Starting phenix.real_space_refine
on Fri Jan 17 06:56:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xor_38538/01_2025/8xor_38538.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xor_38538/01_2025/8xor_38538.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xor_38538/01_2025/8xor_38538.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xor_38538/01_2025/8xor_38538.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xor_38538/01_2025/8xor_38538.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xor_38538/01_2025/8xor_38538.cif"
  }
  resolution = 3.0
  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=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1900 atoms to isotropic.
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      58      5.16       5
     C    5801      2.51       5
     N    1478      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8979
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2481
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2481
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 120
          Unresolved non-hydrogen angles: 147
          Unresolved non-hydrogen dihedrals: 95
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 91
    Chain: "C"
      Number of atoms: 353
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 353
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "A"
      Number of atoms: 1848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1848
          Classifications: {'peptide': 234}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 65
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 50
    Chain: "E"
      Number of atoms: 1729
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1729
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "R"
      Number of atoms: 2400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2400
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 11, 'TRANS': 293}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 168
          Unusual residues: {'CLR': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 5.44, per 1000 atoms: 0.61
  Number of scatterers: 8979
  At special positions: 0
  Unit cell: (116.739, 116.739, 103.887, 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      58     16.00
     O    1642      8.00
     N    1478      7.00
     C    5801      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 175 " - pdb=" SG  CYS R 254 " 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: 2.50
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2184

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 14 sheets defined
      40.2% alpha, 23.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.19
  Creating SS restraints...
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'C' and resid 12 through 24
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.708A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 26
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 210 through 218
      removed outlier: 4.212A  pdb=" N   ASN A 216 " --> pdb=" O   GLN A 213 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   ASP A 217 " --> pdb=" O   CYS A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 245
      removed outlier: 4.222A  pdb=" N   GLN A 234 " --> pdb=" O   TYR A 230 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLU A 235 " --> pdb=" O   ASN A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 252
      removed outlier: 4.458A  pdb=" N   THR A 251 " --> pdb=" O   TRP A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 270
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 279 through 285
    Processing helix  chain 'A' and resid 300 through 318
      removed outlier: 3.544A  pdb=" N   PHE A 312 " --> pdb=" O   ILE A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 358
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 3.807A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 74 through 76
      No H-bonds generated for 'chain 'E' and resid 74 through 76'
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'R' and resid 89 through 98
    Processing helix  chain 'R' and resid 98 through 127
      removed outlier: 5.016A  pdb=" N   VAL R 105 " --> pdb=" O   LEU R 101 " (cutoff:3.500A)
      Proline residue:  R 106  - end of helix
      Proline residue:  R 118  - end of helix
    Processing helix  chain 'R' and resid 135 through 164
      removed outlier: 3.699A  pdb=" N   VAL R 139 " --> pdb=" O   LYS R 135 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL R 154 " --> pdb=" O   LEU R 150 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU R 155 " --> pdb=" O   PHE R 151 " (cutoff:3.500A)
      Proline residue:  R 156  - end of helix
    Processing helix  chain 'R' and resid 170 through 206
      removed outlier: 4.360A  pdb=" N   LEU R 174 " --> pdb=" O   PHE R 170 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 206 through 214
      removed outlier: 3.689A  pdb=" N   LEU R 211 " --> pdb=" O   PRO R 207 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   SER R 212 " --> pdb=" O   MET R 208 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   TRP R 213 " --> pdb=" O   GLN R 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 215 through 240
      Proline residue:  R 236  - end of helix
    Processing helix  chain 'R' and resid 260 through 265
    Processing helix  chain 'R' and resid 265 through 279
    Processing helix  chain 'R' and resid 279 through 299
    Processing helix  chain 'R' and resid 299 through 306
      removed outlier: 4.055A  pdb=" N   SER R 306 " --> pdb=" O   VAL R 302 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 308 through 339
      Proline residue:  R 328  - end of helix
      removed outlier: 3.757A  pdb=" N   PHE R 339 " --> pdb=" O   ALA R 335 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 342 through 361
      removed outlier: 4.143A  pdb=" N   GLU R 347 " --> pdb=" O   THR R 343 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   ALA R 348 " --> pdb=" O   SER R 344 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 362 through 372
      Proline residue:  R 368  - end of helix
    Processing helix  chain 'R' and resid 375 through 380
      removed outlier: 4.274A  pdb=" N   ARG R 380 " --> pdb=" O   SER R 376 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.560A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.601A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.937A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.955A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.674A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.962A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.362A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.347A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.498A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.763A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ASP B 303 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 184 through 191
      removed outlier: 4.617A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 8.240A  pdb=" N   GLY A  40 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ALA A 220 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 6
    Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12
      removed outlier: 6.125A  pdb=" N   TRP E 111 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   ARG E  98 " --> pdb=" O   TRP E 111 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   GLN E 113 " --> pdb=" O   CYS E  96 " (cutoff:3.500A)
      removed outlier: 5.981A  pdb=" N   CYS E  96 " --> pdb=" O   GLN E 113 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142
    Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 148
      removed outlier: 5.896A  pdb=" N   VAL E 147 " --> pdb=" O   GLU E 246 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'R' and resid 87 through 88
      removed outlier: 6.133A  pdb=" N   PHE R  43 " --> pdb=" O   LEU R 258 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 243 through 245

    453 hydrogen bonds defined for protein.
    1272 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: 2.84

  Time building geometry restraints manager: 2.88 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: 2811
        1.34 -     1.46: 1740
        1.46 -     1.58: 4561
        1.58 -     1.70: 0
        1.70 -     1.82: 80
  Bond restraints: 9192
  Sorted by residual:
  bond pdb=" CD2 HIS E 232 "
       pdb=" NE2 HIS E 232 "
    ideal  model  delta    sigma   weight residual
    1.374  1.397 -0.023 1.10e-02 8.26e+03 4.54e+00
  bond pdb=" ND1 HIS E  35 "
       pdb=" CE1 HIS E  35 "
    ideal  model  delta    sigma   weight residual
    1.321  1.342 -0.021 1.00e-02 1.00e+04 4.49e+00
  bond pdb=" C13 CLR R1405 "
       pdb=" C17 CLR R1405 "
    ideal  model  delta    sigma   weight residual
    1.550  1.508  0.042 2.00e-02 2.50e+03 4.33e+00
  bond pdb=" C13 CLR R1403 "
       pdb=" C17 CLR R1403 "
    ideal  model  delta    sigma   weight residual
    1.550  1.509  0.041 2.00e-02 2.50e+03 4.26e+00
  bond pdb=" C13 CLR R1402 "
       pdb=" C17 CLR R1402 "
    ideal  model  delta    sigma   weight residual
    1.550  1.509  0.041 2.00e-02 2.50e+03 4.26e+00
  ... (remaining 9187 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 11885
        1.78 -     3.56: 544
        3.56 -     5.34: 86
        5.34 -     7.13: 18
        7.13 -     8.91: 11
  Bond angle restraints: 12544
  Sorted by residual:
  angle pdb=" OE1 GLN E 231 "
        pdb=" CD  GLN E 231 "
        pdb=" NE2 GLN E 231 "
      ideal   model   delta    sigma   weight residual
     122.60  117.91    4.69 1.00e+00 1.00e+00 2.20e+01
  angle pdb=" CB  HIS E  35 "
        pdb=" CG  HIS E  35 "
        pdb=" CD2 HIS E  35 "
      ideal   model   delta    sigma   weight residual
     131.20  125.34    5.86 1.30e+00 5.92e-01 2.03e+01
  angle pdb=" N   PRO E 236 "
        pdb=" CA  PRO E 236 "
        pdb=" C   PRO E 236 "
      ideal   model   delta    sigma   weight residual
     113.81  107.34    6.47 1.45e+00 4.76e-01 1.99e+01
  angle pdb=" CA  ASP E 137 "
        pdb=" CB  ASP E 137 "
        pdb=" CG  ASP E 137 "
      ideal   model   delta    sigma   weight residual
     112.60  117.00   -4.40 1.00e+00 1.00e+00 1.93e+01
  angle pdb=" CB  HIS E 167 "
        pdb=" CG  HIS E 167 "
        pdb=" CD2 HIS E 167 "
      ideal   model   delta    sigma   weight residual
     131.20  125.78    5.42 1.30e+00 5.92e-01 1.74e+01
  ... (remaining 12539 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.31: 5346
       21.31 -    42.61: 255
       42.61 -    63.92: 56
       63.92 -    85.23: 13
       85.23 -   106.53: 6
  Dihedral angle restraints: 5676
    sinusoidal: 2289
      harmonic: 3387
  Sorted by residual:
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.96   29.04     0      5.00e+00 4.00e-02 3.37e+01
  dihedral pdb=" CA  LEU R  44 "
           pdb=" C   LEU R  44 "
           pdb=" N   LEU R  45 "
           pdb=" CA  LEU R  45 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.18   28.82     0      5.00e+00 4.00e-02 3.32e+01
  dihedral pdb=" CA  THR B 249 "
           pdb=" C   THR B 249 "
           pdb=" N   CYS B 250 "
           pdb=" CA  CYS B 250 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.62   28.38     0      5.00e+00 4.00e-02 3.22e+01
  ... (remaining 5673 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1222
       0.070 -    0.139: 217
       0.139 -    0.209: 14
       0.209 -    0.278: 8
       0.278 -    0.348: 7
  Chirality restraints: 1468
  Sorted by residual:
  chirality pdb=" C13 CLR R1405 "
            pdb=" C12 CLR R1405 "
            pdb=" C14 CLR R1405 "
            pdb=" C17 CLR R1405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.58   -0.35 2.00e-01 2.50e+01 3.02e+00
  chirality pdb=" C13 CLR R1402 "
            pdb=" C12 CLR R1402 "
            pdb=" C14 CLR R1402 "
            pdb=" C17 CLR R1402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.60   -0.33 2.00e-01 2.50e+01 2.77e+00
  chirality pdb=" C13 CLR R1401 "
            pdb=" C12 CLR R1401 "
            pdb=" C14 CLR R1401 "
            pdb=" C17 CLR R1401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.60   -0.33 2.00e-01 2.50e+01 2.74e+00
  ... (remaining 1465 not shown)

  Planarity restraints: 1546
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 101 "   -0.087 2.00e-02 2.50e+03   5.04e-02 5.08e+01
        pdb=" CG  TYR E 101 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 101 "    0.030 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 101 "    0.041 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 101 "    0.038 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 101 "    0.026 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 101 "    0.013 2.00e-02 2.50e+03
        pdb=" OH  TYR E 101 "   -0.085 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E  50 "    0.087 2.00e-02 2.50e+03   4.99e-02 4.99e+01
        pdb=" CG  TYR E  50 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD1 TYR E  50 "   -0.052 2.00e-02 2.50e+03
        pdb=" CD2 TYR E  50 "   -0.049 2.00e-02 2.50e+03
        pdb=" CE1 TYR E  50 "   -0.029 2.00e-02 2.50e+03
        pdb=" CE2 TYR E  50 "   -0.032 2.00e-02 2.50e+03
        pdb=" CZ  TYR E  50 "    0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR E  50 "    0.072 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R 276 "    0.019 2.00e-02 2.50e+03   3.76e-02 1.41e+01
        pdb=" C   ALA R 276 "   -0.065 2.00e-02 2.50e+03
        pdb=" O   ALA R 276 "    0.024 2.00e-02 2.50e+03
        pdb=" N   VAL R 277 "    0.022 2.00e-02 2.50e+03
  ... (remaining 1543 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1655
        2.77 -     3.31: 9047
        3.31 -     3.84: 15053
        3.84 -     4.37: 18390
        4.37 -     4.90: 31188
  Nonbonded interactions: 75333
  Sorted by model distance:
  nonbonded pdb=" OH  TYR R 161 "
            pdb=" OD2 ASP R 256 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG  SER E   7 "
            pdb=" OG  SER E  21 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" CE1 HIS R 143 "
            pdb=" C19 CLR R1405 "
     model   vdw
     2.363 3.680
  nonbonded pdb=" OD2 ASP A   9 "
            pdb=" ND2 ASN E 169 "
     model   vdw
     2.400 3.120
  nonbonded pdb=" OH  TYR A 327 "
            pdb=" OD2 ASP A 348 "
     model   vdw
     2.401 3.040
  ... (remaining 75328 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.060
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  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:13.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
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      :  0.005   0.042   9192  Z= 0.324
  Angle     :  0.901   8.907  12544  Z= 0.511
  Chirality :  0.058   0.348   1468
  Planarity :  0.007   0.056   1546
  Dihedral  : 14.200 106.534   3489
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  4.67 %
    Favored  : 95.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.23), residues: 1144
  helix: -0.42 (0.23), residues: 407
  sheet:  0.27 (0.30), residues: 276
  loop : -0.52 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP E  47 
 HIS   0.011   0.002   HIS E 232 
 PHE   0.030   0.002   PHE E 177 
 TYR   0.087   0.007   TYR E 101 
 ARG   0.043   0.008   ARG E  72 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 162
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  175 GLN cc_start: 0.8333 (pt0) cc_final: 0.8028 (pp30)
REVERT: B  259 GLN cc_start: 0.7626 (pt0) cc_final: 0.7411 (pt0)
REVERT: B  275 SER cc_start: 0.8846 (t) cc_final: 0.8361 (m)
REVERT: B  280 LYS cc_start: 0.9250 (tttt) cc_final: 0.9034 (tttm)
REVERT: A   25 LYS cc_start: 0.7565 (tptt) cc_final: 0.6934 (tmmm)
REVERT: A   27 LYS cc_start: 0.7982 (tmtt) cc_final: 0.7568 (mmtt)
REVERT: A  281 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8810 (mp0)
REVERT: E    3 GLN cc_start: 0.8677 (tt0) cc_final: 0.8342 (tt0)
REVERT: E   73 ASP cc_start: 0.7823 (t0) cc_final: 0.7278 (t0)
REVERT: E  186 GLN cc_start: 0.8566 (tt0) cc_final: 0.8330 (tt0)
REVERT: R   91 ASP cc_start: 0.8560 (p0) cc_final: 0.8269 (p0)
REVERT: R  240 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7898 (mmtm)
REVERT: R  245 GLN cc_start: 0.8573 (tp40) cc_final: 0.8339 (mm-40)
REVERT: R  304 ASN cc_start: 0.9201 (m-40) cc_final: 0.8919 (m110)
REVERT: R  347 GLU cc_start: 0.9067 (mp0) cc_final: 0.8678 (mp0)
REVERT: R  377 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8117 (tp30)
  outliers start: 3
  outliers final: 0
  residues processed: 165
  average time/residue: 1.5426
  time to fit residues: 268.1769
Evaluate side-chains
  116 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0170
   chunk 47 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 58 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   chunk 89 optimal weight:    9.9990
   chunk 34 optimal weight:    7.9990
   chunk 54 optimal weight:   30.0000
   chunk 66 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9990
   overall best weight:    1.6026

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B  62 HIS
B  75 GLN
B 295 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  24 GLN
A 216 ASN
E 194 ASN
R  47 ASN
** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.077410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.056164 restraints weight = 21940.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.2833 rms_B_bonded: 3.14
r_work: 0.2687 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9192  Z= 0.230
  Angle     :  0.664   7.788  12544  Z= 0.347
  Chirality :  0.046   0.263   1468
  Planarity :  0.005   0.047   1546
  Dihedral  :  9.044  56.817   1644
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.21 %
    Favored  : 88.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.25), residues: 1144
  helix:  1.22 (0.27), residues: 410
  sheet:  0.42 (0.30), residues: 261
  loop : -0.21 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 211 
 HIS   0.003   0.001   HIS R 336 
 PHE   0.015   0.002   PHE B 253 
 TYR   0.024   0.002   TYR R 109 
 ARG   0.010   0.001   ARG A 300 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 LYS cc_start: 0.9510 (tppp) cc_final: 0.9262 (mppt)
REVERT: B  175 GLN cc_start: 0.8719 (pt0) cc_final: 0.8311 (pp30)
REVERT: B  228 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.7928 (p0)
REVERT: B  259 GLN cc_start: 0.7950 (pt0) cc_final: 0.7609 (pt0)
REVERT: B  275 SER cc_start: 0.8955 (t) cc_final: 0.8544 (m)
REVERT: B  280 LYS cc_start: 0.9227 (tttt) cc_final: 0.8997 (tttm)
REVERT: A   25 LYS cc_start: 0.7638 (tptt) cc_final: 0.7103 (tmmm)
REVERT: A   27 LYS cc_start: 0.8001 (tmtt) cc_final: 0.7463 (mmtm)
REVERT: A   52 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8680 (pp30)
REVERT: A  281 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8863 (mp0)
REVERT: E    3 GLN cc_start: 0.8787 (tt0) cc_final: 0.8546 (tt0)
REVERT: E   13 GLN cc_start: 0.9276 (tp40) cc_final: 0.8651 (pp30)
REVERT: E   38 ARG cc_start: 0.9196 (ptt180) cc_final: 0.8971 (ptp90)
REVERT: E   73 ASP cc_start: 0.7761 (t0) cc_final: 0.7329 (t0)
REVERT: E   74 ASP cc_start: 0.8360 (m-30) cc_final: 0.8100 (m-30)
REVERT: E  186 GLN cc_start: 0.8862 (tt0) cc_final: 0.8591 (tt0)
REVERT: E  223 ASP cc_start: 0.8580 (m-30) cc_final: 0.8231 (m-30)
REVERT: E  230 MET cc_start: 0.9374 (ttp) cc_final: 0.9151 (ttt)
REVERT: R   91 ASP cc_start: 0.8713 (p0) cc_final: 0.8492 (p0)
REVERT: R  132 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8661 (mmmm)
REVERT: R  134 LYS cc_start: 0.9363 (mtpp) cc_final: 0.9147 (mtpt)
REVERT: R  245 GLN cc_start: 0.8700 (tp40) cc_final: 0.8482 (mm-40)
REVERT: R  347 GLU cc_start: 0.9247 (mp0) cc_final: 0.8645 (mp0)
REVERT: R  362 ILE cc_start: 0.9270 (tt) cc_final: 0.9053 (pp)
  outliers start: 16
  outliers final: 4
  residues processed: 136
  average time/residue: 1.5785
  time to fit residues: 226.9050
Evaluate side-chains
  115 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 110
  time to evaluate  : 1.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain R residue  122 MET
Chi-restraints excluded: chain R residue  358 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 86 optimal weight:    9.9990
   chunk 98 optimal weight:    1.9990
   chunk 81 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 109 optimal weight:    0.7980
   chunk 88 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 21 optimal weight:    8.9990
   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  32 GLN
B  75 GLN
A  28 GLN
** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.077466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.056725 restraints weight = 21973.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 3.06
r_work: 0.2701 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9192  Z= 0.222
  Angle     :  0.613   8.090  12544  Z= 0.322
  Chirality :  0.044   0.235   1468
  Planarity :  0.004   0.050   1546
  Dihedral  :  8.196  59.418   1644
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.94 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.25), residues: 1144
  helix:  1.51 (0.27), residues: 410
  sheet:  0.51 (0.30), residues: 260
  loop : -0.10 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 211 
 HIS   0.002   0.001   HIS A 324 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.016   0.002   TYR R 140 
 ARG   0.006   0.001   ARG E  18 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   22 ARG cc_start: 0.7858 (mpt-90) cc_final: 0.7598 (mpt-90)
REVERT: B   23 LYS cc_start: 0.9499 (tppp) cc_final: 0.9267 (mppt)
REVERT: B  175 GLN cc_start: 0.8781 (pt0) cc_final: 0.8333 (pp30)
REVERT: B  228 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7931 (p0)
REVERT: B  275 SER cc_start: 0.8994 (t) cc_final: 0.8624 (m)
REVERT: B  280 LYS cc_start: 0.9157 (tttt) cc_final: 0.8935 (tttm)
REVERT: C   29 LYS cc_start: 0.8911 (mttm) cc_final: 0.8678 (mmpt)
REVERT: A   25 LYS cc_start: 0.7597 (tptt) cc_final: 0.7205 (tmmm)
REVERT: A   27 LYS cc_start: 0.7934 (tmtt) cc_final: 0.7409 (mmtm)
REVERT: A   52 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8660 (pp30)
REVERT: A  281 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8907 (mp0)
REVERT: E    3 GLN cc_start: 0.8794 (tt0) cc_final: 0.8508 (tt0)
REVERT: E   13 GLN cc_start: 0.9298 (tp40) cc_final: 0.8766 (pp30)
REVERT: E   73 ASP cc_start: 0.7788 (t0) cc_final: 0.7344 (t0)
REVERT: E   74 ASP cc_start: 0.8509 (m-30) cc_final: 0.8230 (m-30)
REVERT: E  140 MET cc_start: 0.9231 (mmm) cc_final: 0.8918 (mmm)
REVERT: E  183 GLN cc_start: 0.8511 (mp10) cc_final: 0.8168 (mm-40)
REVERT: E  186 GLN cc_start: 0.8855 (tt0) cc_final: 0.8599 (tt0)
REVERT: E  192 MET cc_start: 0.8715 (tmm) cc_final: 0.8502 (ttp)
REVERT: E  223 ASP cc_start: 0.8701 (m-30) cc_final: 0.8277 (m-30)
REVERT: E  230 MET cc_start: 0.9324 (ttp) cc_final: 0.8953 (ttp)
REVERT: E  234 GLU cc_start: 0.8143 (tp30) cc_final: 0.7927 (pt0)
REVERT: R  264 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8372 (mt-10)
REVERT: R  347 GLU cc_start: 0.9246 (mp0) cc_final: 0.8547 (mp0)
  outliers start: 13
  outliers final: 6
  residues processed: 129
  average time/residue: 1.5154
  time to fit residues: 206.8445
Evaluate side-chains
  118 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 111
  time to evaluate  : 1.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain E residue  163 LYS
Chi-restraints excluded: chain R residue  122 MET
Chi-restraints excluded: chain R residue  358 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 92 optimal weight:   10.0000
   chunk 48 optimal weight:    9.9990
   chunk 89 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 32 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   chunk 38 optimal weight:    0.5980
   chunk 64 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B  75 GLN
** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.077237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.056671 restraints weight = 21875.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.2847 rms_B_bonded: 3.04
r_work: 0.2699 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9192  Z= 0.215
  Angle     :  0.589   7.985  12544  Z= 0.310
  Chirality :  0.043   0.223   1468
  Planarity :  0.004   0.054   1546
  Dihedral  :  7.717  57.568   1644
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 12.81 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.25), residues: 1144
  helix:  1.62 (0.27), residues: 409
  sheet:  0.44 (0.30), residues: 267
  loop :  0.02 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 211 
 HIS   0.003   0.001   HIS A 329 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.015   0.001   TYR E 235 
 ARG   0.005   0.000   ARG E 160 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 LYS cc_start: 0.9513 (tppp) cc_final: 0.9297 (mppt)
REVERT: B  175 GLN cc_start: 0.8816 (pt0) cc_final: 0.8373 (pp30)
REVERT: B  275 SER cc_start: 0.8978 (t) cc_final: 0.8623 (m)
REVERT: B  280 LYS cc_start: 0.9107 (tttt) cc_final: 0.8897 (tttm)
REVERT: C   29 LYS cc_start: 0.8861 (mttm) cc_final: 0.8488 (mmtt)
REVERT: C   31 SER cc_start: 0.8803 (OUTLIER) cc_final: 0.8271 (m)
REVERT: A   25 LYS cc_start: 0.7575 (tptt) cc_final: 0.7350 (tmmm)
REVERT: A   27 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7350 (mmtm)
REVERT: A   52 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8591 (pp30)
REVERT: A  281 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8896 (mp0)
REVERT: E    3 GLN cc_start: 0.8808 (tt0) cc_final: 0.8514 (tt0)
REVERT: E   13 GLN cc_start: 0.9322 (tp40) cc_final: 0.8783 (pp30)
REVERT: E   73 ASP cc_start: 0.7952 (t0) cc_final: 0.7524 (t0)
REVERT: E   74 ASP cc_start: 0.8609 (m-30) cc_final: 0.8373 (m-30)
REVERT: E  183 GLN cc_start: 0.8556 (mp10) cc_final: 0.8335 (mm-40)
REVERT: E  186 GLN cc_start: 0.8868 (tt0) cc_final: 0.8614 (tt0)
REVERT: E  223 ASP cc_start: 0.8712 (m-30) cc_final: 0.8206 (m-30)
REVERT: E  230 MET cc_start: 0.9325 (ttp) cc_final: 0.8956 (ttp)
REVERT: R  134 LYS cc_start: 0.9313 (mtmm) cc_final: 0.9055 (mtpp)
REVERT: R  242 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8323 (mm-40)
REVERT: R  245 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8305 (tp-100)
REVERT: R  347 GLU cc_start: 0.9248 (mp0) cc_final: 0.8914 (mp0)
  outliers start: 17
  outliers final: 9
  residues processed: 131
  average time/residue: 1.4612
  time to fit residues: 202.6420
Evaluate side-chains
  123 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain A residue   27 LYS
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  140 MET
Chi-restraints excluded: chain R residue  122 MET
Chi-restraints excluded: chain R residue  358 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 29 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 99 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  32 GLN
B  75 GLN
B 176 GLN
B 230 ASN
B 259 GLN
** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.075041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.054181 restraints weight = 22040.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.2791 rms_B_bonded: 3.04
r_work: 0.2643 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   9192  Z= 0.333
  Angle     :  0.626   8.445  12544  Z= 0.331
  Chirality :  0.045   0.250   1468
  Planarity :  0.004   0.055   1546
  Dihedral  :  7.609  59.481   1644
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 14.44 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.25), residues: 1144
  helix:  1.61 (0.27), residues: 409
  sheet:  0.34 (0.31), residues: 267
  loop :  0.01 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 211 
 HIS   0.003   0.001   HIS A 329 
 PHE   0.016   0.002   PHE B 253 
 TYR   0.020   0.002   TYR E 235 
 ARG   0.008   0.000   ARG E 160 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   22 ARG cc_start: 0.7934 (mpt-90) cc_final: 0.7708 (mpt-90)
REVERT: B  175 GLN cc_start: 0.8856 (pt0) cc_final: 0.8426 (pp30)
REVERT: B  275 SER cc_start: 0.8997 (t) cc_final: 0.8615 (m)
REVERT: C   29 LYS cc_start: 0.8868 (mttm) cc_final: 0.8578 (mmtt)
REVERT: C   31 SER cc_start: 0.8956 (t) cc_final: 0.8481 (m)
REVERT: C   32 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8398 (mtmm)
REVERT: A   18 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8629 (mtm)
REVERT: A   25 LYS cc_start: 0.7701 (tptt) cc_final: 0.7423 (tmmm)
REVERT: A   27 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7523 (mmtm)
REVERT: A   52 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8589 (pp30)
REVERT: E    3 GLN cc_start: 0.8863 (tt0) cc_final: 0.8597 (tt0)
REVERT: E   13 GLN cc_start: 0.9388 (tp40) cc_final: 0.8859 (pp30)
REVERT: E   73 ASP cc_start: 0.8092 (t0) cc_final: 0.7637 (t0)
REVERT: E  186 GLN cc_start: 0.8896 (tt0) cc_final: 0.8576 (tt0)
REVERT: E  223 ASP cc_start: 0.8727 (m-30) cc_final: 0.8158 (m-30)
REVERT: E  230 MET cc_start: 0.9388 (ttp) cc_final: 0.9010 (ttp)
REVERT: R  134 LYS cc_start: 0.9312 (mtmm) cc_final: 0.9081 (mtpp)
REVERT: R  245 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8343 (tp-100)
REVERT: R  347 GLU cc_start: 0.9300 (mp0) cc_final: 0.9010 (mm-30)
  outliers start: 19
  outliers final: 7
  residues processed: 121
  average time/residue: 1.4366
  time to fit residues: 184.6187
Evaluate side-chains
  117 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   27 LYS
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  140 MET
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain R residue  122 MET
Chi-restraints excluded: chain R residue  358 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 83 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  75 GLN
B 259 GLN
** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.075304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.054513 restraints weight = 22018.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.2802 rms_B_bonded: 3.05
r_work: 0.2653 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.3097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9192  Z= 0.287
  Angle     :  0.615   8.102  12544  Z= 0.324
  Chirality :  0.044   0.233   1468
  Planarity :  0.004   0.052   1546
  Dihedral  :  7.414  59.499   1644
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.42 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.25), residues: 1144
  helix:  1.74 (0.27), residues: 403
  sheet:  0.33 (0.31), residues: 267
  loop :  0.02 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 211 
 HIS   0.003   0.001   HIS A 329 
 PHE   0.013   0.001   PHE B 253 
 TYR   0.017   0.002   TYR E 235 
 ARG   0.010   0.000   ARG E 160 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 LYS cc_start: 0.9361 (ttpp) cc_final: 0.8788 (ptpp)
REVERT: B  175 GLN cc_start: 0.8863 (pt0) cc_final: 0.8437 (pp30)
REVERT: B  275 SER cc_start: 0.9001 (t) cc_final: 0.8641 (m)
REVERT: C   31 SER cc_start: 0.8943 (t) cc_final: 0.8479 (m)
REVERT: C   32 LYS cc_start: 0.8707 (mtmm) cc_final: 0.8464 (mtmm)
REVERT: C   52 THR cc_start: 0.8489 (m) cc_final: 0.7893 (p)
REVERT: A   18 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8624 (mtm)
REVERT: A   25 LYS cc_start: 0.7697 (tptt) cc_final: 0.7431 (tmmm)
REVERT: A   27 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7502 (mmtm)
REVERT: A   52 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8602 (pp30)
REVERT: A  180 LYS cc_start: 0.8483 (mmpt) cc_final: 0.8058 (mptt)
REVERT: E    3 GLN cc_start: 0.8848 (tt0) cc_final: 0.8582 (tt0)
REVERT: E   73 ASP cc_start: 0.8128 (t0) cc_final: 0.7680 (t0)
REVERT: E  186 GLN cc_start: 0.8914 (tt0) cc_final: 0.8594 (tt0)
REVERT: E  223 ASP cc_start: 0.8726 (m-30) cc_final: 0.8158 (m-30)
REVERT: E  230 MET cc_start: 0.9364 (ttp) cc_final: 0.9008 (ttp)
REVERT: R  134 LYS cc_start: 0.9290 (mtmm) cc_final: 0.9083 (mtpp)
REVERT: R  141 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8736 (mtm)
REVERT: R  245 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8336 (tp-100)
REVERT: R  347 GLU cc_start: 0.9297 (mp0) cc_final: 0.8971 (mm-30)
  outliers start: 19
  outliers final: 9
  residues processed: 120
  average time/residue: 1.4486
  time to fit residues: 184.2706
Evaluate side-chains
  121 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   27 LYS
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  140 MET
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  216 ILE
Chi-restraints excluded: chain R residue  122 MET
Chi-restraints excluded: chain R residue  141 MET
Chi-restraints excluded: chain R residue  358 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 110 optimal weight:    7.9990
   chunk 83 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   chunk 62 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    5.9990
   chunk 43 optimal weight:    7.9990
   chunk 61 optimal weight:    9.9990
   chunk 111 optimal weight:    0.8980
   overall best weight:    3.3386

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
E 183 GLN
** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.074158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.053657 restraints weight = 22329.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.2777 rms_B_bonded: 3.02
r_work: 0.2626 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.3187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   9192  Z= 0.373
  Angle     :  0.640   8.590  12544  Z= 0.338
  Chirality :  0.045   0.258   1468
  Planarity :  0.004   0.055   1546
  Dihedral  :  7.440  59.732   1644
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.18 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.25), residues: 1144
  helix:  1.86 (0.27), residues: 397
  sheet:  0.24 (0.32), residues: 263
  loop :  0.05 (0.29), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 211 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.016   0.002   PHE B 253 
 TYR   0.021   0.002   TYR E 235 
 ARG   0.010   0.000   ARG E 160 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  175 GLN cc_start: 0.8859 (pt0) cc_final: 0.8416 (pp30)
REVERT: B  275 SER cc_start: 0.8920 (t) cc_final: 0.8546 (m)
REVERT: C   29 LYS cc_start: 0.8975 (mttm) cc_final: 0.8677 (mmtt)
REVERT: C   31 SER cc_start: 0.8996 (t) cc_final: 0.8556 (m)
REVERT: C   32 LYS cc_start: 0.8758 (mtmm) cc_final: 0.8470 (mtmm)
REVERT: C   52 THR cc_start: 0.8593 (m) cc_final: 0.8007 (p)
REVERT: A   18 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8636 (mtm)
REVERT: A   25 LYS cc_start: 0.7755 (tptt) cc_final: 0.7477 (tmmm)
REVERT: A   27 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7547 (mmtm)
REVERT: A   52 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8581 (pp30)
REVERT: A  180 LYS cc_start: 0.8548 (mmpt) cc_final: 0.8147 (mptt)
REVERT: E    3 GLN cc_start: 0.8844 (tt0) cc_final: 0.8576 (tt0)
REVERT: E   73 ASP cc_start: 0.8137 (t0) cc_final: 0.7698 (t0)
REVERT: E  140 MET cc_start: 0.9230 (mmm) cc_final: 0.9029 (OUTLIER)
REVERT: E  186 GLN cc_start: 0.8893 (tt0) cc_final: 0.8547 (tt0)
REVERT: E  223 ASP cc_start: 0.8764 (m-30) cc_final: 0.8169 (m-30)
REVERT: E  230 MET cc_start: 0.9367 (ttp) cc_final: 0.8984 (ttp)
REVERT: R  134 LYS cc_start: 0.9293 (mtmm) cc_final: 0.9076 (mtpp)
REVERT: R  141 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8787 (mtm)
REVERT: R  245 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8272 (tp40)
REVERT: R  347 GLU cc_start: 0.9316 (mp0) cc_final: 0.8995 (mm-30)
  outliers start: 23
  outliers final: 10
  residues processed: 122
  average time/residue: 1.4122
  time to fit residues: 183.1436
Evaluate side-chains
  119 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   27 LYS
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  216 ILE
Chi-restraints excluded: chain R residue  122 MET
Chi-restraints excluded: chain R residue  141 MET
Chi-restraints excluded: chain R residue  358 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 108 optimal weight:    0.9980
   chunk 67 optimal weight:    7.9990
   chunk 102 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 259 GLN
R 169 GLN
** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.076662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.055781 restraints weight = 22282.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.2833 rms_B_bonded: 3.11
r_work: 0.2684 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9192  Z= 0.199
  Angle     :  0.599   7.889  12544  Z= 0.317
  Chirality :  0.042   0.209   1468
  Planarity :  0.004   0.049   1546
  Dihedral  :  7.170  59.681   1644
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 17.05 %
    Favored  : 80.89 %
  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:  1.10 (0.26), residues: 1144
  helix:  1.81 (0.27), residues: 403
  sheet:  0.41 (0.32), residues: 263
  loop :  0.08 (0.30), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.011   0.001   PHE R 279 
 TYR   0.020   0.001   TYR E 235 
 ARG   0.012   0.000   ARG E 160 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   22 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7917 (tpp-160)
REVERT: B  175 GLN cc_start: 0.8838 (pt0) cc_final: 0.8460 (pp30)
REVERT: B  220 GLN cc_start: 0.9114 (mt0) cc_final: 0.8758 (mt0)
REVERT: B  275 SER cc_start: 0.9032 (t) cc_final: 0.8718 (m)
REVERT: C   29 LYS cc_start: 0.8965 (mttm) cc_final: 0.8642 (mmtt)
REVERT: C   31 SER cc_start: 0.8990 (t) cc_final: 0.8602 (m)
REVERT: C   32 LYS cc_start: 0.8701 (mtmm) cc_final: 0.8452 (mtmm)
REVERT: C   41 CYS cc_start: 0.8880 (m) cc_final: 0.8654 (m)
REVERT: C   42 GLU cc_start: 0.8460 (pp20) cc_final: 0.8246 (pp20)
REVERT: C   52 THR cc_start: 0.8553 (m) cc_final: 0.8008 (p)
REVERT: A   18 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8620 (mtm)
REVERT: A   22 GLN cc_start: 0.8150 (tp40) cc_final: 0.7752 (tp40)
REVERT: A   25 LYS cc_start: 0.7686 (tptt) cc_final: 0.7431 (tmmm)
REVERT: A   27 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7470 (mmtm)
REVERT: A   52 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8589 (pp30)
REVERT: A  180 LYS cc_start: 0.8651 (mmpt) cc_final: 0.8299 (mptt)
REVERT: E    3 GLN cc_start: 0.8822 (tt0) cc_final: 0.8568 (tt0)
REVERT: E   73 ASP cc_start: 0.8119 (t0) cc_final: 0.7683 (t0)
REVERT: E  186 GLN cc_start: 0.8884 (tt0) cc_final: 0.8580 (tt0)
REVERT: E  223 ASP cc_start: 0.8719 (m-30) cc_final: 0.8111 (m-30)
REVERT: E  230 MET cc_start: 0.9338 (ttp) cc_final: 0.9004 (ttp)
REVERT: R  245 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8228 (tp-100)
REVERT: R  260 GLU cc_start: 0.7790 (pm20) cc_final: 0.7408 (pm20)
REVERT: R  264 GLU cc_start: 0.8537 (mt-10) cc_final: 0.7953 (mp0)
REVERT: R  347 GLU cc_start: 0.9285 (mp0) cc_final: 0.9023 (mm-30)
  outliers start: 19
  outliers final: 11
  residues processed: 126
  average time/residue: 1.3714
  time to fit residues: 183.6655
Evaluate side-chains
  123 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   27 LYS
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain E residue   58 ILE
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  140 MET
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  216 ILE
Chi-restraints excluded: chain R residue  122 MET
Chi-restraints excluded: chain R residue  358 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0270
   chunk 30 optimal weight:   10.0000
   chunk 71 optimal weight:    0.5980
   chunk 8 optimal weight:    4.9990
   chunk 106 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 9 optimal weight:    0.0370
   overall best weight:    1.3320

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.076522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.055743 restraints weight = 21919.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.2835 rms_B_bonded: 3.07
r_work: 0.2687 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.3475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9192  Z= 0.215
  Angle     :  0.603   8.241  12544  Z= 0.319
  Chirality :  0.042   0.227   1468
  Planarity :  0.004   0.049   1546
  Dihedral  :  6.932  58.854   1644
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 18.02 %
    Favored  : 80.13 %
  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:  1.18 (0.26), residues: 1144
  helix:  1.96 (0.27), residues: 397
  sheet:  0.41 (0.33), residues: 246
  loop :  0.12 (0.29), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 211 
 HIS   0.002   0.001   HIS E  35 
 PHE   0.011   0.001   PHE B 253 
 TYR   0.021   0.001   TYR E 235 
 ARG   0.013   0.000   ARG E 160 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 1.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  175 GLN cc_start: 0.8848 (pt0) cc_final: 0.8464 (pp30)
REVERT: B  275 SER cc_start: 0.9087 (t) cc_final: 0.8791 (m)
REVERT: C   29 LYS cc_start: 0.8987 (mttm) cc_final: 0.8716 (mmpt)
REVERT: C   31 SER cc_start: 0.8982 (t) cc_final: 0.8616 (m)
REVERT: C   32 LYS cc_start: 0.8690 (mtmm) cc_final: 0.8427 (mtmm)
REVERT: C   42 GLU cc_start: 0.8470 (pp20) cc_final: 0.8235 (pp20)
REVERT: C   52 THR cc_start: 0.8628 (m) cc_final: 0.8110 (p)
REVERT: A   18 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8604 (mtm)
REVERT: A   22 GLN cc_start: 0.8086 (tp40) cc_final: 0.7616 (tp40)
REVERT: A   25 LYS cc_start: 0.7663 (tptt) cc_final: 0.7409 (tmmm)
REVERT: A   27 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7477 (mmtm)
REVERT: A   52 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8575 (pp30)
REVERT: A  180 LYS cc_start: 0.8627 (mmpt) cc_final: 0.8273 (mptt)
REVERT: A  251 THR cc_start: 0.9519 (OUTLIER) cc_final: 0.9208 (t)
REVERT: E    3 GLN cc_start: 0.8745 (tt0) cc_final: 0.8491 (tt0)
REVERT: E   73 ASP cc_start: 0.8137 (t0) cc_final: 0.7686 (t0)
REVERT: E  186 GLN cc_start: 0.8888 (tt0) cc_final: 0.8588 (tt0)
REVERT: E  223 ASP cc_start: 0.8709 (m-30) cc_final: 0.8102 (m-30)
REVERT: E  230 MET cc_start: 0.9332 (ttp) cc_final: 0.9014 (ttp)
REVERT: R  173 GLU cc_start: 0.8352 (mp0) cc_final: 0.7412 (mm-30)
REVERT: R  347 GLU cc_start: 0.9289 (mp0) cc_final: 0.9066 (mm-30)
  outliers start: 17
  outliers final: 11
  residues processed: 118
  average time/residue: 1.3819
  time to fit residues: 173.2803
Evaluate side-chains
  119 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   27 LYS
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain E residue   58 ILE
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain E residue  140 MET
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  216 ILE
Chi-restraints excluded: chain R residue  122 MET
Chi-restraints excluded: chain R residue  358 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 86 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0070
   chunk 61 optimal weight:    9.9990
   chunk 70 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 111 optimal weight:    0.9990
   overall best weight:    1.1202

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.077112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.056631 restraints weight = 21936.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 3.05
r_work: 0.2705 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.3597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9192  Z= 0.202
  Angle     :  0.604   8.161  12544  Z= 0.320
  Chirality :  0.042   0.214   1468
  Planarity :  0.004   0.047   1546
  Dihedral  :  6.801  59.565   1644
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 18.46 %
    Favored  : 80.13 %
  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:  1.15 (0.26), residues: 1144
  helix:  1.86 (0.27), residues: 405
  sheet:  0.46 (0.33), residues: 253
  loop :  0.10 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 211 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.010   0.001   PHE R 279 
 TYR   0.018   0.001   TYR E 235 
 ARG   0.006   0.000   ARG E 160 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  175 GLN cc_start: 0.8843 (pt0) cc_final: 0.8443 (pp30)
REVERT: B  215 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7713 (pp20)
REVERT: B  275 SER cc_start: 0.9078 (t) cc_final: 0.8798 (m)
REVERT: C   29 LYS cc_start: 0.9010 (mttm) cc_final: 0.8666 (mmtt)
REVERT: C   31 SER cc_start: 0.9048 (t) cc_final: 0.8726 (m)
REVERT: C   32 LYS cc_start: 0.8642 (mtmm) cc_final: 0.8416 (mtmm)
REVERT: C   42 GLU cc_start: 0.8476 (pp20) cc_final: 0.8233 (pp20)
REVERT: C   52 THR cc_start: 0.8707 (m) cc_final: 0.8236 (p)
REVERT: A   18 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8611 (mtm)
REVERT: A   22 GLN cc_start: 0.8084 (tp40) cc_final: 0.7617 (tp40)
REVERT: A   25 LYS cc_start: 0.7615 (tptt) cc_final: 0.7409 (tmmm)
REVERT: A   27 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7448 (mmtm)
REVERT: A   52 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8563 (pp30)
REVERT: A  180 LYS cc_start: 0.8604 (mmpt) cc_final: 0.8264 (mptt)
REVERT: A  251 THR cc_start: 0.9519 (OUTLIER) cc_final: 0.9223 (t)
REVERT: A  325 ILE cc_start: 0.9086 (mt) cc_final: 0.8615 (tp)
REVERT: E    3 GLN cc_start: 0.8716 (tt0) cc_final: 0.8486 (tt0)
REVERT: E   73 ASP cc_start: 0.8155 (t0) cc_final: 0.7715 (t0)
REVERT: E  160 ARG cc_start: 0.8949 (mtm110) cc_final: 0.8746 (mtm110)
REVERT: E  186 GLN cc_start: 0.8889 (tt0) cc_final: 0.8581 (tt0)
REVERT: E  223 ASP cc_start: 0.8720 (m-30) cc_final: 0.8107 (m-30)
REVERT: E  230 MET cc_start: 0.9300 (ttp) cc_final: 0.8980 (ttp)
REVERT: R   91 ASP cc_start: 0.8874 (p0) cc_final: 0.8621 (p0)
REVERT: R  173 GLU cc_start: 0.8354 (mp0) cc_final: 0.7429 (mm-30)
REVERT: R  260 GLU cc_start: 0.7727 (pm20) cc_final: 0.7178 (pm20)
REVERT: R  264 GLU cc_start: 0.8539 (mt-10) cc_final: 0.7835 (mp0)
REVERT: R  347 GLU cc_start: 0.9267 (mp0) cc_final: 0.9055 (mm-30)
  outliers start: 13
  outliers final: 9
  residues processed: 118
  average time/residue: 1.4023
  time to fit residues: 176.0312
Evaluate side-chains
  118 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   27 LYS
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain E residue  140 MET
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  216 ILE
Chi-restraints excluded: chain R residue  122 MET
Chi-restraints excluded: chain R residue  358 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 76 optimal weight:   10.0000
   chunk 69 optimal weight:    6.9990
   chunk 67 optimal weight:    0.2980
   chunk 29 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 72 optimal weight:    9.9990
   chunk 49 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 81 optimal weight:    6.9990
   chunk 18 optimal weight:    0.4980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  32 GLN
** R 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.077766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.056884 restraints weight = 22034.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 3.10
r_work: 0.2719 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.3693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9192  Z= 0.188
  Angle     :  0.590   8.216  12544  Z= 0.312
  Chirality :  0.042   0.210   1468
  Planarity :  0.004   0.046   1546
  Dihedral  :  6.638  59.234   1644
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 18.68 %
    Favored  : 80.13 %
  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:  1.22 (0.26), residues: 1144
  helix:  1.93 (0.27), residues: 399
  sheet:  0.50 (0.33), residues: 252
  loop :  0.14 (0.29), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 211 
 HIS   0.002   0.000   HIS E  35 
 PHE   0.010   0.001   PHE R 279 
 TYR   0.017   0.001   TYR E 235 
 ARG   0.007   0.000   ARG E 160 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6109.65 seconds
wall clock time: 109 minutes 1.40 seconds (6541.40 seconds total)