Starting phenix.real_space_refine
on Sun Apr  5 00:39:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9p80_71359/04_2026/9p80_71359.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9p80_71359/04_2026/9p80_71359.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9p80_71359/04_2026/9p80_71359.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9p80_71359/04_2026/9p80_71359.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9p80_71359/04_2026/9p80_71359.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9p80_71359/04_2026/9p80_71359.cif"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.022
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      37      5.16       5
     C    4116      2.51       5
     N    1105      2.21       5
     O    1175      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6433
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2330
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2330
          Classifications: {'peptide': 332}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 63}
          Link IDs: {'PTRANS': 5, 'TRANS': 326}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 223
          Unresolved non-hydrogen angles: 276
          Unresolved non-hydrogen dihedrals: 172
          Unresolved non-hydrogen chiralities: 17
          Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 10, 'GLU:plan': 6, 'ASP:plan': 8, 'ASN:plan1': 5, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 138
    Chain: "C"
      Number of atoms: 311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 311
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 88
          Unresolved non-hydrogen angles: 105
          Unresolved non-hydrogen dihedrals: 71
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 43
    Chain: "R"
      Number of atoms: 2172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2172
          Classifications: {'peptide': 302}
          Incomplete info: {'truncation_to_alanine': 72}
          Link IDs: {'PTRANS': 10, 'TRANS': 291}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 236
          Unresolved non-hydrogen angles: 298
          Unresolved non-hydrogen dihedrals: 192
          Unresolved non-hydrogen chiralities: 28
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 2, 'TYR:plan': 2, 'PHE:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 5, 'HIS:plan': 4}
          Unresolved non-hydrogen planarities: 109
    Chain: "L"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 58
          Classifications: {'peptide': 6}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
    Chain: "A"
      Number of atoms: 1562
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1562
          Classifications: {'peptide': 216}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 54}
          Link IDs: {'PTRANS': 2, 'TRANS': 213}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 182
          Unresolved non-hydrogen angles: 214
          Unresolved non-hydrogen dihedrals: 152
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 4, 'HIS:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 76
  Time building chain proxies: 1.61, per 1000 atoms: 0.25
  Number of scatterers: 6433
  At special positions: 0
  Unit cell: (91.52, 90.688, 116.48, 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      37     16.00
     O    1175      8.00
     N    1105      7.00
     C    4116      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 141 " - pdb=" SG  CYS R 224 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 262.3 milliseconds
  

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1716

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 9 sheets defined
      48.2% alpha, 19.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 11 through 23
    Processing helix  chain 'C' and resid 29 through 43
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'R' and resid 59 through 89
    Processing helix  chain 'R' and resid 98 through 119
      removed outlier: 3.726A  pdb=" N   ALA R 119 " --> pdb=" O   THR R 115 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 119 through 127
    Processing helix  chain 'R' and resid 138 through 172
      removed outlier: 3.962A  pdb=" N   ARG R 142 " --> pdb=" O   ASP R 138 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   TYR R 145 " --> pdb=" O   CYS R 141 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 181 through 201
    Processing helix  chain 'R' and resid 202 through 206
    Processing helix  chain 'R' and resid 218 through 220
      No H-bonds generated for 'chain 'R' and resid 218 through 220'
    Processing helix  chain 'R' and resid 229 through 245
    Processing helix  chain 'R' and resid 245 through 270
      removed outlier: 3.641A  pdb=" N   VAL R 251 " --> pdb=" O   PHE R 247 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ASN R 256 " --> pdb=" O   ILE R 252 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 280 through 329
      removed outlier: 3.801A  pdb=" N   GLN R 296 " --> pdb=" O   PRO R 292 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   VAL R 309 " --> pdb=" O   LEU R 305 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
      removed outlier: 3.903A  pdb=" N   CYS R 327 " --> pdb=" O   ARG R 323 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE R 329 " --> pdb=" O   MET R 325 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 330 through 334
    Processing helix  chain 'R' and resid 335 through 356
      removed outlier: 3.531A  pdb=" N   ASP R 340 " --> pdb=" O   PRO R 336 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   HIS R 343 " --> pdb=" O   TYR R 339 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   MET R 347 " --> pdb=" O   HIS R 343 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   SER R 356 " --> pdb=" O   LEU R 352 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 359 through 368
    Processing helix  chain 'R' and resid 368 through 376
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 3.825A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.543A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.675A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.455A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.120A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.936A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.540A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.882A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.561A  pdb=" N   PHE A 336 " --> pdb=" O   VAL A 332 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52
      removed outlier: 4.323A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.701A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.786A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.944A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.981A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.607A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.004A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.764A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.979A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.803A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.826A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'R' and resid 207 through 211
    Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.266A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.354A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.759A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)

    376 hydrogen bonds defined for protein.
    1089 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: 1.06

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1784
        1.33 -     1.45: 1194
        1.45 -     1.57: 3540
        1.57 -     1.69: 0
        1.69 -     1.81: 50
  Bond restraints: 6568
  Sorted by residual:
  bond pdb=" N   VAL R 367 "
       pdb=" CA  VAL R 367 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.09e-02 8.42e+03 9.89e+00
  bond pdb=" N   ILE L  12 "
       pdb=" CA  ILE L  12 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.034 1.10e-02 8.26e+03 9.39e+00
  bond pdb=" N   LEU B 336 "
       pdb=" CA  LEU B 336 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.19e-02 7.06e+03 8.50e+00
  bond pdb=" N   GLY B 144 "
       pdb=" CA  GLY B 144 "
    ideal  model  delta    sigma   weight residual
    1.450  1.475 -0.026 9.40e-03 1.13e+04 7.47e+00
  bond pdb=" N   PHE B 335 "
       pdb=" CA  PHE B 335 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.034 1.27e-02 6.20e+03 7.27e+00
  ... (remaining 6563 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 8474
        1.20 -     2.40: 419
        2.40 -     3.60: 74
        3.60 -     4.80: 17
        4.80 -     6.00: 7
  Bond angle restraints: 8991
  Sorted by residual:
  angle pdb=" N   LEU B 300 "
        pdb=" CA  LEU B 300 "
        pdb=" C   LEU B 300 "
      ideal   model   delta    sigma   weight residual
     114.75  109.79    4.96 1.26e+00 6.30e-01 1.55e+01
  angle pdb=" CA  GLY B 144 "
        pdb=" C   GLY B 144 "
        pdb=" O   GLY B 144 "
      ideal   model   delta    sigma   weight residual
     121.06  117.54    3.52 9.00e-01 1.23e+00 1.53e+01
  angle pdb=" N   TYR L  11 "
        pdb=" CA  TYR L  11 "
        pdb=" C   TYR L  11 "
      ideal   model   delta    sigma   weight residual
     113.97  109.04    4.93 1.28e+00 6.10e-01 1.49e+01
  angle pdb=" N   ASP A 231 "
        pdb=" CA  ASP A 231 "
        pdb=" C   ASP A 231 "
      ideal   model   delta    sigma   weight residual
     112.13  107.48    4.65 1.37e+00 5.33e-01 1.15e+01
  angle pdb=" N   GLY A 292 "
        pdb=" CA  GLY A 292 "
        pdb=" C   GLY A 292 "
      ideal   model   delta    sigma   weight residual
     111.76  116.34   -4.58 1.43e+00 4.89e-01 1.03e+01
  ... (remaining 8986 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.61: 3412
       17.61 -    35.22: 290
       35.22 -    52.84: 62
       52.84 -    70.45: 18
       70.45 -    88.06: 3
  Dihedral angle restraints: 3785
    sinusoidal: 1141
      harmonic: 2644
  Sorted by residual:
  dihedral pdb=" CA  ASP A 231 "
           pdb=" C   ASP A 231 "
           pdb=" N   LEU A 232 "
           pdb=" CA  LEU A 232 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.85   18.15     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  PHE B 151 "
           pdb=" C   PHE B 151 "
           pdb=" N   LEU B 152 "
           pdb=" CA  LEU B 152 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.95   18.05     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" SG  CYS R 141 "
           pdb=" CB  CYS R 224 "
           pdb=" SG  CYS R 224 "
           pdb=" CA  CYS R 224 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00  -12.12  -60.88     1      2.00e+01 2.50e-03 1.23e+01
  ... (remaining 3782 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 763
       0.041 -    0.081: 236
       0.081 -    0.122: 56
       0.122 -    0.162: 14
       0.162 -    0.203: 2
  Chirality restraints: 1071
  Sorted by residual:
  chirality pdb=" CA  ILE L  12 "
            pdb=" N   ILE L  12 "
            pdb=" C   ILE L  12 "
            pdb=" CB  ILE L  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  LEU B 139 "
            pdb=" N   LEU B 139 "
            pdb=" C   LEU B 139 "
            pdb=" CB  LEU B 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.31e-01
  chirality pdb=" CA  LEU B 336 "
            pdb=" N   LEU B 336 "
            pdb=" C   LEU B 336 "
            pdb=" CB  LEU B 336 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.06e-01
  ... (remaining 1068 not shown)

  Planarity restraints: 1157
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L   9 "   -0.422 9.50e-02 1.11e+02   1.89e-01 2.19e+01
        pdb=" NE  ARG L   9 "    0.026 2.00e-02 2.50e+03
        pdb=" CZ  ARG L   9 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG L   9 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG L   9 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 281 "    0.027 5.00e-02 4.00e+02   4.12e-02 2.71e+00
        pdb=" N   PRO R 292 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO R 292 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO R 292 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L   8 "    0.135 9.50e-02 1.11e+02   6.03e-02 2.23e+00
        pdb=" NE  ARG L   8 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG L   8 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG L   8 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG L   8 "    0.005 2.00e-02 2.50e+03
  ... (remaining 1154 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1017
        2.76 -     3.29: 6059
        3.29 -     3.83: 11166
        3.83 -     4.36: 12613
        4.36 -     4.90: 22283
  Nonbonded interactions: 53138
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   GLY R  77 "
            pdb=" ND2 ASN R  81 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" O   CYS A 254 "
            pdb=" NZ  LYS A 317 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" O   ALA R 119 "
            pdb=" OH  TYR R 144 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" O   MET R 249 "
            pdb=" OG  SER R 253 "
     model   vdw
     2.356 3.040
  ... (remaining 53133 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.130
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6878
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6569  Z= 0.210
  Angle     :  0.623   6.004   8993  Z= 0.397
  Chirality :  0.043   0.203   1071
  Planarity :  0.007   0.189   1157
  Dihedral  : 14.584  88.061   2066
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 19.04 %
    Favored  : 80.25 %
  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:  1.10 (0.29), residues: 888
  helix:  2.49 (0.27), residues: 383
  sheet:  0.53 (0.38), residues: 169
  loop : -1.33 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 322 
 TYR   0.012   0.001   TYR R 319 
 PHE   0.013   0.001   PHE B 151 
 TRP   0.017   0.002   TRP R 334 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6568)
  covalent geometry    : angle       0.62280 ( 8991)
  SS BOND              : bond        0.00536 (    1)
  SS BOND              : angle       0.80996 (    2)
  hydrogen bonds       : bond        0.12354 (  376)
  hydrogen bonds       : angle       5.20738 ( 1089)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 89
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  245 GLU cc_start: 0.6560 (pp20) cc_final: 0.6243 (pp20)
  outliers start: 4
  outliers final: 2
  residues processed: 92
  average time/residue: 0.5141
  time to fit residues: 49.8558
Evaluate side-chains
  81 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain A residue  267 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
R 210 GLN
R 365 ASN
A  52 GLN
A 255 ASN
A 322 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.231823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.183032 restraints weight = 6729.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.4138 rms_B_bonded: 1.89
r_work: 0.4044 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3937 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.0798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6569  Z= 0.129
  Angle     :  0.499   5.590   8993  Z= 0.275
  Chirality :  0.041   0.151   1071
  Planarity :  0.004   0.043   1157
  Dihedral  :  4.575  50.119    963
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 17.62 %
    Favored  : 79.36 %
  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:  1.30 (0.29), residues: 888
  helix:  2.68 (0.26), residues: 381
  sheet:  0.51 (0.38), residues: 171
  loop : -1.16 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 322 
 TYR   0.014   0.001   TYR R 319 
 PHE   0.016   0.001   PHE B 151 
 TRP   0.015   0.002   TRP R 334 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6568)
  covalent geometry    : angle       0.49886 ( 8991)
  SS BOND              : bond        0.00501 (    1)
  SS BOND              : angle       1.05015 (    2)
  hydrogen bonds       : bond        0.04188 (  376)
  hydrogen bonds       : angle       4.32637 ( 1089)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.277 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7710 (mm)
REVERT: B  298 ASP cc_start: 0.5345 (OUTLIER) cc_final: 0.4794 (t0)
REVERT: R  366 LEU cc_start: 0.6213 (OUTLIER) cc_final: 0.6007 (pp)
REVERT: A  245 GLU cc_start: 0.6806 (pp20) cc_final: 0.6453 (pp20)
  outliers start: 17
  outliers final: 5
  residues processed: 102
  average time/residue: 0.3725
  time to fit residues: 40.6057
Evaluate side-chains
  92 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  366 LEU
Chi-restraints excluded: chain A residue  267 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 48 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 73 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 4 optimal weight:    8.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
R  81 ASN
R 210 GLN
R 240 ASN
R 350 ASN
R 365 ASN
A  52 GLN
A 269 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.228988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.179499 restraints weight = 6660.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.4103 rms_B_bonded: 1.89
r_work: 0.4011 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3900 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
moved from start:          0.1262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6569  Z= 0.183
  Angle     :  0.566   5.679   8993  Z= 0.312
  Chirality :  0.044   0.163   1071
  Planarity :  0.004   0.046   1157
  Dihedral  :  4.896  48.550    963
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 16.55 %
    Favored  : 79.54 %
  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:  1.01 (0.28), residues: 888
  helix:  2.40 (0.26), residues: 380
  sheet:  0.38 (0.38), residues: 171
  loop : -1.25 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R 322 
 TYR   0.016   0.002   TYR R 319 
 PHE   0.023   0.002   PHE B 151 
 TRP   0.013   0.002   TRP B  63 
 HIS   0.005   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 6568)
  covalent geometry    : angle       0.56542 ( 8991)
  SS BOND              : bond        0.00562 (    1)
  SS BOND              : angle       1.22961 (    2)
  hydrogen bonds       : bond        0.04890 (  376)
  hydrogen bonds       : angle       4.48691 ( 1089)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.212 
Fit side-chains
REVERT: R  120 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.5641 (ttt)
REVERT: R  366 LEU cc_start: 0.6119 (OUTLIER) cc_final: 0.5819 (pp)
REVERT: A  245 GLU cc_start: 0.6866 (pp20) cc_final: 0.6526 (pp20)
  outliers start: 22
  outliers final: 10
  residues processed: 101
  average time/residue: 0.4166
  time to fit residues: 44.6741
Evaluate side-chains
  89 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  265 VAL
Chi-restraints excluded: chain R residue  299 ARG
Chi-restraints excluded: chain R residue  366 LEU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  267 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 37 optimal weight:    0.3980
   chunk 70 optimal weight:    3.9990
   chunk 50 optimal weight:    8.9990
   chunk 53 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 0 optimal weight:   30.0000
   chunk 16 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
B 156 GLN
R 210 GLN
R 350 ASN
A  52 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.230514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.181545 restraints weight = 6724.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.4123 rms_B_bonded: 1.89
r_work: 0.4031 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3923 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.1278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6569  Z= 0.135
  Angle     :  0.519  10.088   8993  Z= 0.279
  Chirality :  0.042   0.153   1071
  Planarity :  0.004   0.044   1157
  Dihedral  :  4.665  49.865    963
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.79 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.17 (0.29), residues: 888
  helix:  2.58 (0.26), residues: 381
  sheet:  0.41 (0.38), residues: 171
  loop : -1.22 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 322 
 TYR   0.010   0.001   TYR R 319 
 PHE   0.018   0.001   PHE B 151 
 TRP   0.014   0.002   TRP B  82 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6568)
  covalent geometry    : angle       0.51847 ( 8991)
  SS BOND              : bond        0.00514 (    1)
  SS BOND              : angle       1.04356 (    2)
  hydrogen bonds       : bond        0.04182 (  376)
  hydrogen bonds       : angle       4.24740 ( 1089)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.219 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7769 (mm)
REVERT: B  298 ASP cc_start: 0.5455 (OUTLIER) cc_final: 0.4689 (t0)
REVERT: R  366 LEU cc_start: 0.6006 (OUTLIER) cc_final: 0.5716 (pp)
REVERT: A  245 GLU cc_start: 0.6980 (pp20) cc_final: 0.6604 (pp20)
REVERT: A  248 LYS cc_start: 0.6858 (ptpp) cc_final: 0.6497 (ptpp)
  outliers start: 18
  outliers final: 8
  residues processed: 101
  average time/residue: 0.3986
  time to fit residues: 42.8201
Evaluate side-chains
  94 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  265 VAL
Chi-restraints excluded: chain R residue  366 LEU
Chi-restraints excluded: chain A residue  267 PHE
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain A residue  343 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 78 optimal weight:    8.9990
   chunk 86 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0770
   chunk 54 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9980
   chunk 44 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
R 210 GLN
R 350 ASN
A  52 GLN
A 269 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.231995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.183132 restraints weight = 6789.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.4137 rms_B_bonded: 1.91
r_work: 0.4044 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3936 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7042
moved from start:          0.1346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6569  Z= 0.113
  Angle     :  0.489   8.471   8993  Z= 0.261
  Chirality :  0.041   0.147   1071
  Planarity :  0.003   0.044   1157
  Dihedral  :  4.454  51.013    963
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 18.15 %
    Favored  : 78.83 %
  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:  1.33 (0.29), residues: 888
  helix:  2.74 (0.26), residues: 380
  sheet:  0.49 (0.39), residues: 169
  loop : -1.15 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 322 
 TYR   0.009   0.001   TYR R 319 
 PHE   0.015   0.001   PHE B 151 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 6568)
  covalent geometry    : angle       0.48923 ( 8991)
  SS BOND              : bond        0.00476 (    1)
  SS BOND              : angle       0.94847 (    2)
  hydrogen bonds       : bond        0.03746 (  376)
  hydrogen bonds       : angle       4.07921 ( 1089)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.281 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7743 (mm)
REVERT: B  298 ASP cc_start: 0.5322 (OUTLIER) cc_final: 0.4697 (t0)
REVERT: R  366 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5680 (pp)
REVERT: A  245 GLU cc_start: 0.6891 (pp20) cc_final: 0.6508 (pp20)
REVERT: A  248 LYS cc_start: 0.6857 (ptpp) cc_final: 0.6523 (ptpp)
  outliers start: 17
  outliers final: 11
  residues processed: 101
  average time/residue: 0.4101
  time to fit residues: 44.0125
Evaluate side-chains
  96 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  265 VAL
Chi-restraints excluded: chain R residue  299 ARG
Chi-restraints excluded: chain R residue  366 LEU
Chi-restraints excluded: chain A residue  267 PHE
Chi-restraints excluded: chain A residue  304 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 29 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0970
   chunk 9 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
R 210 GLN
A  52 GLN
A 269 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.231774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.182906 restraints weight = 6724.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.4134 rms_B_bonded: 1.89
r_work: 0.4045 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3935 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
moved from start:          0.1419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6569  Z= 0.116
  Angle     :  0.493   7.837   8993  Z= 0.264
  Chirality :  0.041   0.149   1071
  Planarity :  0.003   0.044   1157
  Dihedral  :  4.407  51.118    963
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 17.97 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.29), residues: 888
  helix:  2.80 (0.26), residues: 380
  sheet:  0.54 (0.39), residues: 169
  loop : -1.11 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 322 
 TYR   0.009   0.001   TYR R 319 
 PHE   0.015   0.001   PHE B 151 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 6568)
  covalent geometry    : angle       0.49326 ( 8991)
  SS BOND              : bond        0.00449 (    1)
  SS BOND              : angle       0.96616 (    2)
  hydrogen bonds       : bond        0.03761 (  376)
  hydrogen bonds       : angle       4.06133 ( 1089)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.232 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7722 (mm)
REVERT: B  298 ASP cc_start: 0.5320 (OUTLIER) cc_final: 0.4664 (t0)
REVERT: R  120 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.5515 (ttt)
REVERT: A  245 GLU cc_start: 0.6866 (pp20) cc_final: 0.6476 (pp20)
REVERT: A  248 LYS cc_start: 0.6828 (ptpp) cc_final: 0.6495 (ptpp)
  outliers start: 17
  outliers final: 10
  residues processed: 101
  average time/residue: 0.3969
  time to fit residues: 42.7438
Evaluate side-chains
  97 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  265 VAL
Chi-restraints excluded: chain A residue  267 PHE
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain A residue  343 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 13 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
R 210 GLN
A  52 GLN
A 269 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.229479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.180065 restraints weight = 6672.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.4107 rms_B_bonded: 1.89
r_work: 0.4015 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3908 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6569  Z= 0.163
  Angle     :  0.552   7.262   8993  Z= 0.297
  Chirality :  0.043   0.158   1071
  Planarity :  0.004   0.045   1157
  Dihedral  :  4.722  49.922    963
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 17.79 %
    Favored  : 79.18 %
  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:  1.25 (0.29), residues: 888
  helix:  2.61 (0.26), residues: 382
  sheet:  0.49 (0.39), residues: 170
  loop : -1.16 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R 322 
 TYR   0.010   0.001   TYR R 319 
 PHE   0.021   0.002   PHE B 151 
 TRP   0.012   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 6568)
  covalent geometry    : angle       0.55184 ( 8991)
  SS BOND              : bond        0.00452 (    1)
  SS BOND              : angle       1.15588 (    2)
  hydrogen bonds       : bond        0.04469 (  376)
  hydrogen bonds       : angle       4.30747 ( 1089)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.217 
Fit side-chains
REVERT: B  298 ASP cc_start: 0.5533 (OUTLIER) cc_final: 0.4613 (t0)
REVERT: A  245 GLU cc_start: 0.7034 (pp20) cc_final: 0.6650 (pp20)
  outliers start: 17
  outliers final: 10
  residues processed: 100
  average time/residue: 0.3847
  time to fit residues: 41.0805
Evaluate side-chains
  90 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  265 VAL
Chi-restraints excluded: chain A residue  267 PHE
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain A residue  343 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 37 optimal weight:    0.1980
   chunk 59 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 44 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0770
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
R 210 GLN
A  52 GLN
A 269 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4641 r_free = 0.4641 target = 0.232758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.184218 restraints weight = 6733.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.4148 rms_B_bonded: 1.89
r_work: 0.4057 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3948 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7025
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6569  Z= 0.103
  Angle     :  0.480   7.637   8993  Z= 0.254
  Chirality :  0.040   0.145   1071
  Planarity :  0.003   0.043   1157
  Dihedral  :  4.309  51.978    963
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 18.51 %
    Favored  : 78.83 %
  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:  1.43 (0.29), residues: 888
  helix:  2.85 (0.26), residues: 380
  sheet:  0.55 (0.40), residues: 169
  loop : -1.14 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 322 
 TYR   0.007   0.001   TYR B 264 
 PHE   0.013   0.001   PHE B 151 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 6568)
  covalent geometry    : angle       0.47951 ( 8991)
  SS BOND              : bond        0.00405 (    1)
  SS BOND              : angle       0.85881 (    2)
  hydrogen bonds       : bond        0.03469 (  376)
  hydrogen bonds       : angle       3.98173 ( 1089)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.229 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7705 (mm)
REVERT: B  298 ASP cc_start: 0.5315 (OUTLIER) cc_final: 0.4694 (t0)
REVERT: R  190 SER cc_start: 0.7195 (m) cc_final: 0.6773 (p)
REVERT: R  319 TYR cc_start: 0.6884 (t80) cc_final: 0.6181 (t80)
REVERT: A  245 GLU cc_start: 0.6994 (pp20) cc_final: 0.6594 (pp20)
REVERT: A  248 LYS cc_start: 0.6753 (ptpp) cc_final: 0.6440 (ptpp)
  outliers start: 15
  outliers final: 6
  residues processed: 100
  average time/residue: 0.3956
  time to fit residues: 42.2082
Evaluate side-chains
  93 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  265 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 28 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
R 210 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.231281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.182229 restraints weight = 6829.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.4126 rms_B_bonded: 1.91
r_work: 0.4036 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3927 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7050
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6569  Z= 0.125
  Angle     :  0.508   7.439   8993  Z= 0.271
  Chirality :  0.041   0.152   1071
  Planarity :  0.003   0.044   1157
  Dihedral  :  4.295  51.117    961
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.22 %
    Favored  : 78.47 %
  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:  1.43 (0.29), residues: 888
  helix:  2.83 (0.26), residues: 381
  sheet:  0.56 (0.39), residues: 171
  loop : -1.15 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 322 
 TYR   0.009   0.001   TYR R 319 
 PHE   0.017   0.001   PHE B 151 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6568)
  covalent geometry    : angle       0.50783 ( 8991)
  SS BOND              : bond        0.00396 (    1)
  SS BOND              : angle       0.93611 (    2)
  hydrogen bonds       : bond        0.03861 (  376)
  hydrogen bonds       : angle       4.10768 ( 1089)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.190 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7755 (mm)
REVERT: B  298 ASP cc_start: 0.5348 (OUTLIER) cc_final: 0.4639 (t0)
REVERT: R  190 SER cc_start: 0.7206 (m) cc_final: 0.6785 (p)
REVERT: A  245 GLU cc_start: 0.6983 (pp20) cc_final: 0.6575 (pp20)
REVERT: A  248 LYS cc_start: 0.6850 (ptpp) cc_final: 0.6518 (ptpp)
  outliers start: 13
  outliers final: 6
  residues processed: 93
  average time/residue: 0.4062
  time to fit residues: 40.2996
Evaluate side-chains
  90 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  265 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 87 optimal weight:    0.0870
   chunk 59 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0670
   chunk 1 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    0.7698

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

Flipped N/Q/H residues before XYZ refinement:
R 210 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.231615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.182730 restraints weight = 6610.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.4132 rms_B_bonded: 1.87
r_work: 0.4039 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3936 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6569  Z= 0.120
  Angle     :  0.503   8.210   8993  Z= 0.267
  Chirality :  0.041   0.148   1071
  Planarity :  0.003   0.044   1157
  Dihedral  :  4.278  51.430    961
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.22 %
    Favored  : 78.47 %
  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:  1.43 (0.29), residues: 888
  helix:  2.85 (0.26), residues: 381
  sheet:  0.55 (0.39), residues: 171
  loop : -1.16 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 322 
 TYR   0.011   0.001   TYR B 264 
 PHE   0.016   0.001   PHE B 151 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6568)
  covalent geometry    : angle       0.50280 ( 8991)
  SS BOND              : bond        0.00400 (    1)
  SS BOND              : angle       0.90193 (    2)
  hydrogen bonds       : bond        0.03775 (  376)
  hydrogen bonds       : angle       4.08560 ( 1089)

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.168 
Fit side-chains
REVERT: B   49 ARG cc_start: 0.8041 (mmt-90) cc_final: 0.7800 (mmt-90)
REVERT: B  146 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7750 (mm)
REVERT: B  298 ASP cc_start: 0.5395 (OUTLIER) cc_final: 0.4702 (t0)
REVERT: R  190 SER cc_start: 0.7218 (m) cc_final: 0.6799 (p)
REVERT: A  245 GLU cc_start: 0.6996 (pp20) cc_final: 0.6591 (pp20)
REVERT: A  248 LYS cc_start: 0.6873 (ptpp) cc_final: 0.6546 (ptpp)
  outliers start: 13
  outliers final: 8
  residues processed: 94
  average time/residue: 0.3974
  time to fit residues: 39.7982
Evaluate side-chains
  95 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  138 GLU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  298 ASP
Chi-restraints excluded: chain R residue  105 LEU
Chi-restraints excluded: chain R residue  265 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  343 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0980
   chunk 63 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 86 optimal weight:    4.9990
   chunk 28 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
R 210 GLN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4624 r_free = 0.4624 target = 0.230587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.181552 restraints weight = 6677.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.4122 rms_B_bonded: 1.89
r_work: 0.4030 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3922 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6569  Z= 0.132
  Angle     :  0.519   8.443   8993  Z= 0.277
  Chirality :  0.042   0.153   1071
  Planarity :  0.003   0.044   1157
  Dihedral  :  4.378  50.833    961
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.04 %
    Favored  : 78.65 %
  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:  1.38 (0.29), residues: 888
  helix:  2.79 (0.26), residues: 381
  sheet:  0.51 (0.39), residues: 171
  loop : -1.16 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 322 
 TYR   0.010   0.001   TYR B 264 
 PHE   0.017   0.001   PHE B 151 
 TRP   0.013   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6568)
  covalent geometry    : angle       0.51929 ( 8991)
  SS BOND              : bond        0.00404 (    1)
  SS BOND              : angle       0.94882 (    2)
  hydrogen bonds       : bond        0.03998 (  376)
  hydrogen bonds       : angle       4.16488 ( 1089)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3573.38 seconds
wall clock time: 61 minutes 17.53 seconds (3677.53 seconds total)