Starting phenix.real_space_refine
on Tue Mar 11 14:29:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8geh_29970/03_2025/8geh_29970.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8geh_29970/03_2025/8geh_29970.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8geh_29970/03_2025/8geh_29970.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8geh_29970/03_2025/8geh_29970.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8geh_29970/03_2025/8geh_29970.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8geh_29970/03_2025/8geh_29970.cif"
  }
  resolution = 4.0
  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=   0.021
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      11      5.16       5
     C    3853      2.51       5
     N    1069      2.21       5
     O    1062      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: 5995
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 1812
          Classifications: {'peptide': 301}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 198}
          Link IDs: {'PTRANS': 8, 'TRANS': 292}
          Chain breaks: 8
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 714
          Unresolved non-hydrogen angles: 889
          Unresolved non-hydrogen dihedrals: 578
          Unresolved non-hydrogen chiralities: 44
          Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 19, 'PHE:plan': 5, 'GLU:plan': 23, 'ARG:plan': 20}
          Unresolved non-hydrogen planarities: 438
    Chain: "B"
      Number of atoms: 2133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2133
          Classifications: {'peptide': 331}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 135}
          Link IDs: {'PTRANS': 5, 'TRANS': 325}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 408
          Unresolved non-hydrogen angles: 509
          Unresolved non-hydrogen dihedrals: 309
          Unresolved non-hydrogen chiralities: 33
          Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 24, 'ASN:plan1': 12, 'HIS:plan': 1, 'ASN%COO:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 12}
          Unresolved non-hydrogen planarities: 244
    Chain: "G"
      Number of atoms: 312
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 312
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 42
    Chain: "R"
      Number of atoms: 1723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 1723
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 160}
          Link IDs: {'PTRANS': 7, 'TRANS': 270}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 521
          Unresolved non-hydrogen angles: 664
          Unresolved non-hydrogen dihedrals: 409
          Unresolved non-hydrogen chiralities: 71
          Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 236
    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: 5.67, per 1000 atoms: 0.95
  Number of scatterers: 5995
  At special positions: 0
  Unit cell: (68.9, 98.58, 128.26, 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      11     16.00
     O    1062      8.00
     N    1069      7.00
     C    3853      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: 1.66
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1826

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 8 sheets defined
      50.1% alpha, 14.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 40
      removed outlier: 3.551A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 51
    Processing helix  chain 'A' and resid 52 through 61
      removed outlier: 4.009A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 114
    Processing helix  chain 'A' and resid 125 through 133
    Processing helix  chain 'A' and resid 144 through 148
    Processing helix  chain 'A' and resid 174 through 181
    Processing helix  chain 'A' and resid 195 through 200
    Processing helix  chain 'A' and resid 233 through 238
      removed outlier: 3.850A  pdb=" N   CYS A 237 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   PHE A 238 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 233 through 238'
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.907A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 4.429A  pdb=" N   ARG A 317 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.757A  pdb=" N   ALA A 337 " --> pdb=" O   ARG A 333 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 390
    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 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 14 through 24
      removed outlier: 3.591A  pdb=" N   GLU G  22 " --> pdb=" O   GLN G  18 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA G  23 " --> pdb=" O   LEU G  19 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 32 through 61
      removed outlier: 3.634A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   VAL R  54 " --> pdb=" O   GLY R  50 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 86
      removed outlier: 4.158A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   THR R  73 " --> pdb=" O   ASN R  69 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   SER R  74 " --> pdb=" O   TYR R  70 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 86 through 97
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 3.654A  pdb=" N   VAL R 117 " --> pdb=" O   ASP R 113 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 163
    Processing helix  chain 'R' and resid 165 through 172
      removed outlier: 3.892A  pdb=" N   ILE R 169 " --> pdb=" O   SER R 165 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 181 through 187
      removed outlier: 3.963A  pdb=" N   TYR R 185 " --> pdb=" O   ALA R 181 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA R 186 " --> pdb=" O   ILE R 182 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.597A  pdb=" N   ILE R 201 " --> pdb=" O   GLN R 197 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 236
      removed outlier: 3.615A  pdb=" N   SER R 236 " --> pdb=" O   LYS R 232 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 270 through 293
      removed outlier: 3.523A  pdb=" N   ILE R 277 " --> pdb=" O   LYS R 273 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ILE R 278 " --> pdb=" O   THR R 274 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TRP R 286 " --> pdb=" O   PHE R 282 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
    Processing helix  chain 'R' and resid 294 through 299
      removed outlier: 4.271A  pdb=" N   ILE R 298 " --> pdb=" O   ILE R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 326
      removed outlier: 3.631A  pdb=" N   ILE R 309 " --> pdb=" O   LYS R 305 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 3.768A  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 209 through 212
      removed outlier: 5.744A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU A  44 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.808A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.200A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ILE B  80 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.776A  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: 6.350A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.209A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.821A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.412A  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: 6.657A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.625A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU B 210 " --> pdb=" O   GLN B 220 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.336A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.312A  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 278
      removed outlier: 5.692A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    373 hydrogen bonds defined for protein.
    1089 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.05

  Time building geometry restraints manager: 1.93 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: 2024
        1.34 -     1.46: 1381
        1.46 -     1.57: 2692
        1.57 -     1.69: 0
        1.69 -     1.81: 14
  Bond restraints: 6111
  Sorted by residual:
  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 6.99e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.572 -0.049 2.00e-02 2.50e+03 6.10e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.442 -0.048 2.00e-02 2.50e+03 5.72e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 2.00e-02 2.50e+03 4.91e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" NAN G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.451  1.487 -0.036 2.00e-02 2.50e+03 3.30e+00
  ... (remaining 6106 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.09: 8216
        1.09 -     2.17: 175
        2.17 -     3.26: 28
        3.26 -     4.34: 10
        4.34 -     5.43: 7
  Bond angle restraints: 8436
  Sorted by residual:
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     113.20  109.44    3.76 9.60e-01 1.09e+00 1.53e+01
  angle pdb=" N   GLY B 202 "
        pdb=" CA  GLY B 202 "
        pdb=" C   GLY B 202 "
      ideal   model   delta    sigma   weight residual
     111.46  114.89   -3.43 1.75e+00 3.27e-01 3.83e+00
  angle pdb=" C   VAL A 214 "
        pdb=" N   ASP A 215 "
        pdb=" CA  ASP A 215 "
      ideal   model   delta    sigma   weight residual
     121.54  125.12   -3.58 1.91e+00 2.74e-01 3.51e+00
  angle pdb=" CAG G1I R 501 "
        pdb=" CAH G1I R 501 "
        pdb=" CAI G1I R 501 "
      ideal   model   delta    sigma   weight residual
     110.89  116.32   -5.43 3.00e+00 1.11e-01 3.27e+00
  angle pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
        pdb=" N   CYS B 271 "
      ideal   model   delta    sigma   weight residual
     118.71  116.64    2.07 1.15e+00 7.56e-01 3.24e+00
  ... (remaining 8431 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.91: 3159
       10.91 -    21.82: 157
       21.82 -    32.74: 77
       32.74 -    43.65: 36
       43.65 -    54.56: 9
  Dihedral angle restraints: 3438
    sinusoidal: 644
      harmonic: 2794
  Sorted by residual:
  dihedral pdb=" CA  HIS B 183 "
           pdb=" C   HIS B 183 "
           pdb=" N   THR B 184 "
           pdb=" CA  THR B 184 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.10  -15.90     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CA  ARG A 380 "
           pdb=" CB  ARG A 380 "
           pdb=" CG  ARG A 380 "
           pdb=" CD  ARG A 380 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -109.66   49.66     3      1.50e+01 4.44e-03 8.80e+00
  dihedral pdb=" CA  ARG B  49 "
           pdb=" CB  ARG B  49 "
           pdb=" CG  ARG B  49 "
           pdb=" CD  ARG B  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  132.13   47.87     3      1.50e+01 4.44e-03 8.56e+00
  ... (remaining 3435 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 730
       0.034 -    0.068: 233
       0.068 -    0.102: 68
       0.102 -    0.136: 18
       0.136 -    0.171: 2
  Chirality restraints: 1051
  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    2.57   -0.17 2.00e-01 2.50e+01 7.27e-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    2.57   -0.14 2.00e-01 2.50e+01 4.82e-01
  chirality pdb=" CA  ILE B 157 "
            pdb=" N   ILE B 157 "
            pdb=" C   ILE B 157 "
            pdb=" CB  ILE B 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.65e-01
  ... (remaining 1048 not shown)

  Planarity restraints: 1096
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 167 "   -0.021 5.00e-02 4.00e+02   3.25e-02 1.69e+00
        pdb=" N   PRO R 168 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO R 168 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO R 168 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.017 5.00e-02 4.00e+02   2.57e-02 1.05e+00
        pdb=" N   PRO B 236 "   -0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B  87 "    0.005 2.00e-02 2.50e+03   1.00e-02 1.00e+00
        pdb=" C   THR B  87 "   -0.017 2.00e-02 2.50e+03
        pdb=" O   THR B  87 "    0.006 2.00e-02 2.50e+03
        pdb=" N   ASN B  88 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1093 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1650
        2.80 -     3.33: 5824
        3.33 -     3.85: 9406
        3.85 -     4.38: 9766
        4.38 -     4.90: 17270
  Nonbonded interactions: 43916
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 282 "
            pdb=" NE2 HIS A 357 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" ND1 HIS B 142 "
            pdb=" OG  SER B 161 "
     model   vdw
     2.331 3.120
  nonbonded pdb=" NE1 TRP A 277 "
            pdb=" O   SER A 349 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" NH2 ARG B  49 "
            pdb=" O   PHE G  61 "
     model   vdw
     2.357 3.120
  ... (remaining 43911 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:             1.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     21.330
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
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   0.053   6111  Z= 0.181
  Angle     :  0.433   5.428   8436  Z= 0.241
  Chirality :  0.039   0.171   1051
  Planarity :  0.002   0.032   1096
  Dihedral  : 10.847  54.562   1612
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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:  1.54 (0.28), residues: 930
  helix:  2.42 (0.24), residues: 415
  sheet:  0.67 (0.44), residues: 163
  loop : -0.52 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 297 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.014   0.001   TYR R 141 
 ARG   0.004   0.000   ARG A 385 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.692 
Fit side-chains
REVERT: A  380 ARG cc_start: 0.8813 (tmm-80) cc_final: 0.8369 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1488
  time to fit residues: 12.6339
Evaluate side-chains
  44 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 80 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 74 optimal weight:   10.0000
   chunk 28 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 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 = 0.3346 r_free = 0.3346 target = 0.084243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.072966 restraints weight = 22069.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.074425 restraints weight = 13372.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.075158 restraints weight = 9289.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6111  Z= 0.217
  Angle     :  0.451   4.906   8436  Z= 0.260
  Chirality :  0.040   0.145   1051
  Planarity :  0.003   0.030   1096
  Dihedral  :  3.792  15.151   1000
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 10.06 %
    Favored  : 89.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.90 (0.28), residues: 930
  helix:  2.81 (0.24), residues: 429
  sheet:  0.50 (0.42), residues: 180
  loop : -0.46 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 297 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.015   0.001   TYR R 199 
 ARG   0.003   0.000   ARG A 385 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.683 
Fit side-chains
REVERT: A  380 ARG cc_start: 0.8768 (tmm-80) cc_final: 0.8325 (ttm170)
REVERT: B   17 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8466 (tm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 48
  average time/residue: 0.1140
  time to fit residues: 8.7218
Evaluate side-chains
  45 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 66 optimal weight:    0.0170
   chunk 84 optimal weight:    0.4980
   chunk 31 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0980
   chunk 1 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 42 optimal weight:    9.9990
   chunk 81 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.5220

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 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 = 0.3386 r_free = 0.3386 target = 0.086449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.075132 restraints weight = 21844.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.076612 restraints weight = 13085.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.077615 restraints weight = 9000.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6111  Z= 0.120
  Angle     :  0.386   4.960   8436  Z= 0.218
  Chirality :  0.039   0.140   1051
  Planarity :  0.003   0.030   1096
  Dihedral  :  3.469  17.533   1000
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 15.09 %
    Favored  : 84.28 %
  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:  2.20 (0.28), residues: 930
  helix:  3.13 (0.24), residues: 428
  sheet:  0.79 (0.42), residues: 169
  loop : -0.46 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 297 
 HIS   0.002   0.001   HIS B  54 
 PHE   0.006   0.001   PHE B 199 
 TYR   0.013   0.001   TYR R 199 
 ARG   0.002   0.000   ARG A 385 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.685 
Fit side-chains
REVERT: A  380 ARG cc_start: 0.8697 (tmm-80) cc_final: 0.8156 (ttt90)
REVERT: B   17 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8477 (tm-30)
REVERT: R   82 MET cc_start: 0.8106 (tmm) cc_final: 0.7890 (tmm)
REVERT: R  141 TYR cc_start: 0.7339 (t80) cc_final: 0.7080 (t80)
REVERT: R  199 TYR cc_start: 0.8725 (t80) cc_final: 0.8384 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 57
  average time/residue: 0.1277
  time to fit residues: 10.9437
Evaluate side-chains
  48 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 63 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 88 optimal weight:   10.0000
   chunk 83 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 82 optimal weight:    6.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 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 = 0.3330 r_free = 0.3330 target = 0.083637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.072123 restraints weight = 22617.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.073593 restraints weight = 13776.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.074674 restraints weight = 9554.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6111  Z= 0.226
  Angle     :  0.437   5.260   8436  Z= 0.248
  Chirality :  0.039   0.150   1051
  Planarity :  0.003   0.028   1096
  Dihedral  :  3.736  17.270   1000
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 16.67 %
    Favored  : 81.45 %
  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:  2.13 (0.29), residues: 930
  helix:  3.16 (0.25), residues: 431
  sheet:  0.39 (0.41), residues: 180
  loop : -0.46 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 297 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.015   0.001   TYR R 199 
 ARG   0.004   0.000   ARG A 385 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.691 
Fit side-chains
REVERT: A  380 ARG cc_start: 0.8757 (tmm-80) cc_final: 0.8504 (tmm-80)
REVERT: A  381 ASP cc_start: 0.9083 (m-30) cc_final: 0.8529 (m-30)
REVERT: A  385 ARG cc_start: 0.8473 (mtt90) cc_final: 0.7791 (mtt90)
REVERT: R  141 TYR cc_start: 0.7639 (t80) cc_final: 0.7380 (t80)
  outliers start: 6
  outliers final: 5
  residues processed: 50
  average time/residue: 0.1297
  time to fit residues: 9.8708
Evaluate side-chains
  49 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 46 optimal weight:    6.9990
   chunk 73 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 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 = 0.3353 r_free = 0.3353 target = 0.084766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.073320 restraints weight = 22130.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.074738 restraints weight = 13362.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.075896 restraints weight = 9297.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6111  Z= 0.153
  Angle     :  0.394   5.094   8436  Z= 0.224
  Chirality :  0.038   0.140   1051
  Planarity :  0.002   0.028   1096
  Dihedral  :  3.536  17.640   1000
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 19.50 %
    Favored  : 78.62 %
  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:  2.24 (0.29), residues: 930
  helix:  3.23 (0.25), residues: 431
  sheet:  0.42 (0.41), residues: 178
  loop : -0.35 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 297 
 HIS   0.002   0.001   HIS B 183 
 PHE   0.009   0.001   PHE B 199 
 TYR   0.016   0.001   TYR R 199 
 ARG   0.002   0.000   ARG A 385 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.630 
Fit side-chains
REVERT: A  380 ARG cc_start: 0.8723 (tmm-80) cc_final: 0.8190 (ttt90)
REVERT: A  385 ARG cc_start: 0.8461 (mtt90) cc_final: 0.7797 (mtt90)
REVERT: B  273 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8546 (mp)
REVERT: R  141 TYR cc_start: 0.7604 (t80) cc_final: 0.7267 (t80)
  outliers start: 6
  outliers final: 3
  residues processed: 47
  average time/residue: 0.1245
  time to fit residues: 8.9436
Evaluate side-chains
  46 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 88 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 93 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0870
   chunk 9 optimal weight:   20.0000
   chunk 81 optimal weight:    7.9990
   chunk 84 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.9760

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 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 = 0.3348 r_free = 0.3348 target = 0.084523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.073069 restraints weight = 21729.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.074517 restraints weight = 13316.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.075392 restraints weight = 9281.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6111  Z= 0.161
  Angle     :  0.400   5.115   8436  Z= 0.225
  Chirality :  0.039   0.142   1051
  Planarity :  0.002   0.028   1096
  Dihedral  :  3.530  16.859   1000
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 18.55 %
    Favored  : 77.99 %
  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:  2.25 (0.29), residues: 930
  helix:  3.27 (0.25), residues: 431
  sheet:  0.33 (0.40), residues: 178
  loop : -0.35 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 297 
 HIS   0.002   0.001   HIS R  93 
 PHE   0.009   0.001   PHE B 199 
 TYR   0.016   0.001   TYR R 199 
 ARG   0.001   0.000   ARG B 256 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.656 
Fit side-chains
REVERT: A  380 ARG cc_start: 0.8732 (tmm-80) cc_final: 0.8206 (ttt90)
REVERT: A  385 ARG cc_start: 0.8450 (mtt90) cc_final: 0.7825 (mtt90)
REVERT: B  273 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8564 (mp)
REVERT: R  141 TYR cc_start: 0.7644 (t80) cc_final: 0.7325 (t80)
  outliers start: 11
  outliers final: 4
  residues processed: 55
  average time/residue: 0.1213
  time to fit residues: 10.3447
Evaluate side-chains
  48 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 87 optimal weight:    9.9990
   chunk 62 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 92 optimal weight:    3.9990
   chunk 80 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9990
   chunk 23 optimal weight:    8.9990
   chunk 72 optimal weight:    0.8980
   chunk 86 optimal weight:    0.7980
   chunk 4 optimal weight:    0.2980
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 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 = 0.3362 r_free = 0.3362 target = 0.085243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.073802 restraints weight = 22013.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.075244 restraints weight = 13282.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.076339 restraints weight = 9212.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6111  Z= 0.139
  Angle     :  0.426   9.177   8436  Z= 0.228
  Chirality :  0.039   0.137   1051
  Planarity :  0.002   0.028   1096
  Dihedral  :  3.447  16.825   1000
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 20.13 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.30 (0.29), residues: 930
  helix:  3.31 (0.25), residues: 431
  sheet:  0.46 (0.40), residues: 174
  loop : -0.37 (0.35), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP B 297 
 HIS   0.002   0.001   HIS R  93 
 PHE   0.009   0.001   PHE B 199 
 TYR   0.014   0.001   TYR R 199 
 ARG   0.001   0.000   ARG B 283 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A  380 ARG cc_start: 0.8731 (tmm-80) cc_final: 0.8222 (ttt90)
REVERT: A  385 ARG cc_start: 0.8496 (mtt90) cc_final: 0.8052 (mtt90)
REVERT: B  273 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8568 (mp)
REVERT: R  141 TYR cc_start: 0.7693 (t80) cc_final: 0.7319 (t80)
  outliers start: 8
  outliers final: 4
  residues processed: 53
  average time/residue: 0.1249
  time to fit residues: 10.0293
Evaluate side-chains
  48 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 70 optimal weight:    8.9990
   chunk 13 optimal weight:    8.9990
   chunk 27 optimal weight:    0.2980
   chunk 57 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 73 optimal weight:    0.6980
   chunk 40 optimal weight:    7.9990
   chunk 46 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9980
   chunk 83 optimal weight:    9.9990
   overall best weight:    1.5984

-------------------------------------------------------------------------------
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 = 0.3326 r_free = 0.3326 target = 0.083531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.071909 restraints weight = 22441.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.073323 restraints weight = 13709.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.074154 restraints weight = 9583.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6111  Z= 0.238
  Angle     :  0.466   9.004   8436  Z= 0.254
  Chirality :  0.039   0.145   1051
  Planarity :  0.003   0.027   1096
  Dihedral  :  3.735  16.991   1000
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 21.38 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.09 (0.29), residues: 930
  helix:  3.24 (0.25), residues: 433
  sheet:  0.10 (0.39), residues: 180
  loop : -0.52 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP B 297 
 HIS   0.002   0.001   HIS R  93 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.019   0.001   TYR B 264 
 ARG   0.001   0.000   ARG B 256 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.716 
Fit side-chains
REVERT: A  380 ARG cc_start: 0.8783 (tmm-80) cc_final: 0.8265 (ttt90)
REVERT: A  385 ARG cc_start: 0.8467 (mtt90) cc_final: 0.7977 (mtt90)
REVERT: B  273 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8583 (mp)
  outliers start: 8
  outliers final: 5
  residues processed: 50
  average time/residue: 0.1284
  time to fit residues: 9.8516
Evaluate side-chains
  48 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain R residue  281 THR
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 89 optimal weight:    4.9990
   chunk 21 optimal weight:    8.9990
   chunk 55 optimal weight:    4.9990
   chunk 5 optimal weight:    7.9990
   chunk 85 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 12 optimal weight:    8.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3345 r_free = 0.3345 target = 0.084642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.073309 restraints weight = 21850.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.074698 restraints weight = 13099.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.075827 restraints weight = 9146.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6111  Z= 0.176
  Angle     :  0.439   9.034   8436  Z= 0.238
  Chirality :  0.039   0.140   1051
  Planarity :  0.003   0.027   1096
  Dihedral  :  3.636  18.576   1000
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 22.64 %
    Favored  : 75.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.11 (0.29), residues: 930
  helix:  3.23 (0.25), residues: 433
  sheet:  0.12 (0.39), residues: 178
  loop : -0.45 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP B 297 
 HIS   0.002   0.001   HIS R  93 
 PHE   0.010   0.001   PHE B 199 
 TYR   0.015   0.001   TYR R 199 
 ARG   0.001   0.000   ARG B 256 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.679 
Fit side-chains
REVERT: A  380 ARG cc_start: 0.8752 (tmm-80) cc_final: 0.8254 (ttt90)
REVERT: A  385 ARG cc_start: 0.8483 (mtt90) cc_final: 0.8004 (mtt90)
REVERT: B  273 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8629 (mp)
  outliers start: 6
  outliers final: 5
  residues processed: 47
  average time/residue: 0.1271
  time to fit residues: 9.2364
Evaluate side-chains
  48 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0980
   chunk 85 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0060
   chunk 36 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 40 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0030
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.3606

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 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 = 0.3387 r_free = 0.3387 target = 0.086612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.075188 restraints weight = 21806.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.076724 restraints weight = 13224.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.077831 restraints weight = 9142.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.018   6111  Z= 0.105
  Angle     :  0.409   8.991   8436  Z= 0.219
  Chirality :  0.038   0.139   1051
  Planarity :  0.002   0.027   1096
  Dihedral  :  3.330  16.628   1000
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 22.64 %
    Favored  : 75.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.26 (0.29), residues: 930
  helix:  3.38 (0.25), residues: 431
  sheet:  0.32 (0.39), residues: 174
  loop : -0.48 (0.35), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 313 
 HIS   0.002   0.000   HIS B 183 
 PHE   0.008   0.001   PHE B 241 
 TYR   0.010   0.001   TYR R 199 
 ARG   0.001   0.000   ARG B  68 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.675 
Fit side-chains
REVERT: A  380 ARG cc_start: 0.8702 (tmm-80) cc_final: 0.8199 (ttt90)
REVERT: A  385 ARG cc_start: 0.8455 (mtt90) cc_final: 0.7992 (mtt90)
REVERT: B  273 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8650 (mp)
  outliers start: 6
  outliers final: 3
  residues processed: 56
  average time/residue: 0.1254
  time to fit residues: 10.5696
Evaluate side-chains
  50 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain R residue  297 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 86 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 34 optimal weight:   10.0000
   chunk 81 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 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 = 0.3370 r_free = 0.3370 target = 0.085699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.074202 restraints weight = 22255.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.075687 restraints weight = 13433.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.076812 restraints weight = 9271.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6111  Z= 0.147
  Angle     :  0.440   8.751   8436  Z= 0.230
  Chirality :  0.040   0.175   1051
  Planarity :  0.002   0.027   1096
  Dihedral  :  3.362  14.158   1000
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 23.27 %
    Favored  : 75.16 %
  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:  2.25 (0.29), residues: 930
  helix:  3.36 (0.25), residues: 433
  sheet:  0.30 (0.40), residues: 174
  loop : -0.47 (0.35), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 297 
 HIS   0.004   0.001   HIS A 387 
 PHE   0.009   0.001   PHE B 199 
 TYR   0.015   0.001   TYR B 111 
 ARG   0.002   0.000   ARG A 389 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1678.62 seconds
wall clock time: 30 minutes 6.05 seconds (1806.05 seconds total)