Starting phenix.real_space_refine
on Thu Jun  5 12:42:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8geb_29964/06_2025/8geb_29964.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8geb_29964/06_2025/8geb_29964.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8geb_29964/06_2025/8geb_29964.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8geb_29964/06_2025/8geb_29964.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8geb_29964/06_2025/8geb_29964.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8geb_29964/06_2025/8geb_29964.cif"
  }
  resolution = 3.6
  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=   0.028
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      36      5.16       5
     C    4017      2.51       5
     N    1091      2.21       5
     O    1079      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6223
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1650
          Classifications: {'peptide': 233}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 79}
          Link IDs: {'PTRANS': 6, 'TRANS': 226}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 299
          Unresolved non-hydrogen angles: 364
          Unresolved non-hydrogen dihedrals: 238
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 12}
          Unresolved non-hydrogen planarities: 198
    Chain: "B"
      Number of atoms: 2301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2301
          Classifications: {'peptide': 329}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 77}
          Link IDs: {'PTRANS': 5, 'TRANS': 323}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 227
          Unresolved non-hydrogen angles: 287
          Unresolved non-hydrogen dihedrals: 167
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 6, 'ASP:plan': 19}
          Unresolved non-hydrogen planarities: 158
    Chain: "G"
      Number of atoms: 319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 319
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 84
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "R"
      Number of atoms: 1938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 1938
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 97}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 330
          Unresolved non-hydrogen angles: 416
          Unresolved non-hydrogen dihedrals: 267
          Unresolved non-hydrogen chiralities: 36
          Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 162
    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: 4.83, per 1000 atoms: 0.78
  Number of scatterers: 6223
  At special positions: 0
  Unit cell: (68.9, 98.58, 127.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1079      8.00
     N    1091      7.00
     C    4017      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.77
  Conformation dependent library (CDL) restraints added in 906.9 milliseconds
  

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1694

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      47.5% alpha, 16.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 39
      removed outlier: 4.420A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 233 through 237
      removed outlier: 4.043A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.735A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.641A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 8 through 26
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.522A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 14 through 24
      removed outlier: 3.546A  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: 3.683A  pdb=" N   ILE R  38 " --> pdb=" O   VAL R  34 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   VAL R  39 " --> pdb=" O   GLY R  35 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   MET R  40 " --> pdb=" O   MET R  36 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 3.895A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 171
      Proline residue:  R 168  - end of helix
      removed outlier: 3.506A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 270 through 298
      removed outlier: 4.111A  pdb=" N   CYS R 285 " --> pdb=" O   THR R 281 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.169A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 318
    Processing helix  chain 'R' and resid 321 through 327
      removed outlier: 3.611A  pdb=" N   ILE R 325 " --> pdb=" O   PHE R 321 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 329 through 340
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214
      removed outlier: 6.848A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.683A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 50
      removed outlier: 5.914A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   THR B 329 " --> pdb=" O   LYS B 337 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 61
      removed outlier: 7.102A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.507A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.317A  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 151
      removed outlier: 6.523A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.310A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   CYS B 166 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.506A  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: 6.807A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.187A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.544A  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: 3.790A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.272A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)

    373 hydrogen bonds defined for protein.
    1086 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: 1.98

  Time building geometry restraints manager: 2.07 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1987
        1.34 -     1.45: 886
        1.45 -     1.57: 3436
        1.57 -     1.69: 1
        1.69 -     1.81: 48
  Bond restraints: 6358
  Sorted by residual:
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.575 -0.052 2.00e-02 2.50e+03 6.78e+00
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.449 -0.052 2.00e-02 2.50e+03 6.77e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.441 -0.047 2.00e-02 2.50e+03 5.49e+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 4.89e+00
  bond pdb=" CA  ALA B  73 "
       pdb=" CB  ALA B  73 "
    ideal  model  delta    sigma   weight residual
    1.532  1.496  0.035 1.82e-02 3.02e+03 3.79e+00
  ... (remaining 6353 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 8572
        1.70 -     3.41: 121
        3.41 -     5.11: 13
        5.11 -     6.82: 6
        6.82 -     8.52: 2
  Bond angle restraints: 8714
  Sorted by residual:
  angle pdb=" N   ILE B 269 "
        pdb=" CA  ILE B 269 "
        pdb=" C   ILE B 269 "
      ideal   model   delta    sigma   weight residual
     109.34  117.26   -7.92 2.08e+00 2.31e-01 1.45e+01
  angle pdb=" CB  MET B 188 "
        pdb=" CG  MET B 188 "
        pdb=" SD  MET B 188 "
      ideal   model   delta    sigma   weight residual
     112.70  104.18    8.52 3.00e+00 1.11e-01 8.06e+00
  angle pdb=" N   CYS B 271 "
        pdb=" CA  CYS B 271 "
        pdb=" C   CYS B 271 "
      ideal   model   delta    sigma   weight residual
     110.59  114.37   -3.78 1.45e+00 4.76e-01 6.79e+00
  angle pdb=" N   SER B  74 "
        pdb=" CA  SER B  74 "
        pdb=" C   SER B  74 "
      ideal   model   delta    sigma   weight residual
     109.85  113.95   -4.10 1.58e+00 4.01e-01 6.73e+00
  angle pdb=" C   VAL R 295 "
        pdb=" N   HIS R 296 "
        pdb=" CA  HIS R 296 "
      ideal   model   delta    sigma   weight residual
     121.14  116.74    4.40 1.75e+00 3.27e-01 6.31e+00
  ... (remaining 8709 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.71: 3352
       16.71 -    33.41: 249
       33.41 -    50.12: 45
       50.12 -    66.82: 9
       66.82 -    83.53: 2
  Dihedral angle restraints: 3657
    sinusoidal: 1051
      harmonic: 2606
  Sorted by residual:
  dihedral pdb=" CA  ILE R 298 "
           pdb=" C   ILE R 298 "
           pdb=" N   GLN R 299 "
           pdb=" CA  GLN R 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.25   16.75     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  MET B 262 "
           pdb=" C   MET B 262 "
           pdb=" N   THR B 263 "
           pdb=" CA  THR B 263 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.40   16.60     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.49   16.51     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 3654 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 650
       0.030 -    0.060: 273
       0.060 -    0.090: 84
       0.090 -    0.121: 41
       0.121 -    0.151: 2
  Chirality restraints: 1050
  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    2.55   -0.15 2.00e-01 2.50e+01 5.68e-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   -0.13 2.00e-01 2.50e+01 4.41e-01
  chirality pdb=" CA  ILE A 244 "
            pdb=" N   ILE A 244 "
            pdb=" C   ILE A 244 "
            pdb=" CB  ILE A 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.62e-01
  ... (remaining 1047 not shown)

  Planarity restraints: 1106
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 322 "    0.029 5.00e-02 4.00e+02   4.37e-02 3.06e+00
        pdb=" N   PRO R 323 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO R 323 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO R 323 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "   -0.020 5.00e-02 4.00e+02   2.95e-02 1.39e+00
        pdb=" N   PRO B 194 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 320 "    0.018 5.00e-02 4.00e+02   2.73e-02 1.19e+00
        pdb=" N   PRO A 321 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 321 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 321 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1103 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 2190
        2.85 -     3.36: 5967
        3.36 -     3.87: 10203
        3.87 -     4.39: 10707
        4.39 -     4.90: 19725
  Nonbonded interactions: 48792
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP R 113 "
            pdb=" OH  TYR R 316 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" OG  SER B 279 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" NH1 ARG B 137 "
            pdb=" O   ILE B 171 "
     model   vdw
     2.373 3.120
  nonbonded pdb=" OD1 ASP R 113 "
            pdb=" OAM G1I R 501 "
     model   vdw
     2.375 3.040
  nonbonded pdb=" O   ARG A 283 "
            pdb=" NH1 ARG A 356 "
     model   vdw
     2.380 3.120
  ... (remaining 48787 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:             1.610
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.870
  Find NCS groups from input model:        0.100
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
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   0.052   6359  Z= 0.163
  Angle     :  0.520   8.519   8716  Z= 0.275
  Chirality :  0.040   0.151   1050
  Planarity :  0.003   0.044   1106
  Dihedral  : 12.499  83.527   1960
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  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:  1.44 (0.29), residues: 875
  helix:  2.72 (0.26), residues: 396
  sheet:  0.15 (0.41), residues: 162
  loop : -0.95 (0.32), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 281 
 HIS   0.006   0.001   HIS B 266 
 PHE   0.007   0.001   PHE A 212 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.007   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13781 (  373)
  hydrogen bonds       : angle       5.93691 ( 1086)
  SS BOND              : bond        0.00379 (    1)
  SS BOND              : angle       0.28311 (    2)
  covalent geometry    : bond        0.00333 ( 6358)
  covalent geometry    : angle       0.52000 ( 8714)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.715 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1398
  time to fit residues: 17.1316
Evaluate side-chains
  64 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9980
   chunk 37 optimal weight:    0.4980
   chunk 22 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 68 optimal weight:    0.5980
   chunk 26 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.126083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.108358 restraints weight = 10259.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.111432 restraints weight = 5859.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.113533 restraints weight = 4037.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.0803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6359  Z= 0.142
  Angle     :  0.466   5.484   8716  Z= 0.253
  Chirality :  0.040   0.141   1050
  Planarity :  0.003   0.043   1106
  Dihedral  :  4.404  30.821    959
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 10.00 %
    Favored  : 88.80 %
  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:  1.47 (0.29), residues: 875
  helix:  2.74 (0.26), residues: 399
  sheet:  0.19 (0.40), residues: 161
  loop : -0.97 (0.32), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.008   0.001   PHE B 235 
 TYR   0.013   0.001   TYR R 199 
 ARG   0.008   0.001   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03725 (  373)
  hydrogen bonds       : angle       4.58749 ( 1086)
  SS BOND              : bond        0.00417 (    1)
  SS BOND              : angle       0.36058 (    2)
  covalent geometry    : bond        0.00329 ( 6358)
  covalent geometry    : angle       0.46571 ( 8714)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.664 
Fit side-chains
REVERT: B  258 ASP cc_start: 0.8257 (t70) cc_final: 0.7915 (t0)
REVERT: R   58 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8323 (mp)
  outliers start: 6
  outliers final: 5
  residues processed: 76
  average time/residue: 0.1290
  time to fit residues: 14.5350
Evaluate side-chains
  71 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 267 GLN
R 170 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.124763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.107509 restraints weight = 10781.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.110113 restraints weight = 6430.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.112156 restraints weight = 4573.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6359  Z= 0.181
  Angle     :  0.481   5.644   8716  Z= 0.261
  Chirality :  0.040   0.146   1050
  Planarity :  0.003   0.042   1106
  Dihedral  :  4.403  27.965    959
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 15.20 %
    Favored  : 81.80 %
  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:  1.36 (0.29), residues: 875
  helix:  2.64 (0.26), residues: 399
  sheet:  0.18 (0.41), residues: 156
  loop : -1.02 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.012   0.001   PHE B 235 
 TYR   0.014   0.001   TYR R 199 
 ARG   0.004   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03853 (  373)
  hydrogen bonds       : angle       4.45010 ( 1086)
  SS BOND              : bond        0.00631 (    1)
  SS BOND              : angle       0.58854 (    2)
  covalent geometry    : bond        0.00426 ( 6358)
  covalent geometry    : angle       0.48142 ( 8714)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.713 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8705 (ttmm)
REVERT: B  188 MET cc_start: 0.7943 (mmm) cc_final: 0.7650 (mmt)
REVERT: B  233 CYS cc_start: 0.8256 (t) cc_final: 0.8026 (t)
REVERT: B  258 ASP cc_start: 0.8223 (t70) cc_final: 0.7957 (t0)
REVERT: R   58 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8380 (mp)
  outliers start: 15
  outliers final: 11
  residues processed: 81
  average time/residue: 0.1223
  time to fit residues: 14.9862
Evaluate side-chains
  80 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  136 THR
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0270
   chunk 10 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 87 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   chunk 8 optimal weight:    0.3980
   chunk 80 optimal weight:    0.0000
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.3642

-------------------------------------------------------------------------------
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 = 0.3656 r_free = 0.3656 target = 0.128566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.111237 restraints weight = 10727.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.114132 restraints weight = 6326.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.116198 restraints weight = 4418.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.1299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6359  Z= 0.101
  Angle     :  0.419   5.532   8716  Z= 0.229
  Chirality :  0.039   0.205   1050
  Planarity :  0.003   0.041   1106
  Dihedral  :  4.092  28.245    959
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 16.20 %
    Favored  : 81.40 %
  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:  1.61 (0.29), residues: 875
  helix:  2.97 (0.26), residues: 393
  sheet:  0.17 (0.40), residues: 164
  loop : -0.95 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.009   0.001   PHE A 212 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.003   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03315 (  373)
  hydrogen bonds       : angle       4.09239 ( 1086)
  SS BOND              : bond        0.00211 (    1)
  SS BOND              : angle       0.24309 (    2)
  covalent geometry    : bond        0.00225 ( 6358)
  covalent geometry    : angle       0.41903 ( 8714)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.737 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.8910 (mtpt) cc_final: 0.8664 (ttmm)
REVERT: B  233 CYS cc_start: 0.8207 (t) cc_final: 0.7867 (t)
REVERT: B  258 ASP cc_start: 0.8157 (t70) cc_final: 0.7900 (t0)
  outliers start: 12
  outliers final: 9
  residues processed: 80
  average time/residue: 0.1259
  time to fit residues: 15.3006
Evaluate side-chains
  77 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 56 optimal weight:    0.1980
   chunk 2 optimal weight:    0.3980
   chunk 50 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3639 r_free = 0.3639 target = 0.126223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.108378 restraints weight = 10390.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.111483 restraints weight = 5895.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.113625 restraints weight = 4043.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.1383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6359  Z= 0.112
  Angle     :  0.446   8.665   8716  Z= 0.235
  Chirality :  0.039   0.183   1050
  Planarity :  0.003   0.038   1106
  Dihedral  :  4.009  28.376    959
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 17.20 %
    Favored  : 80.40 %
  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:  1.62 (0.29), residues: 875
  helix:  2.98 (0.25), residues: 393
  sheet:  0.23 (0.40), residues: 161
  loop : -0.97 (0.33), residues: 321

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   0.009   0.001   PHE A 212 
 TYR   0.012   0.001   TYR R 199 
 ARG   0.004   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03312 (  373)
  hydrogen bonds       : angle       4.00661 ( 1086)
  SS BOND              : bond        0.00294 (    1)
  SS BOND              : angle       0.24736 (    2)
  covalent geometry    : bond        0.00257 ( 6358)
  covalent geometry    : angle       0.44570 ( 8714)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.697 
Fit side-chains
REVERT: B   82 TRP cc_start: 0.8072 (OUTLIER) cc_final: 0.7299 (m-90)
REVERT: B  233 CYS cc_start: 0.8172 (t) cc_final: 0.7878 (t)
REVERT: B  258 ASP cc_start: 0.8156 (t70) cc_final: 0.7891 (t0)
  outliers start: 12
  outliers final: 11
  residues processed: 83
  average time/residue: 0.1234
  time to fit residues: 15.4469
Evaluate side-chains
  81 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  324 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 7 optimal weight:    0.0370
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0170
   chunk 1 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 78 optimal weight:    0.0570
   overall best weight:    0.3214

-------------------------------------------------------------------------------
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 = 0.3664 r_free = 0.3664 target = 0.128151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.110545 restraints weight = 10275.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.113676 restraints weight = 5829.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.115749 restraints weight = 3977.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6359  Z= 0.092
  Angle     :  0.429   7.972   8716  Z= 0.226
  Chirality :  0.039   0.189   1050
  Planarity :  0.003   0.037   1106
  Dihedral  :  3.859  28.421    959
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 16.60 %
    Favored  : 80.20 %
  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:  1.75 (0.29), residues: 875
  helix:  3.11 (0.25), residues: 393
  sheet:  0.17 (0.40), residues: 162
  loop : -0.87 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.002   0.001   HIS B 311 
 PHE   0.010   0.001   PHE A 212 
 TYR   0.010   0.001   TYR R 199 
 ARG   0.005   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03064 (  373)
  hydrogen bonds       : angle       3.82626 ( 1086)
  SS BOND              : bond        0.00124 (    1)
  SS BOND              : angle       0.09366 (    2)
  covalent geometry    : bond        0.00202 ( 6358)
  covalent geometry    : angle       0.42876 ( 8714)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.662 
Fit side-chains
REVERT: A  274 LYS cc_start: 0.9195 (ttmm) cc_final: 0.8924 (ttmm)
REVERT: B   82 TRP cc_start: 0.8107 (OUTLIER) cc_final: 0.7258 (m-10)
REVERT: B  233 CYS cc_start: 0.8114 (t) cc_final: 0.7795 (t)
REVERT: B  258 ASP cc_start: 0.8123 (t70) cc_final: 0.7849 (t0)
  outliers start: 16
  outliers final: 12
  residues processed: 84
  average time/residue: 0.1216
  time to fit residues: 15.7443
Evaluate side-chains
  81 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  324 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 58 optimal weight:    0.5980
   chunk 29 optimal weight:    0.1980
   chunk 62 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0980
   chunk 69 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.3656 r_free = 0.3656 target = 0.127548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.109763 restraints weight = 10363.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.112910 restraints weight = 5929.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.115015 restraints weight = 4049.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6359  Z= 0.104
  Angle     :  0.438   7.682   8716  Z= 0.232
  Chirality :  0.039   0.169   1050
  Planarity :  0.003   0.037   1106
  Dihedral  :  3.837  27.870    959
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 16.60 %
    Favored  : 79.60 %
  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:  1.74 (0.29), residues: 875
  helix:  3.11 (0.25), residues: 393
  sheet:  0.21 (0.40), residues: 160
  loop : -0.89 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 281 
 HIS   0.002   0.001   HIS B 225 
 PHE   0.010   0.001   PHE A 212 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.004   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03163 (  373)
  hydrogen bonds       : angle       3.79676 ( 1086)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       0.17008 (    2)
  covalent geometry    : bond        0.00235 ( 6358)
  covalent geometry    : angle       0.43833 ( 8714)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.681 
Fit side-chains
REVERT: B   82 TRP cc_start: 0.8089 (OUTLIER) cc_final: 0.7239 (m-10)
REVERT: B  233 CYS cc_start: 0.8131 (t) cc_final: 0.7821 (t)
REVERT: B  234 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8523 (t80)
REVERT: B  258 ASP cc_start: 0.8123 (t70) cc_final: 0.7867 (t0)
  outliers start: 19
  outliers final: 14
  residues processed: 85
  average time/residue: 0.1285
  time to fit residues: 16.7189
Evaluate side-chains
  84 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  324 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 9 optimal weight:    0.0870
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   chunk 23 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.6960

-------------------------------------------------------------------------------
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 = 0.3632 r_free = 0.3632 target = 0.125676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.107738 restraints weight = 10431.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.110855 restraints weight = 6010.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.112925 restraints weight = 4121.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6359  Z= 0.127
  Angle     :  0.458   7.184   8716  Z= 0.241
  Chirality :  0.039   0.166   1050
  Planarity :  0.003   0.038   1106
  Dihedral  :  3.929  28.686    959
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 17.20 %
    Favored  : 79.20 %
  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:  1.66 (0.29), residues: 875
  helix:  2.99 (0.26), residues: 399
  sheet:  0.07 (0.40), residues: 162
  loop : -0.88 (0.33), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 281 
 HIS   0.002   0.001   HIS B 225 
 PHE   0.009   0.001   PHE A 212 
 TYR   0.013   0.001   TYR R 199 
 ARG   0.004   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03331 (  373)
  hydrogen bonds       : angle       3.85130 ( 1086)
  SS BOND              : bond        0.00382 (    1)
  SS BOND              : angle       0.34904 (    2)
  covalent geometry    : bond        0.00293 ( 6358)
  covalent geometry    : angle       0.45776 ( 8714)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.726 
Fit side-chains
REVERT: B   82 TRP cc_start: 0.8109 (OUTLIER) cc_final: 0.7375 (m-10)
REVERT: B  233 CYS cc_start: 0.8188 (t) cc_final: 0.7909 (t)
REVERT: B  234 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8579 (t80)
REVERT: B  258 ASP cc_start: 0.8221 (t70) cc_final: 0.8001 (t0)
  outliers start: 18
  outliers final: 13
  residues processed: 83
  average time/residue: 0.1115
  time to fit residues: 14.5229
Evaluate side-chains
  81 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  324 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 82 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.3602 r_free = 0.3602 target = 0.124155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.106711 restraints weight = 10820.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.109514 restraints weight = 6547.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.111255 restraints weight = 4626.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6359  Z= 0.186
  Angle     :  0.516   7.275   8716  Z= 0.273
  Chirality :  0.041   0.199   1050
  Planarity :  0.003   0.038   1106
  Dihedral  :  4.223  30.222    959
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 18.20 %
    Favored  : 78.60 %
  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:  1.40 (0.29), residues: 875
  helix:  2.73 (0.26), residues: 399
  sheet: -0.11 (0.39), residues: 169
  loop : -0.92 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 281 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.013   0.001   PHE B 235 
 TYR   0.015   0.002   TYR R 199 
 ARG   0.004   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03776 (  373)
  hydrogen bonds       : angle       4.12730 ( 1086)
  SS BOND              : bond        0.00652 (    1)
  SS BOND              : angle       0.69135 (    2)
  covalent geometry    : bond        0.00441 ( 6358)
  covalent geometry    : angle       0.51598 ( 8714)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.723 
Fit side-chains
REVERT: B   82 TRP cc_start: 0.8196 (OUTLIER) cc_final: 0.7562 (m-10)
REVERT: B  233 CYS cc_start: 0.8301 (t) cc_final: 0.8100 (t)
REVERT: B  258 ASP cc_start: 0.8298 (t70) cc_final: 0.8072 (t0)
REVERT: R  316 TYR cc_start: 0.8241 (m-10) cc_final: 0.7810 (m-10)
  outliers start: 16
  outliers final: 14
  residues processed: 81
  average time/residue: 0.1234
  time to fit residues: 15.6171
Evaluate side-chains
  81 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  324 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 40 optimal weight:    0.3980
   chunk 24 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 63 optimal weight:    0.4980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3631 r_free = 0.3631 target = 0.126352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.109204 restraints weight = 10763.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.111994 restraints weight = 6353.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.113959 restraints weight = 4454.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6359  Z= 0.123
  Angle     :  0.468   7.238   8716  Z= 0.247
  Chirality :  0.040   0.213   1050
  Planarity :  0.003   0.036   1106
  Dihedral  :  4.073  29.486    959
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 18.60 %
    Favored  : 78.40 %
  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:  1.48 (0.29), residues: 875
  helix:  2.85 (0.26), residues: 399
  sheet: -0.17 (0.39), residues: 169
  loop : -0.90 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 281 
 HIS   0.002   0.001   HIS B 311 
 PHE   0.010   0.001   PHE A 212 
 TYR   0.013   0.001   TYR R 199 
 ARG   0.004   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03406 (  373)
  hydrogen bonds       : angle       3.95333 ( 1086)
  SS BOND              : bond        0.00325 (    1)
  SS BOND              : angle       0.35108 (    2)
  covalent geometry    : bond        0.00284 ( 6358)
  covalent geometry    : angle       0.46781 ( 8714)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.766 
Fit side-chains
REVERT: B   82 TRP cc_start: 0.8134 (OUTLIER) cc_final: 0.7442 (m-10)
REVERT: B  233 CYS cc_start: 0.8250 (t) cc_final: 0.7990 (t)
REVERT: B  234 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8559 (t80)
REVERT: R  316 TYR cc_start: 0.7930 (m-10) cc_final: 0.7728 (m-10)
  outliers start: 15
  outliers final: 13
  residues processed: 84
  average time/residue: 0.1347
  time to fit residues: 17.8595
Evaluate side-chains
  82 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  324 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 84 optimal weight:    0.4980
   chunk 63 optimal weight:    0.9990
   chunk 85 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0770
   chunk 47 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.5938

-------------------------------------------------------------------------------
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 = 0.3635 r_free = 0.3635 target = 0.126632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.109448 restraints weight = 10766.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.112230 restraints weight = 6363.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.114015 restraints weight = 4479.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6359  Z= 0.123
  Angle     :  0.479   7.156   8716  Z= 0.255
  Chirality :  0.040   0.218   1050
  Planarity :  0.003   0.036   1106
  Dihedral  :  4.017  28.918    959
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 19.40 %
    Favored  : 77.60 %
  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:  1.50 (0.29), residues: 875
  helix:  2.89 (0.26), residues: 399
  sheet: -0.23 (0.39), residues: 163
  loop : -0.89 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 281 
 HIS   0.002   0.001   HIS B 311 
 PHE   0.010   0.001   PHE A 212 
 TYR   0.013   0.001   TYR R 199 
 ARG   0.004   0.000   ARG R  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03406 (  373)
  hydrogen bonds       : angle       3.92263 ( 1086)
  SS BOND              : bond        0.00314 (    1)
  SS BOND              : angle       0.31097 (    2)
  covalent geometry    : bond        0.00282 ( 6358)
  covalent geometry    : angle       0.47919 ( 8714)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2098.82 seconds
wall clock time: 37 minutes 38.67 seconds (2258.67 seconds total)