Starting phenix.real_space_refine
on Wed Jan 15 18:05:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zjd_60141/01_2025/8zjd_60141.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zjd_60141/01_2025/8zjd_60141.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zjd_60141/01_2025/8zjd_60141.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zjd_60141/01_2025/8zjd_60141.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zjd_60141/01_2025/8zjd_60141.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zjd_60141/01_2025/8zjd_60141.cif"
  }
  resolution = 3.06
  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=   0.007 sd=   0.058
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    5617      2.51       5
     N    1521      2.21       5
     O    1627      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8820
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2204
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 16, 'TRANS': 268}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 16
    Chain: "L"
      Number of atoms: 94
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 94
          Classifications: {'peptide': 11}
          Link IDs: {'TRANS': 10}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2555
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 36
    Chain: "S"
      Number of atoms: 1741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1741
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 10, 'TRANS': 218}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "G"
      Number of atoms: 386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 386
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 3, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "A"
      Number of atoms: 1840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1840
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 5, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 21
  Time building chain proxies: 5.42, per 1000 atoms: 0.61
  Number of scatterers: 8820
  At special positions: 0
  Unit cell: (97.09, 115.34, 129.21, 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      55     16.00
     O    1627      8.00
     N    1521      7.00
     C    5617      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 115 " - pdb=" SG  CYS R 191 " distance=2.33

  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: 2.33
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2142

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 13 sheets defined
      40.7% alpha, 22.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'R' and resid 43 through 69
      removed outlier: 3.823A  pdb=" N   LEU R  47 " --> pdb=" O   TRP R  43 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ARG R  69 " --> pdb=" O   TYR R  65 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 75 through 94
    Processing helix  chain 'R' and resid 95 through 103
      removed outlier: 3.624A  pdb=" N   ALA R 100 " --> pdb=" O   VAL R  96 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 111 through 146
    Processing helix  chain 'R' and resid 148 through 152
      removed outlier: 3.571A  pdb=" N   HIS R 152 " --> pdb=" O   ARG R 149 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 155 through 174
    Processing helix  chain 'R' and resid 175 through 180
      removed outlier: 4.307A  pdb=" N   ALA R 179 " --> pdb=" O   ALA R 175 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 197 through 213
    Processing helix  chain 'R' and resid 213 through 234
    Processing helix  chain 'R' and resid 244 through 289
      removed outlier: 5.285A  pdb=" N   ALA R 256 " --> pdb=" O   GLU R 252 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   VAL R 257 " --> pdb=" O   ARG R 253 " (cutoff:3.500A)
      Proline residue:  R 278  - end of helix
    Processing helix  chain 'R' and resid 298 through 324
      removed outlier: 3.729A  pdb=" N   SER R 316 " --> pdb=" O   SER R 312 " (cutoff:3.500A)
      Proline residue:  R 320  - end of helix
    Processing helix  chain 'R' and resid 327 through 337
    Processing helix  chain 'L' and resid 212 through 216
    Processing helix  chain 'B' and resid 10 through 31
      removed outlier: 4.435A  pdb=" N   GLN B  14 " --> pdb=" O   ASP B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 39
    Processing helix  chain 'B' and resid 271 through 275
      removed outlier: 3.781A  pdb=" N   ILE B 275 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 27 through 31
    Processing helix  chain 'S' and resid 52 through 55
    Processing helix  chain 'S' and resid 61 through 64
      removed outlier: 3.588A  pdb=" N   LYS S  64 " --> pdb=" O   ASP S  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 61 through 64'
    Processing helix  chain 'S' and resid 73 through 75
      No H-bonds generated for 'chain 'S' and resid 73 through 75'
    Processing helix  chain 'S' and resid 86 through 90
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.580A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 28 through 43
    Processing helix  chain 'G' and resid 44 through 47
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.603A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 57
    Processing helix  chain 'A' and resid 214 through 223
      removed outlier: 4.427A  pdb=" N   ILE A 219 " --> pdb=" O   ARG A 216 " (cutoff:3.500A)
      removed outlier: 5.619A  pdb=" N   HIS A 220 " --> pdb=" O   LYS A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 237
      No H-bonds generated for 'chain 'A' and resid 235 through 237'
    Processing helix  chain 'A' and resid 248 through 262
    Processing helix  chain 'A' and resid 277 through 285
    Processing helix  chain 'A' and resid 289 through 293
    Processing helix  chain 'A' and resid 303 through 317
    Processing helix  chain 'A' and resid 337 through 358
    Processing sheet with id=AA1, first strand: chain 'R' and resid 181 through 184
    Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 57
      removed outlier: 4.171A  pdb=" N   PHE B 340 " --> pdb=" O   SER B 336 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER B 336 " --> pdb=" O   PHE B 340 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   CYS B 322 " --> pdb=" O   GLY B 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68
      removed outlier: 3.763A  pdb=" N   LYS B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   LEU B  84 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ALA B  97 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ILE B  86 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110
      removed outlier: 6.787A  pdb=" N   GLY B 120 " --> pdb=" O   MET B 106 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   CYS B 108 " --> pdb=" O   ALA B 118 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   ALA B 118 " --> pdb=" O   CYS B 108 " (cutoff:3.500A)
      removed outlier: 4.927A  pdb=" N   TYR B 110 " --> pdb=" O   TYR B 116 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   TYR B 116 " --> pdb=" O   TYR B 110 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   CYS B 126 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   GLU B 143 " --> pdb=" O   CYS B 126 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   ILE B 128 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ARG B 139 " --> pdb=" O   ASN B 130 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156
      removed outlier: 4.388A  pdb=" N   THR B 170 " --> pdb=" O   SER B 166 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ASP B 175 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   GLN B 181 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197
      removed outlier: 6.798A  pdb=" N   GLY B 207 " --> pdb=" O   MET B 193 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   LEU B 195 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   VAL B 205 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
      removed outlier: 5.047A  pdb=" N   LEU B 197 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   LEU B 203 " --> pdb=" O   LEU B 197 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   SER B 212 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ALA B 213 " --> pdb=" O   THR B 226 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   THR B 226 " --> pdb=" O   ALA B 213 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   LEU B 215 " --> pdb=" O   ARG B 224 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   MET B 222 " --> pdb=" O   ASP B 217 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239
      removed outlier: 3.620A  pdb=" N   MET B 267 " --> pdb=" O   LEU B 257 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   ASP B 259 " --> pdb=" O   GLU B 265 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   GLU B 265 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 282 through 283
      removed outlier: 3.781A  pdb=" N   CYS B 299 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLY B 311 " --> pdb=" O   VAL B 301 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ASP B 303 " --> pdb=" O   ARG B 309 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   ARG B 309 " --> pdb=" O   ASP B 303 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 2 through 5
      removed outlier: 5.411A  pdb=" N   GLY S  15 " --> pdb=" O   SER S  84 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 9 through 11
      removed outlier: 6.951A  pdb=" N   MET S  33 " --> pdb=" O   TYR S  49 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   TYR S  49 " --> pdb=" O   MET S  33 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   TRP S  35 " --> pdb=" O   VAL S  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 141
    Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148
      removed outlier: 6.714A  pdb=" N   VAL S 147 " --> pdb=" O   GLU S 246 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 192 through 197
      removed outlier: 9.849A  pdb=" N   SER A 227 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   LYS A  35 " --> pdb=" O   SER A 227 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   MET A 229 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   LEU A  37 " --> pdb=" O   MET A 229 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   LEU A 231 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   LEU A  39 " --> pdb=" O   LEU A 231 " (cutoff:3.500A)
      removed outlier: 8.898A  pdb=" N   ALA A 233 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   ILE A 228 " --> pdb=" O   ILE A 272 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   PHE A 274 " --> pdb=" O   ILE A 228 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   PHE A 230 " --> pdb=" O   PHE A 274 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   ASN A 276 " --> pdb=" O   PHE A 230 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   VAL A 232 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)

    469 hydrogen bonds defined for protein.
    1308 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: 2.58

  Time building geometry restraints manager: 2.70 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1432
        1.31 -     1.44: 2527
        1.44 -     1.56: 4973
        1.56 -     1.69: 1
        1.69 -     1.82: 79
  Bond restraints: 9012
  Sorted by residual:
  bond pdb=" CA  VAL R 138 "
       pdb=" C   VAL R 138 "
    ideal  model  delta    sigma   weight residual
    1.525  1.465  0.060 1.27e-02 6.20e+03 2.25e+01
  bond pdb=" C   ASP R 139 "
       pdb=" O   ASP R 139 "
    ideal  model  delta    sigma   weight residual
    1.236  1.188  0.048 1.19e-02 7.06e+03 1.61e+01
  bond pdb=" CA  LYS A 356 "
       pdb=" C   LYS A 356 "
    ideal  model  delta    sigma   weight residual
    1.522  1.466  0.056 1.40e-02 5.10e+03 1.59e+01
  bond pdb=" C   ARG R 140 "
       pdb=" O   ARG R 140 "
    ideal  model  delta    sigma   weight residual
    1.236  1.188  0.048 1.25e-02 6.40e+03 1.48e+01
  bond pdb=" CA  ASP R 139 "
       pdb=" C   ASP R 139 "
    ideal  model  delta    sigma   weight residual
    1.524  1.475  0.049 1.29e-02 6.01e+03 1.46e+01
  ... (remaining 9007 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 11956
        1.92 -     3.83: 246
        3.83 -     5.75: 32
        5.75 -     7.67: 5
        7.67 -     9.59: 5
  Bond angle restraints: 12244
  Sorted by residual:
  angle pdb=" N   ASP B  81 "
        pdb=" CA  ASP B  81 "
        pdb=" C   ASP B  81 "
      ideal   model   delta    sigma   weight residual
     113.16  103.83    9.33 1.24e+00 6.50e-01 5.67e+01
  angle pdb=" N   TYR A 358 "
        pdb=" CA  TYR A 358 "
        pdb=" C   TYR A 358 "
      ideal   model   delta    sigma   weight residual
     112.97  106.95    6.02 1.06e+00 8.90e-01 3.22e+01
  angle pdb=" N   VAL R 249 "
        pdb=" CA  VAL R 249 "
        pdb=" C   VAL R 249 "
      ideal   model   delta    sigma   weight residual
     110.74  105.63    5.11 9.10e-01 1.21e+00 3.15e+01
  angle pdb=" N   VAL R 138 "
        pdb=" CA  VAL R 138 "
        pdb=" C   VAL R 138 "
      ideal   model   delta    sigma   weight residual
     113.16  106.38    6.78 1.49e+00 4.50e-01 2.07e+01
  angle pdb=" N   ASP R 139 "
        pdb=" CA  ASP R 139 "
        pdb=" C   ASP R 139 "
      ideal   model   delta    sigma   weight residual
     111.40  105.88    5.52 1.22e+00 6.72e-01 2.05e+01
  ... (remaining 12239 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 4796
       17.79 -    35.57: 397
       35.57 -    53.36: 100
       53.36 -    71.15: 14
       71.15 -    88.94: 10
  Dihedral angle restraints: 5317
    sinusoidal: 1999
      harmonic: 3318
  Sorted by residual:
  dihedral pdb=" CB  CYS R 115 "
           pdb=" SG  CYS R 115 "
           pdb=" SG  CYS R 191 "
           pdb=" CB  CYS R 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    4.06   88.94     1      1.00e+01 1.00e-02 9.42e+01
  dihedral pdb=" CA  GLN S  12 "
           pdb=" C   GLN S  12 "
           pdb=" N   PRO S  13 "
           pdb=" CA  PRO S  13 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.33  -19.67     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  LYS B  83 "
           pdb=" C   LYS B  83 "
           pdb=" N   LEU B  84 "
           pdb=" CA  LEU B  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.47   19.53     0      5.00e+00 4.00e-02 1.53e+01
  ... (remaining 5314 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 1300
       0.091 -    0.182: 84
       0.182 -    0.272: 6
       0.272 -    0.363: 2
       0.363 -    0.454: 1
  Chirality restraints: 1393
  Sorted by residual:
  chirality pdb=" CA  ASN A 359 "
            pdb=" N   ASN A 359 "
            pdb=" C   ASN A 359 "
            pdb=" CB  ASN A 359 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.15e+00
  chirality pdb=" CA  VAL R 249 "
            pdb=" N   VAL R 249 "
            pdb=" C   VAL R 249 "
            pdb=" CB  VAL R 249 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.76   -0.32 2.00e-01 2.50e+01 2.57e+00
  chirality pdb=" CA  LEU R 245 "
            pdb=" N   LEU R 245 "
            pdb=" C   LEU R 245 "
            pdb=" CB  LEU R 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.97e+00
  ... (remaining 1390 not shown)

  Planarity restraints: 1557
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET R 136 "   -0.011 2.00e-02 2.50e+03   2.16e-02 4.67e+00
        pdb=" C   MET R 136 "    0.037 2.00e-02 2.50e+03
        pdb=" O   MET R 136 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER R 137 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R 256 "    0.010 2.00e-02 2.50e+03   2.10e-02 4.42e+00
        pdb=" C   ALA R 256 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   ALA R 256 "    0.014 2.00e-02 2.50e+03
        pdb=" N   VAL R 257 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 338 "   -0.009 2.00e-02 2.50e+03   1.87e-02 3.49e+00
        pdb=" C   ASP B 338 "    0.032 2.00e-02 2.50e+03
        pdb=" O   ASP B 338 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   SER B 339 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1554 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 839
        2.74 -     3.28: 9025
        3.28 -     3.82: 14756
        3.82 -     4.36: 17644
        4.36 -     4.90: 31154
  Nonbonded interactions: 73418
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 237 "
            pdb=" OG  SER A 288 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   ARG R 297 "
            pdb=" OH  TYR L 211 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OH  TYR B 150 "
            pdb=" OD2 ASP B 191 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   VAL R  96 "
            pdb=" OG1 THR R  99 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   ASP B 210 "
            pdb=" OD1 ASP B 210 "
     model   vdw
     2.322 3.040
  ... (remaining 73413 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:             0.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.820
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
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      :  0.004   0.060   9012  Z= 0.284
  Angle     :  0.674   9.587  12244  Z= 0.398
  Chirality :  0.046   0.454   1393
  Planarity :  0.004   0.050   1557
  Dihedral  : 14.501  85.750   3172
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 14.67 %
    Favored  : 84.79 %
  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:  0.74 (0.26), residues: 1121
  helix:  1.57 (0.26), residues: 417
  sheet:  0.27 (0.32), residues: 278
  loop : -0.34 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 104 
 HIS   0.002   0.001   HIS B 147 
 PHE   0.016   0.001   PHE L 220 
 TYR   0.015   0.001   TYR R  65 
 ARG   0.010   0.000   ARG L 219 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 156
  time to evaluate  : 1.057 
Fit side-chains
REVERT: R   62 LEU cc_start: 0.8167 (mp) cc_final: 0.7961 (mp)
REVERT: R   71 LYS cc_start: 0.6979 (mmmt) cc_final: 0.6734 (tptp)
REVERT: R   78 ASN cc_start: 0.8894 (m110) cc_final: 0.8665 (m110)
REVERT: R  253 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6590 (ttp-170)
REVERT: R  315 ASN cc_start: 0.8264 (t0) cc_final: 0.8042 (t0)
REVERT: B  222 MET cc_start: 0.7156 (ptt) cc_final: 0.6885 (ptm)
REVERT: B  273 ASN cc_start: 0.8509 (m110) cc_final: 0.8171 (m110)
REVERT: S   45 GLU cc_start: 0.7652 (tt0) cc_final: 0.7443 (tt0)
REVERT: G   31 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8693 (tptt)
REVERT: G   46 GLU cc_start: 0.8252 (mp0) cc_final: 0.7867 (mp0)
  outliers start: 5
  outliers final: 3
  residues processed: 160
  average time/residue: 0.2673
  time to fit residues: 56.8182
Evaluate side-chains
  130 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 126
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   95 CYS
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  190 TYR
Chi-restraints excluded: chain R residue  253 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 84 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 52 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 100 optimal weight:    6.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
R  78 ASN
R  83 ASN
B 273 ASN
S  38 GLN
S 112 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.153165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.109506 restraints weight = 12253.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.90
r_work: 0.3259 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.1323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9012  Z= 0.288
  Angle     :  0.612   6.732  12244  Z= 0.323
  Chirality :  0.044   0.156   1393
  Planarity :  0.004   0.052   1557
  Dihedral  :  5.381  57.918   1250
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 15.10 %
    Favored  : 82.63 %
  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:  0.81 (0.25), residues: 1121
  helix:  1.78 (0.25), residues: 409
  sheet:  0.24 (0.31), residues: 285
  loop : -0.40 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 174 
 HIS   0.004   0.001   HIS B 147 
 PHE   0.012   0.001   PHE S  28 
 TYR   0.015   0.002   TYR B  64 
 ARG   0.005   0.000   ARG A  29 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.968 
Fit side-chains
REVERT: R   71 LYS cc_start: 0.6964 (mmmt) cc_final: 0.6659 (tptp)
REVERT: R  212 LEU cc_start: 0.8287 (mp) cc_final: 0.8016 (mp)
REVERT: R  253 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6444 (ttp-170)
REVERT: R  305 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8094 (tmtt)
REVERT: B  134 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7779 (ttt90)
REVERT: B  135 GLU cc_start: 0.8746 (mp0) cc_final: 0.8417 (mp0)
REVERT: B  222 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6971 (ptm)
REVERT: B  273 ASN cc_start: 0.8675 (m-40) cc_final: 0.8329 (m110)
REVERT: S   81 GLN cc_start: 0.7799 (tp-100) cc_final: 0.7561 (tp-100)
REVERT: G   31 LYS cc_start: 0.8990 (ttpt) cc_final: 0.8597 (tptt)
REVERT: G   46 GLU cc_start: 0.8316 (mp0) cc_final: 0.8009 (mp0)
  outliers start: 21
  outliers final: 10
  residues processed: 150
  average time/residue: 0.2318
  time to fit residues: 47.8943
Evaluate side-chains
  140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  190 TYR
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  305 LYS
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain L residue  214 ASN
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  213 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 10 optimal weight:    0.2980
   chunk 12 optimal weight:    1.9990
   chunk 78 optimal weight:    0.2980
   chunk 62 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
R  83 ASN
B 300 ASN
S  38 GLN
S 112 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.154682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.111998 restraints weight = 12388.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.90
r_work: 0.3283 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9012  Z= 0.171
  Angle     :  0.537   5.830  12244  Z= 0.280
  Chirality :  0.041   0.138   1393
  Planarity :  0.004   0.048   1557
  Dihedral  :  5.089  53.104   1249
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 14.24 %
    Favored  : 83.06 %
  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:  0.92 (0.26), residues: 1121
  helix:  1.98 (0.25), residues: 410
  sheet:  0.27 (0.32), residues: 275
  loop : -0.42 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 344 
 HIS   0.002   0.001   HIS R 309 
 PHE   0.010   0.001   PHE B 246 
 TYR   0.021   0.001   TYR A 237 
 ARG   0.004   0.000   ARG S  86 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.7021 (mmmt) cc_final: 0.6649 (tptp)
REVERT: R  212 LEU cc_start: 0.8123 (mp) cc_final: 0.7878 (mp)
REVERT: R  253 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6321 (ttp-170)
REVERT: B  222 MET cc_start: 0.7317 (ptt) cc_final: 0.7035 (ptm)
REVERT: B  273 ASN cc_start: 0.8687 (m-40) cc_final: 0.8446 (m110)
REVERT: S   66 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7425 (ttp-110)
REVERT: S   81 GLN cc_start: 0.7740 (tp-100) cc_final: 0.7411 (tp-100)
REVERT: S   86 ARG cc_start: 0.7334 (mtp85) cc_final: 0.6833 (mtm-85)
REVERT: S  194 ASN cc_start: 0.6586 (m110) cc_final: 0.6354 (m110)
REVERT: G   31 LYS cc_start: 0.8926 (ttpt) cc_final: 0.8502 (tptt)
REVERT: G   46 GLU cc_start: 0.8268 (mp0) cc_final: 0.7996 (mp0)
  outliers start: 25
  outliers final: 13
  residues processed: 161
  average time/residue: 0.2026
  time to fit residues: 45.3239
Evaluate side-chains
  143 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  190 TYR
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  158 ASP
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain A residue  314 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 24 optimal weight:   20.0000
   chunk 55 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9980
   chunk 86 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 23 optimal weight:    0.1980
   chunk 97 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 91 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
S  38 GLN
S 112 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.154325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.111704 restraints weight = 12227.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 2.88
r_work: 0.3279 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9012  Z= 0.193
  Angle     :  0.540   7.036  12244  Z= 0.280
  Chirality :  0.041   0.137   1393
  Planarity :  0.004   0.055   1557
  Dihedral  :  4.952  49.096   1249
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.40 %
    Favored  : 81.01 %
  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:  0.88 (0.25), residues: 1121
  helix:  2.02 (0.25), residues: 410
  sheet:  0.20 (0.31), residues: 279
  loop : -0.50 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 174 
 HIS   0.006   0.001   HIS R 181 
 PHE   0.010   0.001   PHE B 246 
 TYR   0.013   0.001   TYR R  65 
 ARG   0.004   0.000   ARG B 134 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.7021 (mmmt) cc_final: 0.6698 (tptp)
REVERT: R   78 ASN cc_start: 0.8723 (m-40) cc_final: 0.8486 (m110)
REVERT: R  212 LEU cc_start: 0.8222 (mp) cc_final: 0.7934 (mp)
REVERT: R  253 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6321 (ttp-170)
REVERT: B  222 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.7024 (ptm)
REVERT: B  273 ASN cc_start: 0.8670 (m-40) cc_final: 0.8411 (m110)
REVERT: B  274 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7662 (pp)
REVERT: S   66 ARG cc_start: 0.7738 (mtm-85) cc_final: 0.7380 (ttp-110)
REVERT: S   86 ARG cc_start: 0.7360 (mtp85) cc_final: 0.6853 (mtm-85)
REVERT: G   46 GLU cc_start: 0.8266 (mp0) cc_final: 0.7978 (mp0)
  outliers start: 24
  outliers final: 17
  residues processed: 156
  average time/residue: 0.2132
  time to fit residues: 46.2046
Evaluate side-chains
  152 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  160 LEU
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  190 TYR
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  158 ASP
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue  213 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 86 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0020
   chunk 18 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 88 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9990
   chunk 11 optimal weight:    6.9990
   chunk 69 optimal weight:    3.9990
   overall best weight:    0.7590

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

Flipped N/Q/H residues before XYZ refinement:
R  83 ASN
S  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.156347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.113825 restraints weight = 12266.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 2.90
r_work: 0.3306 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9012  Z= 0.151
  Angle     :  0.520   9.227  12244  Z= 0.267
  Chirality :  0.041   0.135   1393
  Planarity :  0.004   0.051   1557
  Dihedral  :  4.734  48.407   1249
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 17.15 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.26), residues: 1121
  helix:  2.16 (0.25), residues: 409
  sheet:  0.18 (0.32), residues: 275
  loop : -0.44 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 174 
 HIS   0.005   0.001   HIS R 181 
 PHE   0.009   0.001   PHE B 246 
 TYR   0.014   0.001   TYR A 237 
 ARG   0.006   0.000   ARG B 139 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 149
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.6998 (mmmt) cc_final: 0.6665 (tptp)
REVERT: R   78 ASN cc_start: 0.8732 (m-40) cc_final: 0.8512 (m110)
REVERT: R  212 LEU cc_start: 0.8086 (mp) cc_final: 0.7802 (mp)
REVERT: R  253 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6358 (ttp-110)
REVERT: B  222 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7162 (ptm)
REVERT: B  273 ASN cc_start: 0.8650 (m-40) cc_final: 0.8335 (m110)
REVERT: B  274 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7720 (pp)
REVERT: S   86 ARG cc_start: 0.7380 (mtp85) cc_final: 0.6721 (mtt-85)
REVERT: G   46 GLU cc_start: 0.8258 (mp0) cc_final: 0.7964 (mp0)
  outliers start: 22
  outliers final: 16
  residues processed: 163
  average time/residue: 0.2165
  time to fit residues: 49.1664
Evaluate side-chains
  155 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  160 LEU
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue  261 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0670
   chunk 103 optimal weight:    0.9990
   chunk 57 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 13 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 4 optimal weight:    7.9990
   chunk 85 optimal weight:    0.0870
   chunk 50 optimal weight:    4.9990
   overall best weight:    1.0302

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

Flipped N/Q/H residues before XYZ refinement:
R 181 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.155709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.112848 restraints weight = 12366.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.95
r_work: 0.3293 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9012  Z= 0.170
  Angle     :  0.525   7.549  12244  Z= 0.270
  Chirality :  0.041   0.137   1393
  Planarity :  0.004   0.055   1557
  Dihedral  :  4.570  47.831   1247
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.29 %
    Favored  : 81.12 %
  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:  1.00 (0.25), residues: 1121
  helix:  2.21 (0.25), residues: 409
  sheet:  0.19 (0.32), residues: 269
  loop : -0.46 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 174 
 HIS   0.004   0.001   HIS R 181 
 PHE   0.009   0.001   PHE R 282 
 TYR   0.014   0.001   TYR R 190 
 ARG   0.007   0.000   ARG A  29 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.6985 (mmmt) cc_final: 0.6650 (tptp)
REVERT: R  212 LEU cc_start: 0.8143 (mp) cc_final: 0.7864 (mp)
REVERT: R  253 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6287 (ttp-110)
REVERT: B  222 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7185 (ptm)
REVERT: B  273 ASN cc_start: 0.8665 (m-40) cc_final: 0.8405 (m110)
REVERT: B  274 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7674 (pp)
REVERT: S   66 ARG cc_start: 0.7674 (mtm-85) cc_final: 0.7422 (ttp-110)
REVERT: S   86 ARG cc_start: 0.7418 (mtp85) cc_final: 0.6742 (mtt-85)
REVERT: G   46 GLU cc_start: 0.8264 (mp0) cc_final: 0.7970 (mp0)
  outliers start: 24
  outliers final: 18
  residues processed: 162
  average time/residue: 0.2123
  time to fit residues: 47.8487
Evaluate side-chains
  159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  160 LEU
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  158 ASP
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue  261 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 43 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   chunk 105 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 101 optimal weight:    0.8980
   chunk 108 optimal weight:    7.9990
   chunk 87 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
R  83 ASN
R 181 HIS
B  80 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.152605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.109284 restraints weight = 12507.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 2.95
r_work: 0.3227 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   9012  Z= 0.311
  Angle     :  0.597   9.798  12244  Z= 0.307
  Chirality :  0.043   0.163   1393
  Planarity :  0.004   0.053   1557
  Dihedral  :  4.810  46.960   1247
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 17.26 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.83 (0.25), residues: 1121
  helix:  2.10 (0.25), residues: 406
  sheet:  0.01 (0.31), residues: 284
  loop : -0.52 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP S  35 
 HIS   0.004   0.001   HIS R 309 
 PHE   0.013   0.001   PHE S  28 
 TYR   0.020   0.002   TYR B  64 
 ARG   0.006   0.000   ARG B 139 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 138
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.6932 (mmmt) cc_final: 0.6512 (tptp)
REVERT: R  212 LEU cc_start: 0.8388 (mp) cc_final: 0.8142 (mp)
REVERT: R  253 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6284 (ttp-110)
REVERT: B  222 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7078 (ptm)
REVERT: B  225 GLN cc_start: 0.8401 (mp10) cc_final: 0.8130 (mp10)
REVERT: B  273 ASN cc_start: 0.8747 (m-40) cc_final: 0.8450 (m110)
REVERT: B  274 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7730 (pp)
REVERT: B  280 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8233 (m)
REVERT: S   86 ARG cc_start: 0.7481 (mtp85) cc_final: 0.6766 (mtt-85)
REVERT: G   46 GLU cc_start: 0.8266 (mp0) cc_final: 0.7972 (mp0)
  outliers start: 26
  outliers final: 19
  residues processed: 155
  average time/residue: 0.2242
  time to fit residues: 47.7367
Evaluate side-chains
  153 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  143 VAL
Chi-restraints excluded: chain R residue  160 LEU
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  158 ASP
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain S residue   10 LEU
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  214 LEU
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain A residue  261 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 15 optimal weight:   20.0000
   chunk 97 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 74 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 100 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
R  78 ASN
R 181 HIS
S  38 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.153247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.109984 restraints weight = 12525.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 2.96
r_work: 0.3254 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9012  Z= 0.234
  Angle     :  0.565  10.021  12244  Z= 0.288
  Chirality :  0.042   0.164   1393
  Planarity :  0.004   0.052   1557
  Dihedral  :  4.711  44.318   1247
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 18.02 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.25), residues: 1121
  helix:  2.13 (0.25), residues: 406
  sheet:  0.07 (0.32), residues: 269
  loop : -0.57 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 174 
 HIS   0.004   0.001   HIS R 181 
 PHE   0.009   0.001   PHE R 113 
 TYR   0.019   0.001   TYR B  64 
 ARG   0.007   0.000   ARG A  29 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.6944 (mmmt) cc_final: 0.6521 (tptp)
REVERT: R  212 LEU cc_start: 0.8366 (mp) cc_final: 0.8151 (mp)
REVERT: R  253 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6214 (ttp-110)
REVERT: B  222 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7208 (ptm)
REVERT: B  273 ASN cc_start: 0.8741 (m-40) cc_final: 0.8438 (m110)
REVERT: B  274 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7665 (pp)
REVERT: B  280 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8171 (m)
REVERT: S   66 ARG cc_start: 0.7800 (mtm-85) cc_final: 0.7526 (ttp-110)
REVERT: S   86 ARG cc_start: 0.7505 (mtp85) cc_final: 0.6831 (mtt-85)
REVERT: S  220 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7130 (mp0)
REVERT: G   46 GLU cc_start: 0.8275 (mp0) cc_final: 0.7992 (mp0)
  outliers start: 24
  outliers final: 18
  residues processed: 154
  average time/residue: 0.2065
  time to fit residues: 44.3912
Evaluate side-chains
  157 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  160 LEU
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  158 ASP
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  158 SER
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain G residue   53 VAL
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  261 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 58 optimal weight:    0.3980
   chunk 13 optimal weight:    0.3980
   chunk 81 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 86 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 109 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
R 181 HIS
S  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.154268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.112099 restraints weight = 12696.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 2.91
r_work: 0.3272 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9012  Z= 0.167
  Angle     :  0.549  10.145  12244  Z= 0.278
  Chirality :  0.041   0.172   1393
  Planarity :  0.004   0.053   1557
  Dihedral  :  4.567  42.941   1247
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 18.23 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.26), residues: 1121
  helix:  2.16 (0.25), residues: 409
  sheet:  0.10 (0.32), residues: 274
  loop : -0.48 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 174 
 HIS   0.004   0.001   HIS R 181 
 PHE   0.011   0.001   PHE L 220 
 TYR   0.015   0.001   TYR B  64 
 ARG   0.008   0.000   ARG A 302 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 145
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.6959 (mmmt) cc_final: 0.6561 (tptp)
REVERT: R  212 LEU cc_start: 0.8281 (mp) cc_final: 0.8075 (mp)
REVERT: R  253 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.6224 (ttp-110)
REVERT: B  222 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.7151 (ptm)
REVERT: B  225 GLN cc_start: 0.8368 (mp10) cc_final: 0.8130 (mp10)
REVERT: B  273 ASN cc_start: 0.8723 (m-40) cc_final: 0.8423 (m110)
REVERT: B  274 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7696 (pp)
REVERT: B  280 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8108 (m)
REVERT: S   66 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7532 (ttp-110)
REVERT: S   86 ARG cc_start: 0.7515 (mtp85) cc_final: 0.6878 (mtt-85)
REVERT: S  220 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7138 (mp0)
REVERT: A  262 THR cc_start: 0.8447 (m) cc_final: 0.8184 (t)
  outliers start: 22
  outliers final: 17
  residues processed: 157
  average time/residue: 0.2034
  time to fit residues: 44.7328
Evaluate side-chains
  164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  160 LEU
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  158 ASP
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain G residue   53 VAL
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  261 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 79 optimal weight:    8.9990
   chunk 11 optimal weight:    0.6980
   chunk 107 optimal weight:   10.0000
   chunk 63 optimal weight:    6.9990
   chunk 95 optimal weight:    2.9990
   chunk 89 optimal weight:    7.9990
   chunk 58 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
R  78 ASN
R 181 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.153169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.111072 restraints weight = 12683.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 2.90
r_work: 0.3252 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9012  Z= 0.216
  Angle     :  0.558  10.929  12244  Z= 0.284
  Chirality :  0.042   0.161   1393
  Planarity :  0.004   0.054   1557
  Dihedral  :  4.572  42.210   1247
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 18.77 %
    Favored  : 78.96 %
  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:  0.91 (0.25), residues: 1121
  helix:  2.16 (0.25), residues: 408
  sheet:  0.13 (0.33), residues: 263
  loop : -0.52 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 174 
 HIS   0.003   0.001   HIS R 181 
 PHE   0.012   0.001   PHE L 220 
 TYR   0.015   0.001   TYR B  64 
 ARG   0.007   0.000   ARG A 302 

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

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

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2242 Ramachandran restraints generated.
    1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.6946 (mmmt) cc_final: 0.6527 (tptp)
REVERT: R  253 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.6202 (ttp-110)
REVERT: B  222 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.7121 (ptm)
REVERT: B  225 GLN cc_start: 0.8371 (mp10) cc_final: 0.8118 (mp10)
REVERT: B  273 ASN cc_start: 0.8738 (m-40) cc_final: 0.8432 (m110)
REVERT: B  274 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7662 (pp)
REVERT: B  280 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8135 (m)
REVERT: S   66 ARG cc_start: 0.7777 (mtm-85) cc_final: 0.7525 (ttp-110)
REVERT: S   86 ARG cc_start: 0.7464 (mtp85) cc_final: 0.6869 (mtt-85)
REVERT: A  262 THR cc_start: 0.8425 (m) cc_final: 0.7863 (p)
  outliers start: 21
  outliers final: 17
  residues processed: 151
  average time/residue: 0.2096
  time to fit residues: 44.0817
Evaluate side-chains
  159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  115 CYS
Chi-restraints excluded: chain R residue  160 LEU
Chi-restraints excluded: chain R residue  166 ILE
Chi-restraints excluded: chain R residue  200 LEU
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  215 LEU
Chi-restraints excluded: chain R residue  253 ARG
Chi-restraints excluded: chain R residue  321 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  158 ASP
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  274 ILE
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  299 CYS
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain S residue  140 MET
Chi-restraints excluded: chain S residue  226 VAL
Chi-restraints excluded: chain G residue   53 VAL
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  261 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9990
   chunk 105 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 53 optimal weight:   10.0000
   chunk 70 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
R 181 HIS
S  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.154544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.112664 restraints weight = 12634.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 2.89
r_work: 0.3267 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9012  Z= 0.172
  Angle     :  0.550  10.287  12244  Z= 0.280
  Chirality :  0.041   0.158   1393
  Planarity :  0.004   0.052   1557
  Dihedral  :  4.504  41.141   1247
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.99 %
    Favored  : 78.86 %
  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:  0.96 (0.26), residues: 1121
  helix:  2.20 (0.25), residues: 408
  sheet:  0.17 (0.32), residues: 263
  loop : -0.49 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 174 
 HIS   0.004   0.001   HIS R 181 
 PHE   0.012   0.001   PHE L 220 
 TYR   0.014   0.001   TYR B  64 
 ARG   0.007   0.000   ARG A 302 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4626.07 seconds
wall clock time: 83 minutes 8.59 seconds (4988.59 seconds total)