Starting phenix.real_space_refine
on Thu Mar 13 05:35:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zjd_60141/03_2025/8zjd_60141.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zjd_60141/03_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_60141/03_2025/8zjd_60141.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zjd_60141/03_2025/8zjd_60141.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zjd_60141/03_2025/8zjd_60141.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zjd_60141/03_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.55, per 1000 atoms: 0.63
  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: 2.54
  Conformation dependent library (CDL) restraints added in 1.2 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: 1.07
  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: 2.79

  Time building geometry restraints manager: 2.98 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:             1.260
  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:          0.450
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.720
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.790
-------------------------------------------------------------------------------
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  : 0.934 
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: 0.2471
  time to fit residues: 52.7809
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  : 1.032 
-------------------------------------------------------------------------------
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 = 55)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.109504 restraints weight = 12253.722|
|-----------------------------------------------------------------------------|
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  : 1.009 
Fit side-chains
REVERT: R   71 LYS cc_start: 0.6963 (mmmt) cc_final: 0.6658 (tptp)
REVERT: R  212 LEU cc_start: 0.8286 (mp) cc_final: 0.8015 (mp)
REVERT: R  253 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6443 (ttp-170)
REVERT: R  305 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8093 (tmtt)
REVERT: B  134 ARG cc_start: 0.8015 (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: 0.6970 (ptm)
REVERT: B  273 ASN cc_start: 0.8675 (m-40) cc_final: 0.8328 (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: 0.2208
  time to fit residues: 45.5406
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  : 0.993 
-------------------------------------------------------------------------------
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:    0.0870
   chunk 12 optimal weight:    0.9980
   chunk 78 optimal weight:    0.2980
   chunk 62 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.6560

-------------------------------------------------------------------------------
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 = 0.3964 r_free = 0.3964 target = 0.156651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.113717 restraints weight = 12447.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 2.93
r_work: 0.3303 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9012  Z= 0.151
  Angle     :  0.531   5.934  12244  Z= 0.278
  Chirality :  0.041   0.138   1393
  Planarity :  0.004   0.048   1557
  Dihedral  :  5.065  53.139   1249
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 14.46 %
    Favored  : 83.17 %
  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:  0.95 (0.26), residues: 1121
  helix:  1.98 (0.26), residues: 411
  sheet:  0.28 (0.32), residues: 275
  loop : -0.39 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 344 
 HIS   0.002   0.001   HIS B 147 
 PHE   0.010   0.001   PHE B 246 
 TYR   0.024   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
  171 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 149
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.7062 (mmmt) cc_final: 0.6721 (tptp)
REVERT: R  212 LEU cc_start: 0.8082 (mp) cc_final: 0.7844 (mp)
REVERT: R  253 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6320 (ttp-170)
REVERT: B  134 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7815 (ttt90)
REVERT: B  222 MET cc_start: 0.7313 (ptt) cc_final: 0.7030 (ptm)
REVERT: B  273 ASN cc_start: 0.8664 (m-40) cc_final: 0.8371 (m110)
REVERT: S   66 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7426 (ttp-110)
REVERT: S   81 GLN cc_start: 0.7753 (tp-100) cc_final: 0.7420 (tp-100)
REVERT: S   86 ARG cc_start: 0.7337 (mtp85) cc_final: 0.6758 (mtm-85)
REVERT: S  194 ASN cc_start: 0.6529 (m110) cc_final: 0.6298 (m110)
REVERT: G   31 LYS cc_start: 0.8926 (ttpt) cc_final: 0.8498 (tptt)
REVERT: G   46 GLU cc_start: 0.8277 (mp0) cc_final: 0.7971 (mp0)
  outliers start: 22
  outliers final: 9
  residues processed: 164
  average time/residue: 0.2020
  time to fit residues: 46.3030
Evaluate side-chains
  144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 134
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
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  317 ASP
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:    4.9990
   chunk 102 optimal weight:    0.9990
   chunk 86 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 91 optimal weight:    5.9990
   chunk 98 optimal weight:    0.9980
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.3945 r_free = 0.3945 target = 0.154783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.112157 restraints weight = 12221.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 2.88
r_work: 0.3288 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.1897

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= 0.186
  Angle     :  0.532   6.521  12244  Z= 0.277
  Chirality :  0.041   0.137   1393
  Planarity :  0.004   0.055   1557
  Dihedral  :  4.924  49.364   1249
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.97 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.25), residues: 1121
  helix:  2.02 (0.25), residues: 410
  sheet:  0.19 (0.31), residues: 285
  loop : -0.46 (0.31), residues: 426

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   0.010   0.001   PHE B 246 
 TYR   0.013   0.001   TYR R  65 
 ARG   0.003   0.000   ARG A  29 

*********************** 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
  171 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.7027 (mmmt) cc_final: 0.6712 (tptp)
REVERT: R   78 ASN cc_start: 0.8724 (m-40) cc_final: 0.8486 (m110)
REVERT: R  212 LEU cc_start: 0.8214 (mp) cc_final: 0.7925 (mp)
REVERT: R  253 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6333 (ttp-170)
REVERT: B  222 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.7024 (ptm)
REVERT: B  273 ASN cc_start: 0.8665 (m-40) cc_final: 0.8356 (m110)
REVERT: B  274 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7664 (pp)
REVERT: S   86 ARG cc_start: 0.7381 (mtp85) cc_final: 0.6713 (mtt-85)
REVERT: S  194 ASN cc_start: 0.6545 (m110) cc_final: 0.6320 (m110)
REVERT: G   46 GLU cc_start: 0.8261 (mp0) cc_final: 0.7970 (mp0)
  outliers start: 24
  outliers final: 18
  residues processed: 162
  average time/residue: 0.2253
  time to fit residues: 50.5639
Evaluate side-chains
  156 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
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  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  213 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 11 optimal weight:    9.9990
   chunk 69 optimal weight:    4.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3946 r_free = 0.3946 target = 0.155040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.112221 restraints weight = 12341.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.93
r_work: 0.3290 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9012  Z= 0.176
  Angle     :  0.532   9.644  12244  Z= 0.273
  Chirality :  0.041   0.136   1393
  Planarity :  0.004   0.051   1557
  Dihedral  :  4.781  48.491   1249
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 16.94 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.26), residues: 1121
  helix:  2.10 (0.25), residues: 409
  sheet:  0.17 (0.32), residues: 275
  loop : -0.43 (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   0.013   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
  167 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 145
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.7010 (mmmt) cc_final: 0.6671 (tptp)
REVERT: R  212 LEU cc_start: 0.8140 (mp) cc_final: 0.7847 (mp)
REVERT: R  253 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6342 (ttp-110)
REVERT: B  222 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.7112 (ptm)
REVERT: B  273 ASN cc_start: 0.8668 (m-40) cc_final: 0.8357 (m110)
REVERT: B  274 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7717 (pp)
REVERT: S   86 ARG cc_start: 0.7390 (mtp85) cc_final: 0.6739 (mtt-85)
REVERT: G   46 GLU cc_start: 0.8264 (mp0) cc_final: 0.7971 (mp0)
  outliers start: 22
  outliers final: 17
  residues processed: 158
  average time/residue: 0.2435
  time to fit residues: 54.0931
Evaluate side-chains
  155 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 1.971 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 88 optimal weight:    0.0070
   chunk 103 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 96 optimal weight:    9.9990
   chunk 3 optimal weight:    4.9990
   chunk 13 optimal weight:    9.9990
   chunk 62 optimal weight:    0.9990
   chunk 4 optimal weight:    7.9990
   chunk 85 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    1.7404

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

Flipped N/Q/H residues before XYZ refinement:
** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.153416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.110359 restraints weight = 12392.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 2.93
r_work: 0.3263 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2130

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     :  0.555   8.160  12244  Z= 0.287
  Chirality :  0.042   0.140   1393
  Planarity :  0.004   0.055   1557
  Dihedral  :  4.723  47.783   1247
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 16.83 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.26), residues: 1121
  helix:  2.07 (0.25), residues: 410
  sheet:  0.08 (0.31), residues: 278
  loop : -0.44 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 174 
 HIS   0.004   0.001   HIS R 181 
 PHE   0.010   0.001   PHE R 282 
 TYR   0.017   0.001   TYR R 190 
 ARG   0.006   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
  163 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.6965 (mmmt) cc_final: 0.6604 (tptp)
REVERT: R  212 LEU cc_start: 0.8284 (mp) cc_final: 0.8022 (mp)
REVERT: R  253 ARG cc_start: 0.6855 (OUTLIER) cc_final: 0.6276 (ttp-110)
REVERT: B  222 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.7127 (ptm)
REVERT: B  273 ASN cc_start: 0.8705 (m-40) cc_final: 0.8441 (m110)
REVERT: B  274 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7656 (pp)
REVERT: S   86 ARG cc_start: 0.7433 (mtp85) cc_final: 0.6741 (mtt-85)
REVERT: G   46 GLU cc_start: 0.8256 (mp0) cc_final: 0.7965 (mp0)
  outliers start: 23
  outliers final: 18
  residues processed: 154
  average time/residue: 0.2012
  time to fit residues: 43.5739
Evaluate side-chains
  154 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 43 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 105 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 101 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   chunk 87 optimal weight:    6.9990
   chunk 102 optimal weight:    0.7980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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  80 GLN
S  38 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.155463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.113057 restraints weight = 12358.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.91
r_work: 0.3308 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9012  Z= 0.159
  Angle     :  0.540   9.490  12244  Z= 0.275
  Chirality :  0.041   0.153   1393
  Planarity :  0.004   0.051   1557
  Dihedral  :  4.599  46.377   1247
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.91 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.26), residues: 1121
  helix:  2.13 (0.25), residues: 410
  sheet:  0.17 (0.31), residues: 274
  loop : -0.43 (0.30), residues: 437

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   0.008   0.001   PHE B 246 
 TYR   0.015   0.001   TYR R 190 
 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
  173 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.7043 (mmmt) cc_final: 0.6725 (tptp)
REVERT: R  212 LEU cc_start: 0.8252 (mp) cc_final: 0.7995 (mp)
REVERT: R  253 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6261 (ttp-110)
REVERT: B  222 MET cc_start: 0.7437 (ptt) cc_final: 0.7153 (ptm)
REVERT: B  225 GLN cc_start: 0.8401 (mp10) cc_final: 0.8126 (mp10)
REVERT: B  273 ASN cc_start: 0.8695 (m-40) cc_final: 0.8425 (m110)
REVERT: B  274 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7710 (pp)
REVERT: B  280 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8184 (m)
REVERT: S   66 ARG cc_start: 0.7733 (mtm-85) cc_final: 0.7505 (ttp-110)
REVERT: S   86 ARG cc_start: 0.7518 (mtp85) cc_final: 0.6844 (mtt-85)
REVERT: G   46 GLU cc_start: 0.8267 (mp0) cc_final: 0.7978 (mp0)
  outliers start: 24
  outliers final: 18
  residues processed: 163
  average time/residue: 0.1997
  time to fit residues: 46.2534
Evaluate side-chains
  161 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 140
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
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  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 A residue   41 THR
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:    0.8980
   chunk 97 optimal weight:    0.0010
   chunk 67 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 74 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.1590

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

Flipped N/Q/H residues before XYZ refinement:
R 181 HIS
** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.154994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.112234 restraints weight = 12516.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.94
r_work: 0.3291 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9012  Z= 0.183
  Angle     :  0.549   9.537  12244  Z= 0.279
  Chirality :  0.041   0.153   1393
  Planarity :  0.004   0.055   1557
  Dihedral  :  4.554  45.825   1247
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 18.23 %
    Favored  : 79.07 %
  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:  2.17 (0.25), residues: 410
  sheet:  0.14 (0.31), residues: 274
  loop : -0.42 (0.30), residues: 437

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 B 246 
 TYR   0.017   0.001   TYR B  64 
 ARG   0.008   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
  168 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.7020 (mmmt) cc_final: 0.6627 (tptp)
REVERT: R  212 LEU cc_start: 0.8262 (mp) cc_final: 0.8016 (mp)
REVERT: R  253 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6221 (ttp-110)
REVERT: B  222 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.7162 (ptm)
REVERT: B  273 ASN cc_start: 0.8709 (m-40) cc_final: 0.8435 (m110)
REVERT: B  274 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7652 (pp)
REVERT: B  280 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8194 (m)
REVERT: S   66 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7519 (ttp-110)
REVERT: S   86 ARG cc_start: 0.7517 (mtp85) cc_final: 0.6841 (mtt-85)
REVERT: G   46 GLU cc_start: 0.8275 (mp0) cc_final: 0.7975 (mp0)
REVERT: A  239 GLN cc_start: 0.6954 (mm110) cc_final: 0.6752 (mm-40)
  outliers start: 25
  outliers final: 19
  residues processed: 157
  average time/residue: 0.1997
  time to fit residues: 44.6575
Evaluate side-chains
  164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
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  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:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 89 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 109 optimal weight:    3.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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
** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  38 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.153906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.110970 restraints weight = 12524.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 2.94
r_work: 0.3255 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2358

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= 0.259
  Angle     :  0.581  10.978  12244  Z= 0.296
  Chirality :  0.042   0.150   1393
  Planarity :  0.004   0.053   1557
  Dihedral  :  4.670  45.425   1247
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.12 %
    Favored  : 79.07 %
  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:  0.89 (0.26), residues: 1121
  helix:  2.10 (0.25), residues: 409
  sheet:  0.12 (0.32), residues: 264
  loop : -0.47 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 174 
 HIS   0.004   0.001   HIS S  34 
 PHE   0.011   0.001   PHE R 113 
 TYR   0.028   0.002   TYR A 237 
 ARG   0.007   0.000   ARG A  29 

*********************** 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
  169 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 143
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.7008 (mmmt) cc_final: 0.6561 (tptp)
REVERT: R   88 ASP cc_start: 0.8691 (t0) cc_final: 0.8454 (t0)
REVERT: R  212 LEU cc_start: 0.8342 (mp) cc_final: 0.8123 (mp)
REVERT: R  253 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6230 (ttp-110)
REVERT: B  222 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7222 (ptm)
REVERT: B  225 GLN cc_start: 0.8404 (mp10) cc_final: 0.8156 (mp10)
REVERT: B  273 ASN cc_start: 0.8751 (m-40) cc_final: 0.8451 (m110)
REVERT: B  274 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7719 (pp)
REVERT: B  280 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8205 (m)
REVERT: S   66 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7540 (ttp-110)
REVERT: S   86 ARG cc_start: 0.7527 (mtp85) cc_final: 0.6887 (mtt-85)
REVERT: G   46 GLU cc_start: 0.8279 (mp0) cc_final: 0.7983 (mp0)
  outliers start: 26
  outliers final: 20
  residues processed: 157
  average time/residue: 0.1983
  time to fit residues: 43.6001
Evaluate side-chains
  160 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
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   78 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 79 optimal weight:    6.9990
   chunk 11 optimal weight:    0.6980
   chunk 107 optimal weight:    0.6980
   chunk 63 optimal weight:    6.9990
   chunk 95 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
R 181 HIS
** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  38 GLN
A 239 GLN
** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.154940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.113072 restraints weight = 12669.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 2.94
r_work: 0.3278 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9012  Z= 0.162
  Angle     :  0.550  10.875  12244  Z= 0.279
  Chirality :  0.041   0.158   1393
  Planarity :  0.004   0.052   1557
  Dihedral  :  4.533  44.127   1247
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 18.77 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.26), residues: 1121
  helix:  2.14 (0.25), residues: 409
  sheet:  0.17 (0.32), residues: 263
  loop : -0.46 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 174 
 HIS   0.004   0.001   HIS R 181 
 PHE   0.009   0.001   PHE B 204 
 TYR   0.013   0.001   TYR B  64 
 ARG   0.012   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
  171 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
REVERT: R   71 LYS cc_start: 0.6942 (mmmt) cc_final: 0.6520 (tptp)
REVERT: R  212 LEU cc_start: 0.8243 (mp) cc_final: 0.8002 (mp)
REVERT: R  253 ARG cc_start: 0.6740 (OUTLIER) cc_final: 0.6169 (ttp-110)
REVERT: B  222 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.7130 (ptm)
REVERT: B  225 GLN cc_start: 0.8353 (mp10) cc_final: 0.8098 (mp10)
REVERT: B  273 ASN cc_start: 0.8719 (m-40) cc_final: 0.8417 (m110)
REVERT: B  274 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7654 (pp)
REVERT: B  280 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8084 (m)
REVERT: S   37 ARG cc_start: 0.8861 (ptt180) cc_final: 0.8600 (ptt180)
REVERT: S   66 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7547 (ttp-110)
REVERT: S   86 ARG cc_start: 0.7458 (mtp85) cc_final: 0.6865 (mtt-85)
  outliers start: 24
  outliers final: 19
  residues processed: 161
  average time/residue: 0.1993
  time to fit residues: 45.1075
Evaluate side-chains
  169 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 105 optimal weight:    0.3980
   chunk 8 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 53 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   chunk 31 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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
R 181 HIS
** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.154184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.112104 restraints weight = 12662.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 2.90
r_work: 0.3264 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2560

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= 0.191
  Angle     :  0.561  10.789  12244  Z= 0.284
  Chirality :  0.041   0.159   1393
  Planarity :  0.004   0.054   1557
  Dihedral  :  4.529  44.057   1247
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 18.66 %
    Favored  : 78.75 %
  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:  0.97 (0.26), residues: 1121
  helix:  2.13 (0.25), residues: 409
  sheet:  0.19 (0.32), residues: 263
  loop : -0.42 (0.30), residues: 449

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 B 246 
 TYR   0.015   0.001   TYR B  64 
 ARG   0.010   0.000   ARG A  29 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4766.33 seconds
wall clock time: 84 minutes 14.51 seconds (5054.51 seconds total)