 19233.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.092844 restraints weight = 10147.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.094629 restraints weight = 6789.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.095813 restraints weight = 5272.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.096590 restraints weight = 4497.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9084  Z= 0.214
  Angle     :  0.741  11.808  12341  Z= 0.360
  Chirality :  0.045   0.160   1436
  Planarity :  0.005   0.061   1582
  Dihedral  :  4.362  18.840   1252
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.91 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 17.80 %
    Favored  : 80.47 %
  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: -4.12 (0.22), residues: 1145
  helix: -2.08 (0.20), residues: 605
  sheet: -3.33 (0.82), residues: 35
  loop : -3.53 (0.24), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D 566 
 TYR   0.013   0.001   TYR C 182 
 PHE   0.024   0.002   PHE D 235 
 TRP   0.020   0.002   TRP D 427 
 HIS   0.005   0.001   HIS C 303 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00507 /  0.21 ( 9084)
  covalent geometry    : angle       0.74110 /  0.36 (12341)
  hydrogen bonds       : bond        0.04386 /  2.94 (  285)
  hydrogen bonds       : angle       4.31569 /  3.04 (  840)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  121 ASN cc_start: 0.9014 (t0) cc_final: 0.8752 (t0)
REVERT: C  227 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8171 (tm-30)
REVERT: C  539 PHE cc_start: 0.7168 (t80) cc_final: 0.6752 (t80)
REVERT: C  545 MET cc_start: 0.7720 (mtt) cc_final: 0.7390 (mtt)
REVERT: C  563 GLN cc_start: 0.7467 (tp40) cc_final: 0.6949 (tp40)
REVERT: D  162 ASN cc_start: 0.8842 (p0) cc_final: 0.8592 (p0)
REVERT: D  180 MET cc_start: 0.7629 (mtp) cc_final: 0.7345 (mtm)
REVERT: D  278 PHE cc_start: 0.8148 (p90) cc_final: 0.7807 (p90)
REVERT: D  535 GLN cc_start: 0.6834 (mm-40) cc_final: 0.6489 (mm-40)
REVERT: D  547 LEU cc_start: 0.8554 (tp) cc_final: 0.8325 (tp)
  outliers start: 16
  outliers final: 11
  residues processed: 115
  average time/residue: 0.1120
  time to fit residues: 17.3045
Evaluate side-chains
  102 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 TYR
Chi-restraints excluded: chain C residue  226 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   66 PHE
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  209 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 35 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0040
   chunk 29 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    1.1196

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 563 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 = 0.3891 r_free = 0.3891 target = 0.125741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.091164 restraints weight = 18839.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.093887 restraints weight = 9916.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.095779 restraints weight = 6685.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.096952 restraints weight = 5170.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.097685 restraints weight = 4438.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9084  Z= 0.125
  Angle     :  0.609   8.952  12341  Z= 0.296
  Chirality :  0.041   0.143   1436
  Planarity :  0.004   0.047   1582
  Dihedral  :  4.055  19.575   1252
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 19.96 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.52 (0.23), residues: 1145
  helix: -1.38 (0.21), residues: 587
  sheet: -3.88 (0.75), residues: 33
  loop : -3.41 (0.23), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 192 
 TYR   0.008   0.001   TYR C 114 
 PHE   0.015   0.001   PHE C 346 
 TRP   0.012   0.001   TRP D 427 
 HIS   0.003   0.001   HIS C 303 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.12 ( 9084)
  covalent geometry    : angle       0.60869 /  0.30 (12341)
  hydrogen bonds       : bond        0.03215 /  2.16 (  285)
  hydrogen bonds       : angle       3.96528 /  2.77 (  840)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  114 TYR cc_start: 0.6972 (OUTLIER) cc_final: 0.5597 (m-80)
REVERT: C  227 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8213 (tm-30)
REVERT: C  539 PHE cc_start: 0.7239 (t80) cc_final: 0.6864 (t80)
REVERT: C  545 MET cc_start: 0.7755 (mtt) cc_final: 0.7099 (mtm)
REVERT: C  563 GLN cc_start: 0.7520 (tp40) cc_final: 0.6990 (tp40)
REVERT: D  162 ASN cc_start: 0.8692 (p0) cc_final: 0.8440 (p0)
REVERT: D  278 PHE cc_start: 0.8274 (p90) cc_final: 0.7909 (p90)
REVERT: D  302 GLN cc_start: 0.8936 (tp40) cc_final: 0.8609 (tp40)
REVERT: D  304 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8549 (tt)
REVERT: D  535 GLN cc_start: 0.6733 (mm-40) cc_final: 0.6533 (mm-40)
  outliers start: 23
  outliers final: 14
  residues processed: 112
  average time/residue: 0.1026
  time to fit residues: 15.9151
Evaluate side-chains
  104 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 TYR
Chi-restraints excluded: chain C residue  114 TYR
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  544 VAL
Chi-restraints excluded: chain C residue  555 THR
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   66 PHE
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  328 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 33 optimal weight:   20.0000
   chunk 63 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 105 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 99 optimal weight:    0.1980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 121 ASN
C 303 HIS
** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 191 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.127089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.093310 restraints weight = 19150.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.096087 restraints weight = 9818.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.097935 restraints weight = 6472.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.099126 restraints weight = 4979.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.099871 restraints weight = 4235.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.3302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9084  Z= 0.104
  Angle     :  0.586   8.245  12341  Z= 0.282
  Chirality :  0.040   0.147   1436
  Planarity :  0.004   0.049   1582
  Dihedral  :  3.895  19.569   1252
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.34 %
    Favored  : 90.66 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 21.79 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.12 (0.24), residues: 1145
  helix: -1.05 (0.22), residues: 601
  sheet: -3.71 (0.75), residues: 33
  loop : -3.26 (0.25), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 192 
 TYR   0.008   0.001   TYR C 114 
 PHE   0.013   0.001   PHE C 346 
 TRP   0.023   0.001   TRP D  23 
 HIS   0.007   0.001   HIS D  89 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.10 ( 9084)
  covalent geometry    : angle       0.58598 /  0.28 (12341)
  hydrogen bonds       : bond        0.02734 /  1.84 (  285)
  hydrogen bonds       : angle       3.75449 /  2.61 (  840)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 90
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  114 TYR cc_start: 0.6662 (OUTLIER) cc_final: 0.6046 (m-80)
REVERT: C  134 TYR cc_start: 0.8514 (t80) cc_final: 0.8155 (t80)
REVERT: C  227 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8247 (tm-30)
REVERT: C  450 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8355 (tt)
REVERT: C  539 PHE cc_start: 0.7227 (t80) cc_final: 0.6895 (t80)
REVERT: C  545 MET cc_start: 0.7817 (mtt) cc_final: 0.7097 (mtm)
REVERT: D    6 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7458 (pp30)
REVERT: D  153 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9036 (tt)
REVERT: D  162 ASN cc_start: 0.8665 (p0) cc_final: 0.8429 (p0)
REVERT: D  278 PHE cc_start: 0.8276 (p90) cc_final: 0.7908 (p90)
REVERT: D  302 GLN cc_start: 0.8928 (tp40) cc_final: 0.8637 (tp40)
REVERT: D  304 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8521 (tt)
  outliers start: 29
  outliers final: 18
  residues processed: 109
  average time/residue: 0.0989
  time to fit residues: 15.0348
Evaluate side-chains
  105 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 TYR
Chi-restraints excluded: chain C residue   11 TYR
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue  114 TYR
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  544 VAL
Chi-restraints excluded: chain C residue  555 THR
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  153 LEU
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  196 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  328 MET
Chi-restraints excluded: chain D residue  359 SER
Chi-restraints excluded: chain D residue  413 LEU
Chi-restraints excluded: chain D residue  424 HIS
Chi-restraints excluded: chain D residue  524 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 91 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0470
   chunk 102 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    1.4084

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 121 ASN
** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.124696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.089804 restraints weight = 19111.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.092566 restraints weight = 10064.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.094397 restraints weight = 6718.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.095500 restraints weight = 5230.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.096214 restraints weight = 4506.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9084  Z= 0.143
  Angle     :  0.611   8.246  12341  Z= 0.297
  Chirality :  0.042   0.145   1436
  Planarity :  0.004   0.048   1582
  Dihedral  :  4.045  19.651   1252
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.69 %
    Favored  : 90.31 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 21.79 %
    Favored  : 74.11 %
  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: -2.87 (0.25), residues: 1145
  helix: -0.82 (0.22), residues: 601
  sheet: -3.02 (0.67), residues: 55
  loop : -3.21 (0.26), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 115 
 TYR   0.007   0.001   TYR C 114 
 PHE   0.010   0.001   PHE C 346 
 TRP   0.042   0.002   TRP D  23 
 HIS   0.007   0.001   HIS D  89 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.14 ( 9084)
  covalent geometry    : angle       0.61107 /  0.30 (12341)
  hydrogen bonds       : bond        0.03445 /  2.31 (  285)
  hydrogen bonds       : angle       3.93217 /  2.74 (  840)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 85
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  114 TYR cc_start: 0.6843 (OUTLIER) cc_final: 0.5683 (m-80)
REVERT: C  227 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8443 (tm-30)
REVERT: C  446 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8595 (tt)
REVERT: C  539 PHE cc_start: 0.7279 (t80) cc_final: 0.7007 (t80)
REVERT: C  545 MET cc_start: 0.7745 (mtt) cc_final: 0.7048 (mtm)
REVERT: C  563 GLN cc_start: 0.7475 (tp40) cc_final: 0.7052 (tp40)
REVERT: D  153 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9046 (tt)
REVERT: D  162 ASN cc_start: 0.8718 (p0) cc_final: 0.8491 (p0)
REVERT: D  278 PHE cc_start: 0.8366 (p90) cc_final: 0.7971 (p90)
REVERT: D  304 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8512 (tt)
  outliers start: 38
  outliers final: 24
  residues processed: 114
  average time/residue: 0.0906
  time to fit residues: 14.6926
Evaluate side-chains
  107 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 TYR
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue  114 TYR
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain C residue  226 LEU
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  298 THR
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  526 VAL
Chi-restraints excluded: chain C residue  544 VAL
Chi-restraints excluded: chain C residue  555 THR
Chi-restraints excluded: chain D residue   66 PHE
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  153 LEU
Chi-restraints excluded: chain D residue  175 LEU
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  359 SER
Chi-restraints excluded: chain D residue  393 LEU
Chi-restraints excluded: chain D residue  413 LEU
Chi-restraints excluded: chain D residue  424 HIS
Chi-restraints excluded: chain D residue  439 LEU
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  524 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0020
   chunk 62 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.5588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 393 GLN
** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.127078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.092008 restraints weight = 18958.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.094791 restraints weight = 9928.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.096719 restraints weight = 6662.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.097834 restraints weight = 5154.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.098693 restraints weight = 4441.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9084  Z= 0.096
  Angle     :  0.587  14.071  12341  Z= 0.279
  Chirality :  0.040   0.147   1436
  Planarity :  0.004   0.050   1582
  Dihedral  :  3.845  19.948   1252
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.91 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 23.41 %
    Favored  : 73.46 %
  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: -2.59 (0.25), residues: 1145
  helix: -0.58 (0.23), residues: 602
  sheet: -2.88 (0.68), residues: 55
  loop : -3.08 (0.26), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 115 
 TYR   0.007   0.001   TYR C 114 
 PHE   0.011   0.001   PHE C 160 
 TRP   0.024   0.001   TRP D  23 
 HIS   0.001   0.000   HIS C 303 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00220 /  0.10 ( 9084)
  covalent geometry    : angle       0.58695 /  0.28 (12341)
  hydrogen bonds       : bond        0.02522 /  1.70 (  285)
  hydrogen bonds       : angle       3.69587 /  2.58 (  840)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 84
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  114 TYR cc_start: 0.6687 (OUTLIER) cc_final: 0.5780 (m-80)
REVERT: C  134 TYR cc_start: 0.8523 (t80) cc_final: 0.8172 (t80)
REVERT: C  227 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8422 (tm-30)
REVERT: C  446 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8592 (tt)
REVERT: C  539 PHE cc_start: 0.7292 (t80) cc_final: 0.7048 (t80)
REVERT: C  545 MET cc_start: 0.7824 (mtt) cc_final: 0.7602 (mtp)
REVERT: C  563 GLN cc_start: 0.7546 (tp40) cc_final: 0.7124 (tp40)
REVERT: D    6 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7503 (pp30)
REVERT: D  153 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8955 (tt)
REVERT: D  162 ASN cc_start: 0.8599 (p0) cc_final: 0.8359 (p0)
REVERT: D  278 PHE cc_start: 0.8320 (p90) cc_final: 0.7921 (p90)
REVERT: D  304 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8486 (tt)
REVERT: D  534 ARG cc_start: 0.7727 (mmp80) cc_final: 0.7183 (tpp-160)
  outliers start: 29
  outliers final: 18
  residues processed: 106
  average time/residue: 0.0857
  time to fit residues: 13.2486
Evaluate side-chains
  100 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 77
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 TYR
Chi-restraints excluded: chain C residue   11 TYR
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue  114 TYR
Chi-restraints excluded: chain C residue  119 LEU
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  298 THR
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  526 VAL
Chi-restraints excluded: chain C residue  544 VAL
Chi-restraints excluded: chain C residue  555 THR
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue  114 ILE
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  153 LEU
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  424 HIS
Chi-restraints excluded: chain D residue  524 VAL
Chi-restraints excluded: chain D residue  547 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 93 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0030
   chunk 101 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   overall best weight:    0.7390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 535 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 = 0.3897 r_free = 0.3897 target = 0.126808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.091910 restraints weight = 19241.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.094765 restraints weight = 10081.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.096678 restraints weight = 6711.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.097885 restraints weight = 5193.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.098576 restraints weight = 4445.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.3794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9084  Z= 0.104
  Angle     :  0.587  12.958  12341  Z= 0.280
  Chirality :  0.040   0.143   1436
  Planarity :  0.004   0.054   1582
  Dihedral  :  3.823  19.228   1252
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 22.44 %
    Favored  : 73.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.46 (0.25), residues: 1145
  helix: -0.46 (0.23), residues: 608
  sheet: -2.79 (0.69), residues: 55
  loop : -3.08 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 115 
 TYR   0.007   0.001   TYR C 114 
 PHE   0.009   0.001   PHE C 346 
 TRP   0.048   0.001   TRP D  23 
 HIS   0.002   0.000   HIS D 424 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.10 ( 9084)
  covalent geometry    : angle       0.58731 /  0.28 (12341)
  hydrogen bonds       : bond        0.02641 /  1.78 (  285)
  hydrogen bonds       : angle       3.66893 /  2.56 (  840)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 80
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: C  114 TYR cc_start: 0.6710 (OUTLIER) cc_final: 0.5685 (m-80)
REVERT: C  227 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8459 (tm-30)
REVERT: C  446 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8578 (tt)
REVERT: C  563 GLN cc_start: 0.7661 (tp40) cc_final: 0.7176 (tp40)
REVERT: D    6 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7351 (pp30)
REVERT: D  153 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9038 (tt)
REVERT: D  162 ASN cc_start: 0.8607 (p0) cc_final: 0.8379 (p0)
REVERT: D  278 PHE cc_start: 0.8313 (p90) cc_final: 0.7936 (p90)
REVERT: D  304 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8512 (tt)
REVERT: D  459 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7234 (mt)
REVERT: D  534 ARG cc_start: 0.7703 (mmp80) cc_final: 0.7314 (tpp-160)
  outliers start: 36
  outliers final: 22
  residues processed: 106
  average time/residue: 0.0854
  time to fit residues: 13.2809
Evaluate side-chains
  105 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 77
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 TYR
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue  114 TYR
Chi-restraints excluded: chain C residue  119 LEU
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  298 THR
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  526 VAL
Chi-restraints excluded: chain C residue  544 VAL
Chi-restraints excluded: chain C residue  555 THR
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  153 LEU
Chi-restraints excluded: chain D residue  179 PHE
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  196 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  359 SER
Chi-restraints excluded: chain D residue  459 LEU
Chi-restraints excluded: chain D residue  464 VAL
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  524 VAL
Chi-restraints excluded: chain D residue  537 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 30 optimal weight:    0.2980
   chunk 66 optimal weight:    3.9990
   chunk 80 optimal weight:    0.0470
   chunk 32 optimal weight:    0.0970
   chunk 34 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   overall best weight:    1.2880

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 312 HIS
** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.125162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.091116 restraints weight = 19162.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.093815 restraints weight = 10106.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.095613 restraints weight = 6774.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.096788 restraints weight = 5259.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.097477 restraints weight = 4486.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.3998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9084  Z= 0.136
  Angle     :  0.636  12.789  12341  Z= 0.301
  Chirality :  0.041   0.142   1436
  Planarity :  0.004   0.054   1582
  Dihedral  :  3.949  19.521   1252
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.78 %
    Favored  : 90.22 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 23.30 %
    Favored  : 72.92 %
  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: -2.36 (0.26), residues: 1145
  helix: -0.38 (0.23), residues: 609
  sheet: -2.79 (0.69), residues: 55
  loop : -3.03 (0.27), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  99 
 TYR   0.007   0.001   TYR C 114 
 PHE   0.033   0.001   PHE C 539 
 TRP   0.043   0.001   TRP D  23 
 HIS   0.002   0.001   HIS D 424 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.14 ( 9084)
  covalent geometry    : angle       0.63567 /  0.30 (12341)
  hydrogen bonds       : bond        0.03129 /  2.11 (  285)
  hydrogen bonds       : angle       3.86009 /  2.69 (  840)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 81
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
REVERT: C   60 MET cc_start: 0.7714 (mmm) cc_final: 0.7317 (mpp)
REVERT: C  114 TYR cc_start: 0.6660 (OUTLIER) cc_final: 0.5293 (m-80)
REVERT: C  227 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8532 (tm-30)
REVERT: C  446 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8639 (tt)
REVERT: C  450 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8273 (tt)
REVERT: C  563 GLN cc_start: 0.7595 (tp40) cc_final: 0.6988 (tp40)
REVERT: D    6 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7373 (pp30)
REVERT: D  153 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9024 (tt)
REVERT: D  162 ASN cc_start: 0.8682 (p0) cc_final: 0.8472 (p0)
REVERT: D  278 PHE cc_start: 0.8352 (p90) cc_final: 0.7959 (p90)
REVERT: D  304 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8534 (tt)
REVERT: D  534 ARG cc_start: 0.7750 (mmp80) cc_final: 0.7468 (tpp-160)
  outliers start: 35
  outliers final: 26
  residues processed: 106
  average time/residue: 0.0834
  time to fit residues: 13.0360
Evaluate side-chains
  110 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 78
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 TYR
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue  114 TYR
Chi-restraints excluded: chain C residue  119 LEU
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain C residue  226 LEU
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  298 THR
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  526 VAL
Chi-restraints excluded: chain C residue  544 VAL
Chi-restraints excluded: chain C residue  555 THR
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  153 LEU
Chi-restraints excluded: chain D residue  179 PHE
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  196 LEU
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  312 HIS
Chi-restraints excluded: chain D residue  359 SER
Chi-restraints excluded: chain D residue  393 LEU
Chi-restraints excluded: chain D residue  439 LEU
Chi-restraints excluded: chain D residue  464 VAL
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  524 VAL
Chi-restraints excluded: chain D residue  537 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 11 optimal weight:    7.9990
   chunk 77 optimal weight:    1.9990
   chunk 55 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0970
   chunk 98 optimal weight:    4.9990
   chunk 84 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 312 HIS
** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.124925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.091302 restraints weight = 19180.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.093991 restraints weight = 10069.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.095763 restraints weight = 6726.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.096836 restraints weight = 5225.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.097608 restraints weight = 4470.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.4063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9084  Z= 0.132
  Angle     :  0.631  12.485  12341  Z= 0.303
  Chirality :  0.041   0.164   1436
  Planarity :  0.004   0.053   1582
  Dihedral  :  3.990  20.559   1252
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.04 %
    Favored  : 89.96 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 23.09 %
    Favored  : 72.71 %
  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: -2.30 (0.26), residues: 1145
  helix: -0.32 (0.23), residues: 607
  sheet: -2.80 (0.69), residues: 55
  loop : -3.01 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 200 
 TYR   0.012   0.001   TYR D 311 
 PHE   0.029   0.001   PHE C 539 
 TRP   0.038   0.001   TRP D  23 
 HIS   0.002   0.001   HIS D 312 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.13 ( 9084)
  covalent geometry    : angle       0.63136 /  0.30 (12341)
  hydrogen bonds       : bond        0.03082 /  2.07 (  285)
  hydrogen bonds       : angle       3.88602 /  2.70 (  840)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 80
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: C   60 MET cc_start: 0.7707 (mmm) cc_final: 0.7324 (mpp)
REVERT: C  114 TYR cc_start: 0.6679 (OUTLIER) cc_final: 0.5218 (m-80)
REVERT: C  227 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8549 (tm-30)
REVERT: C  446 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8637 (tt)
REVERT: C  563 GLN cc_start: 0.7604 (tp40) cc_final: 0.6982 (tp40)
REVERT: D    6 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7273 (pp30)
REVERT: D  153 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9020 (tt)
REVERT: D  162 ASN cc_start: 0.8679 (p0) cc_final: 0.8470 (p0)
REVERT: D  278 PHE cc_start: 0.8335 (p90) cc_final: 0.7952 (p90)
REVERT: D  304 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8541 (tt)
  outliers start: 39
  outliers final: 27
  residues processed: 108
  average time/residue: 0.0793
  time to fit residues: 12.7270
Evaluate side-chains
  111 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 79
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 TYR
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue  114 TYR
Chi-restraints excluded: chain C residue  119 LEU
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain C residue  226 LEU
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  298 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  526 VAL
Chi-restraints excluded: chain C residue  544 VAL
Chi-restraints excluded: chain C residue  555 THR
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  153 LEU
Chi-restraints excluded: chain D residue  179 PHE
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  196 LEU
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  359 SER
Chi-restraints excluded: chain D residue  393 LEU
Chi-restraints excluded: chain D residue  439 LEU
Chi-restraints excluded: chain D residue  464 VAL
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  524 VAL
Chi-restraints excluded: chain D residue  537 THR
Chi-restraints excluded: chain D residue  547 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 68 optimal weight:    0.2980
   chunk 88 optimal weight:    0.5980
   chunk 22 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0060
   chunk 11 optimal weight:    4.9990
   overall best weight:    0.5800

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 312 HIS
** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.126902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.093166 restraints weight = 19001.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.095888 restraints weight = 9870.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.097739 restraints weight = 6619.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.098951 restraints weight = 5114.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.099743 restraints weight = 4342.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.4060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9084  Z= 0.104
  Angle     :  0.641  12.418  12341  Z= 0.302
  Chirality :  0.040   0.185   1436
  Planarity :  0.004   0.055   1582
  Dihedral  :  3.942  28.559   1252
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.17 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 23.62 %
    Favored  : 72.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.13 (0.26), residues: 1145
  helix: -0.15 (0.23), residues: 603
  sheet: -2.71 (0.70), residues: 55
  loop : -2.94 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 115 
 TYR   0.007   0.001   TYR C 114 
 PHE   0.027   0.001   PHE C 539 
 TRP   0.030   0.001   TRP D  23 
 HIS   0.001   0.000   HIS D 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.10 ( 9084)
  covalent geometry    : angle       0.64106 /  0.30 (12341)
  hydrogen bonds       : bond        0.02596 /  1.75 (  285)
  hydrogen bonds       : angle       3.76304 /  2.59 (  840)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 79
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: C  114 TYR cc_start: 0.6499 (OUTLIER) cc_final: 0.5233 (m-80)
REVERT: C  227 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8540 (tm-30)
REVERT: C  446 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8591 (tt)
REVERT: C  563 GLN cc_start: 0.7584 (tp40) cc_final: 0.6961 (tp40)
REVERT: D  153 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8928 (tt)
REVERT: D  162 ASN cc_start: 0.8591 (p0) cc_final: 0.8368 (p0)
REVERT: D  278 PHE cc_start: 0.8305 (p90) cc_final: 0.7936 (p90)
REVERT: D  304 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8460 (tt)
REVERT: D  459 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7373 (mt)
  outliers start: 33
  outliers final: 24
  residues processed: 103
  average time/residue: 0.0771
  time to fit residues: 11.8028
Evaluate side-chains
  108 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 TYR
Chi-restraints excluded: chain C residue   27 VAL
Chi-restraints excluded: chain C residue  114 TYR
Chi-restraints excluded: chain C residue  119 LEU
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain C residue  226 LEU
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  298 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  458 LEU
Chi-restraints excluded: chain C residue  526 VAL
Chi-restraints excluded: chain C residue  544 VAL
Chi-restraints excluded: chain C residue  555 THR
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  153 LEU
Chi-restraints excluded: chain D residue  179 PHE
Chi-restraints excluded: chain D residue  183 VAL
Chi-restraints excluded: chain D residue  196 LEU
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  359 SER
Chi-restraints excluded: chain D residue  393 LEU
Chi-restraints excluded: chain D residue  424 HIS
Chi-restraints excluded: chain D residue  459 LEU
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  524 VAL
Chi-restraints excluded: chain D residue  537 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 73 optimal weight:    0.0870
   chunk 40 optimal weight:    4.9990
   chunk 77 optimal weight:    0.0870
   chunk 44 optimal weight:    5.9990
   chunk 68 optimal weight:    0.0870
   chunk 84 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9980
   chunk 97 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   overall best weight:    0.3514

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 312 HIS
** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.128163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.094650 restraints weight = 18745.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.097470 restraints weight = 9672.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.099321 restraints weight = 6411.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.100514 restraints weight = 4950.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.101215 restraints weight = 4216.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.4079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9084  Z= 0.100
  Angle     :  0.631  12.242  12341  Z= 0.296
  Chirality :  0.040   0.165   1436
  Planarity :  0.004   0.054   1582
  Dihedral  :  3.817  27.491   1252
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 23.95 %
    Favored  : 73.03 %
  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: -1.98 (0.26), residues: 1145
  helix: -0.03 (0.23), residues: 604
  sheet: -2.47 (0.72), residues: 54
  loop : -2.92 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 115 
 TYR   0.007   0.001   TYR C 114 
 PHE   0.025   0.001   PHE C 539 
 TRP   0.024   0.001   TRP D  23 
 HIS   0.001   0.000   HIS C 303 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00228 /  0.10 ( 9084)
  covalent geometry    : angle       0.63066 /  0.30 (12341)
  hydrogen bonds       : bond        0.02488 /  1.67 (  285)
  hydrogen bonds       : angle       3.65915 /  2.57 (  840)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1565.94 seconds
wall clock time: 27 minutes 37.38 seconds (1657.38 seconds total)