Starting phenix.real_space_refine
on Fri Aug 22 17:52:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ge3_29954/08_2025/8ge3_29954.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ge3_29954/08_2025/8ge3_29954.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ge3_29954/08_2025/8ge3_29954.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ge3_29954/08_2025/8ge3_29954.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ge3_29954/08_2025/8ge3_29954.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ge3_29954/08_2025/8ge3_29954.cif"
  }
  resolution = 3.3
  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=  -0.001 sd=   0.035
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      42      5.16       5
     C    4263      2.51       5
     N    1145      2.21       5
     O    1156      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6606
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1714
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 69}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 246
          Unresolved non-hydrogen angles: 300
          Unresolved non-hydrogen dihedrals: 194
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 7, 'ASN:plan1': 3, 'GLU:plan': 15, 'ASP:plan': 12, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 170
    Chain: "B"
      Number of atoms: 2413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2413
          Classifications: {'peptide': 332}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 5, 'TRANS': 326}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 139
          Unresolved non-hydrogen angles: 173
          Unresolved non-hydrogen dihedrals: 105
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 12, 'GLN:plan1': 4, 'ARG:plan': 6, 'GLU:plan': 5, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 111
    Chain: "G"
      Number of atoms: 345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 345
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "R"
      Number of atoms: 2119
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2119
          Classifications: {'peptide': 286}
          Incomplete info: {'truncation_to_alanine': 54}
          Link IDs: {'PTRANS': 7, 'TRANS': 278}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 188
          Unresolved non-hydrogen angles: 232
          Unresolved non-hydrogen dihedrals: 151
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLU:plan': 9, 'TRP:plan': 1, 'ASP:plan': 5, 'ASN:plan1': 3, 'ARG:plan': 5, 'GLN:plan1': 3}
          Unresolved non-hydrogen planarities: 106
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.66, per 1000 atoms: 0.25
  Number of scatterers: 6606
  At special positions: 0
  Unit cell: (68.9, 97.52, 129.32, 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      42     16.00
     O    1156      8.00
     N    1145      7.00
     C    4263      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " 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: 0.53
  Conformation dependent library (CDL) restraints added in 297.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 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:
      26 helices and 9 sheets defined
      48.8% alpha, 18.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 38
      removed outlier: 3.573A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 3.656A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 3.638A  pdb=" N   ARG A 283 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.761A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 3.507A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.654A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.592A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 26
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.545A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 12 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 31 through 61
      removed outlier: 3.612A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 65
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 3.683A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.237A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 3.688A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 269 through 299
      removed outlier: 3.803A  pdb=" N   THR R 281 " --> pdb=" O   ILE R 277 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.885A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 3.915A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 210
    Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210
      removed outlier: 9.444A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.427A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 52
      removed outlier: 6.133A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.617A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.419A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.619A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.024A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.475A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.711A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.006A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.562A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 278
      removed outlier: 4.139A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    397 hydrogen bonds defined for protein.
    1149 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: 0.90

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2133
        1.35 -     1.46: 1730
        1.46 -     1.58: 2830
        1.58 -     1.70: 0
        1.70 -     1.82: 59
  Bond restraints: 6752
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.451 -0.054 2.00e-02 2.50e+03 7.29e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.565 -0.045 2.00e-02 2.50e+03 5.04e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.439 -0.045 2.00e-02 2.50e+03 5.04e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.566 -0.043 2.00e-02 2.50e+03 4.70e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" OAK G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.353  1.323  0.030 2.00e-02 2.50e+03 2.21e+00
  ... (remaining 6747 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 9086
        1.48 -     2.97: 111
        2.97 -     4.45: 19
        4.45 -     5.93: 12
        5.93 -     7.42: 1
  Bond angle restraints: 9229
  Sorted by residual:
  angle pdb=" C   ASN A 264 "
        pdb=" N   ARG A 265 "
        pdb=" CA  ARG A 265 "
      ideal   model   delta    sigma   weight residual
     121.54  126.19   -4.65 1.91e+00 2.74e-01 5.94e+00
  angle pdb=" CB  GLU R 180 "
        pdb=" CG  GLU R 180 "
        pdb=" CD  GLU R 180 "
      ideal   model   delta    sigma   weight residual
     112.60  116.35   -3.75 1.70e+00 3.46e-01 4.85e+00
  angle pdb=" N   GLY A 329 "
        pdb=" CA  GLY A 329 "
        pdb=" C   GLY A 329 "
      ideal   model   delta    sigma   weight residual
     113.18  108.14    5.04 2.37e+00 1.78e-01 4.52e+00
  angle pdb=" CA  LEU A 296 "
        pdb=" CB  LEU A 296 "
        pdb=" CG  LEU A 296 "
      ideal   model   delta    sigma   weight residual
     116.30  123.72   -7.42 3.50e+00 8.16e-02 4.49e+00
  angle pdb=" C   HIS R 241 "
        pdb=" N   VAL R 242 "
        pdb=" CA  VAL R 242 "
      ideal   model   delta    sigma   weight residual
     121.70  125.38   -3.68 1.80e+00 3.09e-01 4.18e+00
  ... (remaining 9224 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.76: 3557
       15.76 -    31.52: 286
       31.52 -    47.27: 60
       47.27 -    63.03: 5
       63.03 -    78.79: 1
  Dihedral angle restraints: 3909
    sinusoidal: 1267
      harmonic: 2642
  Sorted by residual:
  dihedral pdb=" CA  TRP B 332 "
           pdb=" C   TRP B 332 "
           pdb=" N   ASP B 333 "
           pdb=" CA  ASP B 333 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.28   17.72     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CA  LEU A 266 "
           pdb=" C   LEU A 266 "
           pdb=" N   GLN A 267 "
           pdb=" CA  GLN A 267 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.19   16.81     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.82   16.18     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 3906 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 704
       0.029 -    0.057: 253
       0.057 -    0.086: 93
       0.086 -    0.115: 44
       0.115 -    0.143: 9
  Chirality restraints: 1103
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.54   -0.14 2.00e-01 2.50e+01 5.13e-01
  chirality pdb=" CA  ILE A 288 "
            pdb=" N   ILE A 288 "
            pdb=" C   ILE A 288 "
            pdb=" CB  ILE A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.22e-01
  chirality pdb=" CA  ILE A 244 "
            pdb=" N   ILE A 244 "
            pdb=" C   ILE A 244 "
            pdb=" CB  ILE A 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.82e-01
  ... (remaining 1100 not shown)

  Planarity restraints: 1161
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR R 174 "    0.010 2.00e-02 2.50e+03   1.11e-02 2.47e+00
        pdb=" CG  TYR R 174 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR R 174 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR R 174 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR R 174 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR R 174 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR R 174 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR R 174 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 265 "    0.007 2.00e-02 2.50e+03   1.35e-02 1.83e+00
        pdb=" C   ARG A 265 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   ARG A 265 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LEU A 266 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "    0.022 5.00e-02 4.00e+02   3.32e-02 1.76e+00
        pdb=" N   PRO G  49 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1158 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1127
        2.76 -     3.30: 6359
        3.30 -     3.83: 11208
        3.83 -     4.37: 12378
        4.37 -     4.90: 22691
  Nonbonded interactions: 53763
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OH  TYR R 185 "
            pdb=" O   PHE R 194 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   SER A 252 "
            pdb=" OG  SER A 252 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OG  SER R 203 "
            pdb=" OAL G1I R 501 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OD1 ASN R 293 "
            pdb=" OH  TYR R 308 "
     model   vdw
     2.281 3.040
  ... (remaining 53758 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             2.710
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     7.420
  Find NCS groups from input model:        0.020
  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:0.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
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   0.054   6753  Z= 0.138
  Angle     :  0.478   7.417   9231  Z= 0.252
  Chirality :  0.038   0.143   1103
  Planarity :  0.003   0.033   1161
  Dihedral  : 12.026  78.790   2190
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 aren not related in a simple way.
  whole:  1.74 (0.28), residues: 890
  helix:  2.90 (0.25), residues: 382
  sheet: -0.04 (0.41), residues: 162
  loop : -0.23 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 347 
 TYR   0.028   0.001   TYR R 174 
 PHE   0.015   0.001   PHE B 235 
 TRP   0.009   0.001   TRP R 105 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6752)
  covalent geometry    : angle       0.47778 ( 9229)
  SS BOND              : bond        0.00454 (    1)
  SS BOND              : angle       1.38587 (    2)
  hydrogen bonds       : bond        0.15062 (  393)
  hydrogen bonds       : angle       6.20425 ( 1149)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.189 
Fit side-chains
REVERT: B  322 ASP cc_start: 0.8137 (m-30) cc_final: 0.7924 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0639
  time to fit residues: 8.9701
Evaluate side-chains
  84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.0870
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.2980
   chunk 38 optimal weight:    0.0770
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.4980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.3316

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
R 312 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.142425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.124070 restraints weight = 10451.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 2.19
r_work: 0.3459 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3320 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.0858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6753  Z= 0.107
  Angle     :  0.465   5.504   9231  Z= 0.255
  Chirality :  0.039   0.147   1103
  Planarity :  0.003   0.033   1161
  Dihedral  :  4.292  21.544    978
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  6.79 %
    Favored  : 91.72 %
  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 aren not related in a simple way.
  whole:  1.88 (0.29), residues: 890
  helix:  2.78 (0.25), residues: 396
  sheet:  0.15 (0.41), residues: 166
  loop : -0.03 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  68 
 TYR   0.009   0.001   TYR R 185 
 PHE   0.009   0.001   PHE R 289 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 6752)
  covalent geometry    : angle       0.46476 ( 9229)
  SS BOND              : bond        0.00163 (    1)
  SS BOND              : angle       0.79265 (    2)
  hydrogen bonds       : bond        0.03890 (  393)
  hydrogen bonds       : angle       4.62383 ( 1149)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: A  343 ASP cc_start: 0.8390 (m-30) cc_final: 0.8176 (m-30)
REVERT: B  322 ASP cc_start: 0.8309 (m-30) cc_final: 0.8090 (m-30)
REVERT: R  180 GLU cc_start: 0.7685 (tp30) cc_final: 0.7463 (tp30)
  outliers start: 9
  outliers final: 3
  residues processed: 101
  average time/residue: 0.0664
  time to fit residues: 9.0810
Evaluate side-chains
  85 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain R residue  220 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 80 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 52 optimal weight:    4.9990
   chunk 71 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0050
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  65 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.140020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.121823 restraints weight = 10469.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 2.13
r_work: 0.3434 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6753  Z= 0.126
  Angle     :  0.457   5.659   9231  Z= 0.249
  Chirality :  0.039   0.142   1103
  Planarity :  0.003   0.034   1161
  Dihedral  :  4.264  19.524    978
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  9.60 %
    Favored  : 88.58 %
  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 aren not related in a simple way.
  whole:  1.80 (0.29), residues: 890
  helix:  2.75 (0.25), residues: 396
  sheet:  0.05 (0.39), residues: 171
  loop : -0.10 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.018   0.001   TYR R 174 
 PHE   0.011   0.001   PHE R 289 
 TRP   0.012   0.001   TRP B 339 
 HIS   0.006   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6752)
  covalent geometry    : angle       0.45737 ( 9229)
  SS BOND              : bond        0.00170 (    1)
  SS BOND              : angle       0.55282 (    2)
  hydrogen bonds       : bond        0.03732 (  393)
  hydrogen bonds       : angle       4.32731 ( 1149)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.164 
Fit side-chains
REVERT: B  322 ASP cc_start: 0.8345 (m-30) cc_final: 0.8114 (m-30)
REVERT: R   84 LEU cc_start: 0.8611 (mt) cc_final: 0.8388 (mt)
  outliers start: 11
  outliers final: 9
  residues processed: 103
  average time/residue: 0.0661
  time to fit residues: 9.2096
Evaluate side-chains
  95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0170
   chunk 53 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.7420

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
B  88 ASN
B 183 HIS
R  65 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.136663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.119477 restraints weight = 10481.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 2.09
r_work: 0.3423 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.1285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6753  Z= 0.127
  Angle     :  0.456   5.728   9231  Z= 0.247
  Chirality :  0.039   0.138   1103
  Planarity :  0.003   0.034   1161
  Dihedral  :  4.210  20.331    978
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.09 %
    Favored  : 86.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.76 (0.29), residues: 890
  helix:  2.76 (0.25), residues: 396
  sheet: -0.06 (0.40), residues: 166
  loop : -0.14 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  49 
 TYR   0.018   0.001   TYR R 174 
 PHE   0.011   0.001   PHE R 289 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6752)
  covalent geometry    : angle       0.45576 ( 9229)
  SS BOND              : bond        0.00272 (    1)
  SS BOND              : angle       0.46279 (    2)
  hydrogen bonds       : bond        0.03636 (  393)
  hydrogen bonds       : angle       4.16438 ( 1149)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A  297 LEU cc_start: 0.9202 (tp) cc_final: 0.8877 (tt)
REVERT: B  262 MET cc_start: 0.8220 (tpp) cc_final: 0.7986 (tpp)
REVERT: B  322 ASP cc_start: 0.8351 (m-30) cc_final: 0.8111 (m-30)
REVERT: R   84 LEU cc_start: 0.8599 (mt) cc_final: 0.8370 (mt)
  outliers start: 13
  outliers final: 8
  residues processed: 98
  average time/residue: 0.0618
  time to fit residues: 8.3440
Evaluate side-chains
  95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 78 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0050
   chunk 62 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 23 optimal weight:   20.0000
   chunk 88 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
R  65 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.140244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.122121 restraints weight = 10580.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 2.16
r_work: 0.3431 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.1385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6753  Z= 0.107
  Angle     :  0.448   6.011   9231  Z= 0.241
  Chirality :  0.039   0.135   1103
  Planarity :  0.003   0.033   1161
  Dihedral  :  4.127  20.350    978
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.92 %
    Favored  : 85.93 %
  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 aren not related in a simple way.
  whole:  1.76 (0.29), residues: 890
  helix:  2.82 (0.25), residues: 396
  sheet: -0.27 (0.39), residues: 175
  loop : -0.07 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG R 175 
 TYR   0.015   0.001   TYR R 174 
 PHE   0.010   0.001   PHE R 289 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 6752)
  covalent geometry    : angle       0.44839 ( 9229)
  SS BOND              : bond        0.00141 (    1)
  SS BOND              : angle       0.43921 (    2)
  hydrogen bonds       : bond        0.03459 (  393)
  hydrogen bonds       : angle       4.02662 ( 1149)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  393 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7642 (tt)
REVERT: B  262 MET cc_start: 0.8203 (tpp) cc_final: 0.7983 (tpp)
REVERT: B  322 ASP cc_start: 0.8354 (m-30) cc_final: 0.8131 (m-30)
REVERT: R   65 GLN cc_start: 0.8713 (mt0) cc_final: 0.8282 (mp10)
REVERT: R   84 LEU cc_start: 0.8571 (mt) cc_final: 0.8343 (mt)
  outliers start: 13
  outliers final: 11
  residues processed: 103
  average time/residue: 0.0636
  time to fit residues: 8.8995
Evaluate side-chains
  98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  140 LYS
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 64 optimal weight:    0.4980
   chunk 5 optimal weight:    4.9990
   chunk 9 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.137035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.119158 restraints weight = 10585.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 2.25
r_work: 0.3481 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3348 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.1432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6753  Z= 0.120
  Angle     :  0.460   6.290   9231  Z= 0.248
  Chirality :  0.039   0.136   1103
  Planarity :  0.003   0.034   1161
  Dihedral  :  4.152  20.545    978
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 12.25 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.29), residues: 890
  helix:  2.79 (0.25), residues: 396
  sheet: -0.35 (0.39), residues: 176
  loop : -0.06 (0.37), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.012   0.001   TYR R 174 
 PHE   0.011   0.001   PHE R 289 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 6752)
  covalent geometry    : angle       0.46016 ( 9229)
  SS BOND              : bond        0.00130 (    1)
  SS BOND              : angle       0.39420 (    2)
  hydrogen bonds       : bond        0.03479 (  393)
  hydrogen bonds       : angle       3.99490 ( 1149)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.220 
Fit side-chains
REVERT: B  322 ASP cc_start: 0.8354 (m-30) cc_final: 0.8137 (m-30)
REVERT: R   84 LEU cc_start: 0.8588 (mt) cc_final: 0.8362 (mt)
  outliers start: 16
  outliers final: 11
  residues processed: 98
  average time/residue: 0.0683
  time to fit residues: 9.0972
Evaluate side-chains
  95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain R residue  140 LYS
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 60 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  51 ASN
R  65 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.135808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.118486 restraints weight = 10423.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.10
r_work: 0.3409 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3278 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6753  Z= 0.140
  Angle     :  0.481   7.483   9231  Z= 0.256
  Chirality :  0.040   0.136   1103
  Planarity :  0.003   0.034   1161
  Dihedral  :  4.255  20.964    978
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 12.75 %
    Favored  : 84.77 %
  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 aren not related in a simple way.
  whole:  1.68 (0.29), residues: 890
  helix:  2.76 (0.25), residues: 395
  sheet: -0.37 (0.38), residues: 175
  loop : -0.06 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 175 
 TYR   0.011   0.001   TYR R 199 
 PHE   0.012   0.001   PHE R 289 
 TRP   0.009   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6752)
  covalent geometry    : angle       0.48067 ( 9229)
  SS BOND              : bond        0.00127 (    1)
  SS BOND              : angle       0.34627 (    2)
  hydrogen bonds       : bond        0.03628 (  393)
  hydrogen bonds       : angle       4.02909 ( 1149)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.165 
Fit side-chains
REVERT: B  322 ASP cc_start: 0.8372 (m-30) cc_final: 0.8140 (m-30)
REVERT: R   65 GLN cc_start: 0.8749 (mt0) cc_final: 0.7994 (mp10)
REVERT: R   84 LEU cc_start: 0.8605 (mt) cc_final: 0.8384 (mt)
  outliers start: 15
  outliers final: 12
  residues processed: 98
  average time/residue: 0.0646
  time to fit residues: 8.7144
Evaluate side-chains
  97 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 50 optimal weight:    0.5980
   chunk 14 optimal weight:    5.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.136668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.118183 restraints weight = 10706.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 2.17
r_work: 0.3378 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6753  Z= 0.166
  Angle     :  0.499   6.836   9231  Z= 0.266
  Chirality :  0.040   0.137   1103
  Planarity :  0.003   0.034   1161
  Dihedral  :  4.411  21.778    978
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 12.91 %
    Favored  : 84.77 %
  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 aren not related in a simple way.
  whole:  1.57 (0.29), residues: 890
  helix:  2.66 (0.25), residues: 395
  sheet: -0.48 (0.38), residues: 175
  loop : -0.06 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.012   0.001   TYR R 199 
 PHE   0.013   0.001   PHE R 289 
 TRP   0.010   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 6752)
  covalent geometry    : angle       0.49946 ( 9229)
  SS BOND              : bond        0.00230 (    1)
  SS BOND              : angle       0.30568 (    2)
  hydrogen bonds       : bond        0.03833 (  393)
  hydrogen bonds       : angle       4.11131 ( 1149)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.184 
Fit side-chains
REVERT: B  322 ASP cc_start: 0.8421 (m-30) cc_final: 0.8194 (m-30)
REVERT: R   84 LEU cc_start: 0.8611 (mt) cc_final: 0.8396 (mt)
REVERT: R  180 GLU cc_start: 0.7994 (tp30) cc_final: 0.7730 (tp30)
  outliers start: 14
  outliers final: 12
  residues processed: 96
  average time/residue: 0.0601
  time to fit residues: 7.8763
Evaluate side-chains
  98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 42 optimal weight:    0.6980
   chunk 57 optimal weight:    0.2980
   chunk 45 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 183 HIS
** B 293 ASN ** 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 = 0.3769 r_free = 0.3769 target = 0.138648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.120228 restraints weight = 10637.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 2.18
r_work: 0.3411 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6753  Z= 0.119
  Angle     :  0.470   7.140   9231  Z= 0.249
  Chirality :  0.039   0.135   1103
  Planarity :  0.003   0.031   1161
  Dihedral  :  4.277  21.483    978
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 13.08 %
    Favored  : 84.77 %
  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 aren not related in a simple way.
  whole:  1.65 (0.29), residues: 890
  helix:  2.74 (0.25), residues: 395
  sheet: -0.48 (0.38), residues: 175
  loop : -0.03 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 175 
 TYR   0.009   0.001   TYR R 174 
 PHE   0.010   0.001   PHE R 289 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6752)
  covalent geometry    : angle       0.46963 ( 9229)
  SS BOND              : bond        0.00121 (    1)
  SS BOND              : angle       0.38969 (    2)
  hydrogen bonds       : bond        0.03541 (  393)
  hydrogen bonds       : angle       4.00023 ( 1149)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.7699 (mmtt) cc_final: 0.7490 (mmtt)
REVERT: B  322 ASP cc_start: 0.8386 (m-30) cc_final: 0.8159 (m-30)
REVERT: R   84 LEU cc_start: 0.8581 (mt) cc_final: 0.8354 (mt)
  outliers start: 13
  outliers final: 12
  residues processed: 102
  average time/residue: 0.0581
  time to fit residues: 8.1099
Evaluate side-chains
  102 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0870
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.139216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.120843 restraints weight = 10577.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.17
r_work: 0.3417 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3285 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6753  Z= 0.117
  Angle     :  0.470   7.417   9231  Z= 0.250
  Chirality :  0.039   0.135   1103
  Planarity :  0.003   0.031   1161
  Dihedral  :  4.203  21.433    978
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 13.41 %
    Favored  : 84.11 %
  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 aren not related in a simple way.
  whole:  1.68 (0.29), residues: 890
  helix:  2.77 (0.25), residues: 395
  sheet: -0.46 (0.38), residues: 175
  loop : -0.01 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.010   0.001   TYR R 199 
 PHE   0.010   0.001   PHE R 289 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6752)
  covalent geometry    : angle       0.47028 ( 9229)
  SS BOND              : bond        0.00118 (    1)
  SS BOND              : angle       0.42633 (    2)
  hydrogen bonds       : bond        0.03467 (  393)
  hydrogen bonds       : angle       3.96292 ( 1149)

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

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

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1780 Ramachandran restraints generated.
    890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.211 
Fit side-chains
REVERT: R   84 LEU cc_start: 0.8573 (mt) cc_final: 0.8345 (mt)
REVERT: R  180 GLU cc_start: 0.7995 (tp30) cc_final: 0.7727 (tp30)
  outliers start: 15
  outliers final: 12
  residues processed: 102
  average time/residue: 0.0555
  time to fit residues: 7.7340
Evaluate side-chains
  100 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain R residue   66 THR
Chi-restraints excluded: chain R residue   67 VAL
Chi-restraints excluded: chain R residue  220 SER
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 42 optimal weight:    0.5980
   chunk 57 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 14 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0270
   chunk 46 optimal weight:    0.9980
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
B 293 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.137265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.119356 restraints weight = 10477.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 2.25
r_work: 0.3420 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6753  Z= 0.110
  Angle     :  0.466   7.412   9231  Z= 0.248
  Chirality :  0.039   0.135   1103
  Planarity :  0.003   0.030   1161
  Dihedral  :  4.153  21.035    978
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 13.58 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.29), residues: 890
  helix:  2.80 (0.25), residues: 396
  sheet: -0.44 (0.38), residues: 175
  loop : -0.02 (0.37), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 175 
 TYR   0.009   0.001   TYR R 174 
 PHE   0.009   0.001   PHE R 289 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 6752)
  covalent geometry    : angle       0.46619 ( 9229)
  SS BOND              : bond        0.00130 (    1)
  SS BOND              : angle       0.46861 (    2)
  hydrogen bonds       : bond        0.03413 (  393)
  hydrogen bonds       : angle       3.91963 ( 1149)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1355.71 seconds
wall clock time: 23 minutes 53.25 seconds (1433.25 seconds total)