Starting phenix.real_space_refine
on Thu Mar  6 08:01:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gei_29971/03_2025/8gei_29971.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gei_29971/03_2025/8gei_29971.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gei_29971/03_2025/8gei_29971.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gei_29971/03_2025/8gei_29971.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gei_29971/03_2025/8gei_29971.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gei_29971/03_2025/8gei_29971.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.020
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       2      5.16       5
     C    3449      2.51       5
     N    1003      2.21       5
     O     998      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5452
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 1591
          Classifications: {'peptide': 277}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 203}
          Link IDs: {'PTRANS': 4, 'TRANS': 272}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 738
          Unresolved non-hydrogen angles: 921
          Unresolved non-hydrogen dihedrals: 589
          Unresolved non-hydrogen chiralities: 57
          Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 17, 'TYR:plan': 5, 'ASN:plan1': 16, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 22, 'ARG:plan': 24}
          Unresolved non-hydrogen planarities: 445
    Chain: "B"
      Number of atoms: 1907
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 1907
          Classifications: {'peptide': 328}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 204}
          Link IDs: {'PTRANS': 5, 'TRANS': 322}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 625
          Unresolved non-hydrogen angles: 791
          Unresolved non-hydrogen dihedrals: 482
          Unresolved non-hydrogen chiralities: 68
          Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 3, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 29, 'ASN%COO:plan1': 1, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 15}
          Unresolved non-hydrogen planarities: 327
    Chain: "G"
      Number of atoms: 281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 281
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 112
          Unresolved non-hydrogen angles: 136
          Unresolved non-hydrogen dihedrals: 92
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 58
    Chain: "R"
      Number of atoms: 1658
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 1658
          Classifications: {'peptide': 279}
          Incomplete info: {'truncation_to_alanine': 190}
          Link IDs: {'PTRANS': 7, 'TRANS': 271}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 600
          Unresolved non-hydrogen angles: 770
          Unresolved non-hydrogen dihedrals: 467
          Unresolved non-hydrogen chiralities: 94
          Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 9, 'GLU:plan': 8, 'ARG:plan': 10}
          Unresolved non-hydrogen planarities: 248
    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: 4.49, per 1000 atoms: 0.82
  Number of scatterers: 5452
  At special positions: 0
  Unit cell: (66.78, 96.46, 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       2     16.00
     O     998      8.00
     N    1003      7.00
     C    3449      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.47
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1778

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 8 sheets defined
      49.4% alpha, 13.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 40
      removed outlier: 3.856A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
      removed outlier: 3.768A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 91
      No H-bonds generated for 'chain 'A' and resid 90 through 91'
    Processing helix  chain 'A' and resid 93 through 93
      No H-bonds generated for 'chain 'A' and resid 93 through 93'
    Processing helix  chain 'A' and resid 94 through 106
    Processing helix  chain 'A' and resid 109 through 113
    Processing helix  chain 'A' and resid 124 through 132
    Processing helix  chain 'A' and resid 157 through 166
      removed outlier: 3.509A  pdb=" N   ALA A 161 " --> pdb=" O   GLU A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 238
    Processing helix  chain 'A' and resid 251 through 253
      No H-bonds generated for 'chain 'A' and resid 251 through 253'
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 4.166A  pdb=" N   PHE A 273 " --> pdb=" O   ALA A 269 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   LYS A 274 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.793A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 3.981A  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 351
      removed outlier: 3.510A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 390
      removed outlier: 4.540A  pdb=" N   ARG A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 393
      No H-bonds generated for 'chain 'A' and resid 391 through 393'
    Processing helix  chain 'B' and resid 8 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 14 through 22
    Processing helix  chain 'G' and resid 29 through 43
    Processing helix  chain 'G' and resid 44 through 46
      No H-bonds generated for 'chain 'G' and resid 44 through 46'
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.581A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA R  59 " --> pdb=" O   ILE R  55 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 69 through 85
    Processing helix  chain 'R' and resid 85 through 96
      removed outlier: 3.874A  pdb=" N   PHE R  89 " --> pdb=" O   ALA R  85 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.569A  pdb=" N   SER R 137 " --> pdb=" O   PHE R 133 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 170
      removed outlier: 3.505A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
      removed outlier: 4.680A  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 182 through 187
      removed outlier: 3.787A  pdb=" N   ALA R 186 " --> pdb=" O   ILE R 182 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.526A  pdb=" N   ILE R 201 " --> pdb=" O   GLN R 197 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 4.209A  pdb=" N   ILE R 278 " --> pdb=" O   THR R 274 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   MET R 279 " --> pdb=" O   LEU R 275 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.662A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ILE R 298 " --> pdb=" O   ILE R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 3.531A  pdb=" N   ILE R 309 " --> pdb=" O   LYS R 305 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLY R 315 " --> pdb=" O   LEU R 311 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   TYR R 316 " --> pdb=" O   ASN R 312 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 3.795A  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 339
      removed outlier: 3.787A  pdb=" N   GLU R 338 " --> pdb=" O   ILE R 334 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU R 339 " --> pdb=" O   ALA R 335 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 222
      removed outlier: 6.012A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 5.924A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.783A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.120A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   PHE A 290 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 52
      removed outlier: 3.603A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LEU B  51 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.894A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.199A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.316A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER B  72 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ILE B  80 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105
      removed outlier: 3.691A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.016A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150
      removed outlier: 6.601A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.817A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.689A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.961A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 277
      removed outlier: 5.943A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    353 hydrogen bonds defined for protein.
    1035 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: 1.78

  Time building geometry restraints manager: 1.74 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1923
        1.34 -     1.46: 1362
        1.46 -     1.58: 2263
        1.58 -     1.69: 1
        1.69 -     1.81: 2
  Bond restraints: 5551
  Sorted by residual:
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.600 -0.077 2.00e-02 2.50e+03 1.49e+01
  bond pdb=" CAF G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.519  1.573 -0.054 2.00e-02 2.50e+03 7.16e+00
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.450 -0.053 2.00e-02 2.50e+03 6.96e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.440 -0.046 2.00e-02 2.50e+03 5.37e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" NAN G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.451  1.485 -0.034 2.00e-02 2.50e+03 2.82e+00
  ... (remaining 5546 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 7368
        1.18 -     2.36: 266
        2.36 -     3.55: 40
        3.55 -     4.73: 7
        4.73 -     5.91: 7
  Bond angle restraints: 7688
  Sorted by residual:
  angle pdb=" C   VAL R  86 "
        pdb=" N   VAL R  87 "
        pdb=" CA  VAL R  87 "
      ideal   model   delta    sigma   weight residual
     120.33  122.70   -2.37 8.00e-01 1.56e+00 8.79e+00
  angle pdb=" C   PHE R 321 "
        pdb=" N   ASN R 322 "
        pdb=" CA  ASN R 322 "
      ideal   model   delta    sigma   weight residual
     120.09  123.58   -3.49 1.25e+00 6.40e-01 7.81e+00
  angle pdb=" C   VAL R  87 "
        pdb=" CA  VAL R  87 "
        pdb=" CB  VAL R  87 "
      ideal   model   delta    sigma   weight residual
     114.00  110.43    3.57 1.31e+00 5.83e-01 7.45e+00
  angle pdb=" C   VAL R 210 "
        pdb=" CA  VAL R 210 "
        pdb=" CB  VAL R 210 "
      ideal   model   delta    sigma   weight residual
     114.00  110.89    3.11 1.31e+00 5.83e-01 5.64e+00
  angle pdb=" N   ASN R  69 "
        pdb=" CA  ASN R  69 "
        pdb=" C   ASN R  69 "
      ideal   model   delta    sigma   weight residual
     113.72  110.58    3.14 1.52e+00 4.33e-01 4.27e+00
  ... (remaining 7683 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.95: 3028
       19.95 -    39.91: 60
       39.91 -    59.86: 13
       59.86 -    79.82: 1
       79.82 -    99.77: 3
  Dihedral angle restraints: 3105
    sinusoidal: 386
      harmonic: 2719
  Sorted by residual:
  dihedral pdb=" CAG G1I R 501 "
           pdb=" CAH G1I R 501 "
           pdb=" CAI G1I R 501 "
           pdb=" CAJ G1I R 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -66.05   33.72  -99.77     1      3.00e+01 1.11e-03 1.25e+01
  dihedral pdb=" CAE G1I R 501 "
           pdb=" CAG G1I R 501 "
           pdb=" CAH G1I R 501 "
           pdb=" CAI G1I R 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.24  -51.60   98.84     1      3.00e+01 1.11e-03 1.23e+01
  dihedral pdb=" CA  TYR A 360 "
           pdb=" C   TYR A 360 "
           pdb=" N   PRO A 361 "
           pdb=" CA  PRO A 361 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.66  -17.34     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 3102 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 595
       0.028 -    0.057: 219
       0.057 -    0.085: 75
       0.085 -    0.114: 48
       0.114 -    0.142: 6
  Chirality restraints: 943
  Sorted by residual:
  chirality pdb=" CG  LEU B  51 "
            pdb=" CB  LEU B  51 "
            pdb=" CD1 LEU B  51 "
            pdb=" CD2 LEU B  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.73    0.14 2.00e-01 2.50e+01 5.03e-01
  chirality pdb=" CA  ILE B  81 "
            pdb=" N   ILE B  81 "
            pdb=" C   ILE B  81 "
            pdb=" CB  ILE B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.97e-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   -0.12 2.00e-01 2.50e+01 3.90e-01
  ... (remaining 940 not shown)

  Planarity restraints: 1037
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 331 "   -0.018 5.00e-02 4.00e+02   2.69e-02 1.16e+00
        pdb=" N   PRO A 332 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 332 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 332 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 151 "   -0.008 2.00e-02 2.50e+03   7.37e-03 9.52e-01
        pdb=" CG  PHE B 151 "    0.017 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 151 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 151 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 151 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 151 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 151 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.014 5.00e-02 4.00e+02   2.15e-02 7.42e-01
        pdb=" N   PRO B 236 "   -0.037 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.012 5.00e-02 4.00e+02
  ... (remaining 1034 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1016
        2.76 -     3.30: 5365
        3.30 -     3.83: 8575
        3.83 -     4.37: 8541
        4.37 -     4.90: 14877
  Nonbonded interactions: 38374
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   CYS A 237 "
            pdb=" OH  TYR B  59 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" O   ASN B 155 "
            pdb=" N   ILE B 171 "
     model   vdw
     2.347 3.120
  nonbonded pdb=" O   HIS G  44 "
            pdb=" ND1 HIS G  44 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" OG  SER B 331 "
            pdb=" O   PHE B 335 "
     model   vdw
     2.374 3.040
  ... (remaining 38369 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.550
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
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   0.077   5551  Z= 0.199
  Angle     :  0.543   5.909   7688  Z= 0.333
  Chirality :  0.039   0.142    943
  Planarity :  0.002   0.027   1037
  Dihedral  : 10.593  99.771   1327
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.29), residues: 902
  helix:  2.48 (0.27), residues: 378
  sheet:  0.29 (0.47), residues: 135
  loop : -1.04 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 339 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.017   0.001   PHE B 151 
 TYR   0.007   0.001   TYR A 253 
 ARG   0.001   0.000   ARG B  22 

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.604 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0914
  time to fit residues: 7.2728
Evaluate side-chains
  42 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 46 optimal weight:    9.9990
   chunk 36 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   chunk 27 optimal weight:    9.9990
   chunk 43 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3282 r_free = 0.3282 target = 0.072525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.064060 restraints weight = 30312.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.065079 restraints weight = 20042.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.065803 restraints weight = 14679.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   5551  Z= 0.158
  Angle     :  0.462   8.939   7688  Z= 0.258
  Chirality :  0.041   0.163    943
  Planarity :  0.003   0.027   1037
  Dihedral  :  4.773  40.756    965
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  6.67 %
    Favored  : 92.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.29), residues: 902
  helix:  2.46 (0.25), residues: 414
  sheet: -0.33 (0.43), residues: 152
  loop : -1.09 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 313 
 HIS   0.002   0.001   HIS R 296 
 PHE   0.020   0.002   PHE B 151 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.003   0.000   ARG B 137 

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.541 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 47
  average time/residue: 0.0937
  time to fit residues: 7.5662
Evaluate side-chains
  43 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0050
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    2.9990
   chunk 48 optimal weight:   10.0000
   chunk 78 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    1.7398

-------------------------------------------------------------------------------
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 = 0.3260 r_free = 0.3260 target = 0.071612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.063148 restraints weight = 30777.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.064175 restraints weight = 20296.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.064904 restraints weight = 14799.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5551  Z= 0.199
  Angle     :  0.449   5.324   7688  Z= 0.259
  Chirality :  0.041   0.169    943
  Planarity :  0.003   0.025   1037
  Dihedral  :  4.208  38.400    965
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.29), residues: 902
  helix:  2.75 (0.26), residues: 403
  sheet: -0.22 (0.45), residues: 142
  loop : -1.19 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.008   0.002   HIS B 183 
 PHE   0.024   0.002   PHE B 151 
 TYR   0.013   0.001   TYR R 199 
 ARG   0.001   0.000   ARG B 137 

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.567 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0863
  time to fit residues: 7.1067
Evaluate side-chains
  40 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    7.9990
   chunk 36 optimal weight:    7.9990
   chunk 76 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 18 optimal weight:    0.6980
   chunk 87 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0070
   chunk 44 optimal weight:   20.0000
   overall best weight:    2.1002

-------------------------------------------------------------------------------
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 = 0.3234 r_free = 0.3234 target = 0.070729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.062360 restraints weight = 31958.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.063417 restraints weight = 21052.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.064029 restraints weight = 15166.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.1935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5551  Z= 0.230
  Angle     :  0.467   5.436   7688  Z= 0.269
  Chirality :  0.042   0.198    943
  Planarity :  0.003   0.024   1037
  Dihedral  :  4.212  39.119    965
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.29), residues: 902
  helix:  2.79 (0.26), residues: 403
  sheet: -0.29 (0.46), residues: 127
  loop : -1.38 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.025   0.002   PHE B 151 
 TYR   0.013   0.001   TYR R 199 
 ARG   0.002   0.000   ARG B 137 

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.618 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0826
  time to fit residues: 6.5592
Evaluate side-chains
  40 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 54 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 31 optimal weight:    0.5980
   chunk 83 optimal weight:    7.9990
   chunk 11 optimal weight:   20.0000
   chunk 37 optimal weight:    0.9990
   overall best weight:    2.1186

-------------------------------------------------------------------------------
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 = 0.3228 r_free = 0.3228 target = 0.070498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.062161 restraints weight = 31314.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.063141 restraints weight = 20800.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.063600 restraints weight = 15205.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5551  Z= 0.232
  Angle     :  0.463   5.470   7688  Z= 0.267
  Chirality :  0.041   0.162    943
  Planarity :  0.003   0.024   1037
  Dihedral  :  4.316  39.636    965
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  4.44 %
    Favored  : 95.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.29), residues: 902
  helix:  2.81 (0.26), residues: 405
  sheet: -0.60 (0.44), residues: 140
  loop : -1.40 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.026   0.002   PHE B 151 
 TYR   0.013   0.001   TYR R 199 
 ARG   0.001   0.000   ARG B  22 

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.569 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 45
  average time/residue: 0.0824
  time to fit residues: 6.4896
Evaluate side-chains
  39 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 79 optimal weight:    9.9990
   chunk 37 optimal weight:    0.3980
   chunk 39 optimal weight:    0.7980
   chunk 42 optimal weight:    0.6980
   chunk 59 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   chunk 48 optimal weight:    8.9990
   chunk 32 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3268 r_free = 0.3268 target = 0.072433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.064056 restraints weight = 31078.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.065024 restraints weight = 20437.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.065737 restraints weight = 15064.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5551  Z= 0.124
  Angle     :  0.414   5.330   7688  Z= 0.233
  Chirality :  0.041   0.221    943
  Planarity :  0.002   0.021   1037
  Dihedral  :  3.858  35.635    965
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.29), residues: 902
  helix:  3.01 (0.26), residues: 404
  sheet: -0.64 (0.44), residues: 141
  loop : -1.23 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.006   0.001   HIS B 183 
 PHE   0.018   0.001   PHE B 151 
 TYR   0.008   0.001   TYR R 199 
 ARG   0.001   0.000   ARG B 137 

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.642 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0861
  time to fit residues: 7.4899
Evaluate side-chains
  40 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 87 optimal weight:    5.9990
   chunk 31 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 70 optimal weight:    0.6980
   chunk 72 optimal weight:    8.9990
   chunk 82 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** R 296 HIS ** 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 = 0.3267 r_free = 0.3267 target = 0.072223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.063797 restraints weight = 31228.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.064874 restraints weight = 20608.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.065465 restraints weight = 15027.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5551  Z= 0.139
  Angle     :  0.412   5.795   7688  Z= 0.230
  Chirality :  0.041   0.208    943
  Planarity :  0.002   0.021   1037
  Dihedral  :  3.750  34.223    965
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.29), residues: 902
  helix:  3.09 (0.26), residues: 405
  sheet: -0.68 (0.44), residues: 141
  loop : -1.23 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.019   0.001   PHE B 151 
 TYR   0.009   0.001   TYR R 199 
 ARG   0.001   0.000   ARG B 137 

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.577 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0842
  time to fit residues: 6.6594
Evaluate side-chains
  38 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 36 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   chunk 79 optimal weight:    9.9990
   chunk 88 optimal weight:    2.9990
   chunk 80 optimal weight:    0.4980
   chunk 26 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 37 optimal weight:    0.3980
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
** G  59 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 = 0.3239 r_free = 0.3239 target = 0.071124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.062754 restraints weight = 31139.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.063832 restraints weight = 20647.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.064378 restraints weight = 15124.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5551  Z= 0.201
  Angle     :  0.450   5.776   7688  Z= 0.255
  Chirality :  0.041   0.220    943
  Planarity :  0.002   0.022   1037
  Dihedral  :  4.024  36.847    965
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.29), residues: 902
  helix:  3.03 (0.26), residues: 404
  sheet: -0.74 (0.44), residues: 141
  loop : -1.30 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.024   0.002   PHE B 151 
 TYR   0.013   0.001   TYR R 199 
 ARG   0.001   0.000   ARG A 342 

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.640 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0858
  time to fit residues: 6.9809
Evaluate side-chains
  38 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 7 optimal weight:   20.0000
   chunk 15 optimal weight:   10.0000
   chunk 36 optimal weight:    8.9990
   chunk 85 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 83 optimal weight:    7.9990
   chunk 60 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** G  59 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 = 0.3222 r_free = 0.3222 target = 0.070330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.061962 restraints weight = 31611.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.062690 restraints weight = 21059.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.063506 restraints weight = 15977.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5551  Z= 0.259
  Angle     :  0.490   5.729   7688  Z= 0.283
  Chirality :  0.042   0.256    943
  Planarity :  0.003   0.023   1037
  Dihedral  :  4.273  37.783    965
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.29), residues: 902
  helix:  2.80 (0.26), residues: 410
  sheet: -0.75 (0.47), residues: 127
  loop : -1.63 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 105 
 HIS   0.013   0.002   HIS B  54 
 PHE   0.027   0.002   PHE B 151 
 TYR   0.019   0.001   TYR R 199 
 ARG   0.001   0.000   ARG B  22 

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.558 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.0830
  time to fit residues: 6.3191
Evaluate side-chains
  37 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 42 optimal weight:    0.8980
   chunk 5 optimal weight:   20.0000
   chunk 83 optimal weight:    4.9990
   chunk 37 optimal weight:   10.0000
   chunk 71 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:   20.0000
   chunk 47 optimal weight:    0.5980
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** G  59 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 = 0.3244 r_free = 0.3244 target = 0.071179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.062821 restraints weight = 31678.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.063899 restraints weight = 21116.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.064463 restraints weight = 15389.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   5551  Z= 0.167
  Angle     :  0.431   5.398   7688  Z= 0.244
  Chirality :  0.041   0.217    943
  Planarity :  0.002   0.022   1037
  Dihedral  :  4.024  36.415    965
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.29), residues: 902
  helix:  3.03 (0.26), residues: 399
  sheet: -0.99 (0.46), residues: 134
  loop : -1.41 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 105 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.023   0.002   PHE B 151 
 TYR   0.015   0.001   TYR R 199 
 ARG   0.001   0.000   ARG B  22 

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.632 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0816
  time to fit residues: 6.0756
Evaluate side-chains
  36 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 74 optimal weight:    0.1980
   chunk 29 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 67 optimal weight:    9.9990
   chunk 44 optimal weight:   20.0000
   chunk 64 optimal weight:    0.7980
   chunk 37 optimal weight:    9.9990
   chunk 84 optimal weight:    0.8980
   chunk 11 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
** G  59 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 = 0.3249 r_free = 0.3249 target = 0.071486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.063194 restraints weight = 31473.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.064258 restraints weight = 20755.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.064858 restraints weight = 15005.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5551  Z= 0.166
  Angle     :  0.426   5.364   7688  Z= 0.241
  Chirality :  0.041   0.203    943
  Planarity :  0.002   0.022   1037
  Dihedral  :  3.875  35.099    965
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.29), residues: 902
  helix:  3.15 (0.26), residues: 400
  sheet: -1.06 (0.44), residues: 147
  loop : -1.38 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.022   0.001   PHE B 151 
 TYR   0.013   0.001   TYR R 199 
 ARG   0.001   0.000   ARG B  22 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1534.03 seconds
wall clock time: 27 minutes 6.93 seconds (1626.93 seconds total)