Starting phenix.real_space_refine
on Thu Feb 13 02:07:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8id4_35357/02_2025/8id4_35357.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8id4_35357/02_2025/8id4_35357.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8id4_35357/02_2025/8id4_35357.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8id4_35357/02_2025/8id4_35357.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8id4_35357/02_2025/8id4_35357.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8id4_35357/02_2025/8id4_35357.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.016
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      58      5.16       5
     C    5545      2.51       5
     N    1472      2.21       5
     O    1590      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8665
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2174
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 11, 'TRANS': 273}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 98
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 84
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 6, 'TRP:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 63
    Chain: "A"
      Number of atoms: 1761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1761
          Classifications: {'peptide': 225}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 37
    Chain: "B"
      Number of atoms: 2572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2572
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 23
    Chain: "Y"
      Number of atoms: 404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 404
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "S"
      Number of atoms: 1733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1733
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 28
    Chain: "R"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 21
          Unusual residues: {'EIC': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 5.24, per 1000 atoms: 0.60
  Number of scatterers: 8665
  At special positions: 0
  Unit cell: (106.47, 127.764, 113.568, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      58     16.00
     O    1590      8.00
     N    1472      7.00
     C    5545      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 160 " - pdb=" SG  CYS S 230 " distance=2.04

  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: 2.53
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2126

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 13 sheets defined
      35.9% alpha, 23.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'R' and resid 38 through 69
      removed outlier: 3.619A  pdb=" N   ARG R  67 " --> pdb=" O   VAL R  63 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 77 through 90
      removed outlier: 3.635A  pdb=" N   LEU R  81 " --> pdb=" O   LEU R  77 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   PHE R  82 " --> pdb=" O   VAL R  78 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   LEU R  86 " --> pdb=" O   PHE R  82 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 91 through 101
      removed outlier: 4.018A  pdb=" N   VAL R  95 " --> pdb=" O   ALA R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 109 through 112
      removed outlier: 3.691A  pdb=" N   HIS R 112 " --> pdb=" O   VAL R 109 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 109 through 112'
    Processing helix  chain 'R' and resid 113 through 142
    Processing helix  chain 'R' and resid 152 through 171
    Processing helix  chain 'R' and resid 172 through 174
      No H-bonds generated for 'chain 'R' and resid 172 through 174'
    Processing helix  chain 'R' and resid 201 through 216
      removed outlier: 3.662A  pdb=" N   SER R 206 " --> pdb=" O   PRO R 202 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   TRP R 207 " --> pdb=" O   GLY R 203 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   THR R 213 " --> pdb=" O   VAL R 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 216 through 244
      removed outlier: 3.663A  pdb=" N   THR R 242 " --> pdb=" O   ARG R 238 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   VAL R 243 " --> pdb=" O   LYS R 239 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   SER R 244 " --> pdb=" O   ARG R 240 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 251 through 294
      removed outlier: 3.864A  pdb=" N   SER R 256 " --> pdb=" O   GLN R 252 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ARG R 261 " --> pdb=" O   GLN R 257 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   PHE R 273 " --> pdb=" O   LEU R 269 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   PHE R 274 " --> pdb=" O   MET R 270 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   SER R 278 " --> pdb=" O   PHE R 274 " (cutoff:3.500A)
      Proline residue:  R 279  - end of helix
      removed outlier: 3.849A  pdb=" N   PHE R 292 " --> pdb=" O   LEU R 288 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 301 through 321
      removed outlier: 3.867A  pdb=" N   TRP R 305 " --> pdb=" O   SER R 301 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ASN R 313 " --> pdb=" O   PHE R 309 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   SER R 314 " --> pdb=" O   THR R 310 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ALA R 315 " --> pdb=" O   PHE R 311 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
    Processing helix  chain 'A' and resid 6 through 30
    Processing helix  chain 'A' and resid 31 through 33
      No H-bonds generated for 'chain 'A' and resid 31 through 33'
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.546A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.681A  pdb=" N   TRP A 211 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.785A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.198A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.613A  pdb=" N   GLU A 245 " --> pdb=" O   ASN A 241 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 272
      No H-bonds generated for 'chain 'A' and resid 270 through 272'
    Processing helix  chain 'A' and resid 273 through 278
      removed outlier: 3.655A  pdb=" N   LYS A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.938A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 351
      removed outlier: 3.546A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 24
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'Y' and resid 9 through 24
      removed outlier: 3.636A  pdb=" N   ASN Y  24 " --> pdb=" O   LYS Y  20 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 29 through 44
    Processing helix  chain 'S' and resid 28 through 32
    Processing sheet with id=AA1, first strand: chain 'R' and resid 177 through 181
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.093A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.638A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.850A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.754A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.960A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.992A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.516A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.937A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.534A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.557A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.692A  pdb=" N   THR S 118 " --> pdb=" O   GLY S  10 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLN S  39 " --> pdb=" O   MET S  93 " (cutoff:3.500A)
      removed outlier: 5.808A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.005A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 141 through 142
      removed outlier: 3.522A  pdb=" N   ALA S 212 " --> pdb=" O   SER S 209 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 147 through 149
      removed outlier: 3.792A  pdb=" N   GLU S 247 " --> pdb=" O   VAL S 148 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   LEU S 179 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
      removed outlier: 5.595A  pdb=" N   LEU S 188 " --> pdb=" O   LEU S 179 " (cutoff:3.500A)

    419 hydrogen bonds defined for protein.
    1191 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: 2.56

  Time building geometry restraints manager: 2.49 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2378
        1.33 -     1.45: 1616
        1.45 -     1.57: 4759
        1.57 -     1.70: 2
        1.70 -     1.82: 83
  Bond restraints: 8838
  Sorted by residual:
  bond pdb=" N   THR A 327 "
       pdb=" CA  THR A 327 "
    ideal  model  delta    sigma   weight residual
    1.457  1.529 -0.072 1.29e-02 6.01e+03 3.12e+01
  bond pdb=" CA  PHE R  88 "
       pdb=" C   PHE R  88 "
    ideal  model  delta    sigma   weight residual
    1.524  1.584 -0.061 1.27e-02 6.20e+03 2.28e+01
  bond pdb=" N   ALA A 326 "
       pdb=" CA  ALA A 326 "
    ideal  model  delta    sigma   weight residual
    1.457  1.504 -0.047 1.20e-02 6.94e+03 1.55e+01
  bond pdb=" N   ILE R  89 "
       pdb=" CA  ILE R  89 "
    ideal  model  delta    sigma   weight residual
    1.459  1.509 -0.050 1.34e-02 5.57e+03 1.42e+01
  bond pdb=" CA  ALA A 326 "
       pdb=" C   ALA A 326 "
    ideal  model  delta    sigma   weight residual
    1.524  1.560 -0.037 1.23e-02 6.61e+03 8.84e+00
  ... (remaining 8833 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 11810
        2.46 -     4.92: 147
        4.92 -     7.38: 31
        7.38 -     9.84: 2
        9.84 -    12.29: 2
  Bond angle restraints: 11992
  Sorted by residual:
  angle pdb=" N   ALA A 326 "
        pdb=" CA  ALA A 326 "
        pdb=" C   ALA A 326 "
      ideal   model   delta    sigma   weight residual
     108.38  120.67  -12.29 1.35e+00 5.49e-01 8.29e+01
  angle pdb=" N   SER R 244 "
        pdb=" CA  SER R 244 "
        pdb=" C   SER R 244 "
      ideal   model   delta    sigma   weight residual
     110.28  100.09   10.19 1.48e+00 4.57e-01 4.74e+01
  angle pdb=" N   ARG R  69 "
        pdb=" CA  ARG R  69 "
        pdb=" C   ARG R  69 "
      ideal   model   delta    sigma   weight residual
     112.90  106.20    6.70 1.31e+00 5.83e-01 2.62e+01
  angle pdb=" N   SER R  90 "
        pdb=" CA  SER R  90 "
        pdb=" C   SER R  90 "
      ideal   model   delta    sigma   weight residual
     112.34  105.71    6.63 1.30e+00 5.92e-01 2.60e+01
  angle pdb=" N   ILE R  89 "
        pdb=" CA  ILE R  89 "
        pdb=" C   ILE R  89 "
      ideal   model   delta    sigma   weight residual
     111.44  117.93   -6.49 1.34e+00 5.57e-01 2.34e+01
  ... (remaining 11987 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.82: 4753
       16.82 -    33.64: 377
       33.64 -    50.46: 68
       50.46 -    67.29: 10
       67.29 -    84.11: 9
  Dihedral angle restraints: 5217
    sinusoidal: 1934
      harmonic: 3283
  Sorted by residual:
  dihedral pdb=" C   THR A 327 "
           pdb=" N   THR A 327 "
           pdb=" CA  THR A 327 "
           pdb=" CB  THR A 327 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -145.78   23.78     0      2.50e+00 1.60e-01 9.05e+01
  dihedral pdb=" N   THR A 327 "
           pdb=" C   THR A 327 "
           pdb=" CA  THR A 327 "
           pdb=" CB  THR A 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  145.69  -22.29     0      2.50e+00 1.60e-01 7.95e+01
  dihedral pdb=" CA  ILE R 298 "
           pdb=" C   ILE R 298 "
           pdb=" N   TRP R 299 "
           pdb=" CA  TRP R 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.32   21.68     0      5.00e+00 4.00e-02 1.88e+01
  ... (remaining 5214 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.171: 1391
       0.171 -    0.342: 8
       0.342 -    0.514: 0
       0.514 -    0.685: 0
       0.685 -    0.856: 1
  Chirality restraints: 1400
  Sorted by residual:
  chirality pdb=" CA  THR A 327 "
            pdb=" N   THR A 327 "
            pdb=" C   THR A 327 "
            pdb=" CB  THR A 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.67    0.86 2.00e-01 2.50e+01 1.83e+01
  chirality pdb=" CB  ILE R 197 "
            pdb=" CA  ILE R 197 "
            pdb=" CG1 ILE R 197 "
            pdb=" CG2 ILE R 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.27e+00
  chirality pdb=" CA  SER R 244 "
            pdb=" N   SER R 244 "
            pdb=" C   SER R 244 "
            pdb=" CB  SER R 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 1397 not shown)

  Planarity restraints: 1508
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 171 "    0.052 5.00e-02 4.00e+02   7.81e-02 9.76e+00
        pdb=" N   PRO R 172 "   -0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO R 172 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO R 172 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 324 "    0.015 2.00e-02 2.50e+03   3.11e-02 9.70e+00
        pdb=" C   THR A 324 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   THR A 324 "    0.021 2.00e-02 2.50e+03
        pdb=" N   CYS A 325 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN S  13 "    0.050 5.00e-02 4.00e+02   7.31e-02 8.55e+00
        pdb=" N   PRO S  14 "   -0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO S  14 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO S  14 "    0.041 5.00e-02 4.00e+02
  ... (remaining 1505 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1199
        2.75 -     3.29: 8068
        3.29 -     3.83: 13913
        3.83 -     4.36: 16869
        4.36 -     4.90: 30336
  Nonbonded interactions: 70385
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 128 "
            pdb=" O   ASN B 132 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASP B 154 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 176 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.252 3.040
  ... (remaining 70380 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.020
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
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   0.095   8838  Z= 0.275
  Angle     :  0.732  12.295  11992  Z= 0.427
  Chirality :  0.053   0.856   1400
  Planarity :  0.005   0.078   1508
  Dihedral  : 12.922  84.108   3088
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.69 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.88 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.25), residues: 1112
  helix:  0.33 (0.28), residues: 370
  sheet: -0.43 (0.31), residues: 276
  loop : -1.68 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.022   0.002   PHE R  25 
 TYR   0.024   0.001   TYR S 176 
 ARG   0.012   0.001   ARG S 161 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 131
  time to evaluate  : 0.917 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7674 (mt-10)
REVERT: B  134 ARG cc_start: 0.8079 (ptt90) cc_final: 0.7575 (ptt-90)
REVERT: B  221 THR cc_start: 0.8845 (t) cc_final: 0.8308 (m)
  outliers start: 2
  outliers final: 0
  residues processed: 133
  average time/residue: 0.2559
  time to fit residues: 44.7839
Evaluate side-chains
  118 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.4980
   chunk 84 optimal weight:    0.9980
   chunk 46 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0170
   chunk 87 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 52 optimal weight:   10.0000
   chunk 64 optimal weight:    5.9990
   chunk 100 optimal weight:    7.9990
   overall best weight:    0.9022

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

Flipped N/Q/H residues before XYZ refinement:
R 215 ASN
A 306 GLN
B  17 GLN
B  91 HIS
S  82 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.170797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.132493 restraints weight = 9276.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.28
r_work: 0.3059 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.0949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8838  Z= 0.181
  Angle     :  0.552   7.948  11992  Z= 0.296
  Chirality :  0.042   0.233   1400
  Planarity :  0.004   0.063   1508
  Dihedral  :  5.476  70.342   1227
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.24 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  6.91 %
    Favored  : 92.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.25), residues: 1112
  helix:  0.83 (0.28), residues: 376
  sheet: -0.18 (0.29), residues: 278
  loop : -1.60 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 207 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.019   0.001   PHE R  25 
 TYR   0.016   0.001   TYR S 176 
 ARG   0.005   0.000   ARG R 240 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.939 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8010 (mt-10)
REVERT: A   29 LYS cc_start: 0.7979 (ttmt) cc_final: 0.7535 (tttp)
REVERT: A  197 LYS cc_start: 0.8424 (mmtt) cc_final: 0.8061 (mmtt)
REVERT: B   17 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7241 (pp30)
REVERT: B  217 MET cc_start: 0.8303 (ppp) cc_final: 0.8075 (ppp)
REVERT: S   82 GLN cc_start: 0.7706 (tp40) cc_final: 0.6362 (mp10)
  outliers start: 10
  outliers final: 7
  residues processed: 134
  average time/residue: 0.2518
  time to fit residues: 44.8933
Evaluate side-chains
  127 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  157 VAL
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  271 VAL
Chi-restraints excluded: chain R residue  323 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain S residue    6 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 8 optimal weight:    8.9990
   chunk 59 optimal weight:    3.9990
   chunk 109 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0970
   chunk 24 optimal weight:    6.9990
   overall best weight:    2.8186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.159568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.117763 restraints weight = 9370.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 2.65
r_work: 0.2843 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.1162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   8838  Z= 0.380
  Angle     :  0.634   7.883  11992  Z= 0.338
  Chirality :  0.046   0.225   1400
  Planarity :  0.005   0.065   1508
  Dihedral  :  5.652  70.180   1227
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.23 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  :  9.98 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.72 (0.24), residues: 1112
  helix:  0.69 (0.27), residues: 376
  sheet: -0.18 (0.29), residues: 282
  loop : -1.64 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.015   0.002   PHE B 151 
 TYR   0.013   0.002   TYR S 176 
 ARG   0.004   0.001   ARG S  87 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.942 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8092 (mt-10)
REVERT: B   17 GLN cc_start: 0.7693 (pp30) cc_final: 0.7467 (pp30)
REVERT: B  217 MET cc_start: 0.8340 (ppp) cc_final: 0.7942 (ptm)
REVERT: B  325 MET cc_start: 0.8977 (mtt) cc_final: 0.8542 (mtm)
REVERT: S   82 GLN cc_start: 0.7775 (tp40) cc_final: 0.6309 (mp10)
  outliers start: 15
  outliers final: 12
  residues processed: 130
  average time/residue: 0.2432
  time to fit residues: 42.2269
Evaluate side-chains
  126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  157 VAL
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  271 VAL
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  113 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 93 optimal weight:    0.6980
   chunk 94 optimal weight:    0.2980
   chunk 64 optimal weight:    0.0060
   chunk 41 optimal weight:    2.9990
   chunk 71 optimal weight:    6.9990
   chunk 100 optimal weight:    9.9990
   chunk 78 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 156 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.171132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.131455 restraints weight = 9365.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.84
r_work: 0.3080 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   8838  Z= 0.138
  Angle     :  0.499   6.971  11992  Z= 0.268
  Chirality :  0.041   0.237   1400
  Planarity :  0.004   0.055   1508
  Dihedral  :  5.176  70.453   1227
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.88 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.73 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.28 (0.25), residues: 1112
  helix:  1.27 (0.28), residues: 373
  sheet:  0.02 (0.29), residues: 277
  loop : -1.53 (0.27), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 207 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.019   0.001   PHE R  25 
 TYR   0.012   0.001   TYR S 191 
 ARG   0.004   0.000   ARG S  87 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.999 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8069 (mt-10)
REVERT: B  217 MET cc_start: 0.8309 (ppp) cc_final: 0.7838 (ptm)
REVERT: S   46 GLU cc_start: 0.8425 (tt0) cc_final: 0.8220 (tt0)
REVERT: S   82 GLN cc_start: 0.7864 (tp40) cc_final: 0.6585 (mp10)
  outliers start: 13
  outliers final: 9
  residues processed: 129
  average time/residue: 0.2617
  time to fit residues: 44.3486
Evaluate side-chains
  125 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  271 VAL
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   83 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 102 optimal weight:    7.9990
   chunk 95 optimal weight:    2.9990
   chunk 105 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 156 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.165082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.124624 restraints weight = 9364.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 2.77
r_work: 0.3039 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.1403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   8838  Z= 0.375
  Angle     :  0.610   7.690  11992  Z= 0.326
  Chirality :  0.046   0.227   1400
  Planarity :  0.005   0.065   1508
  Dihedral  :  5.533  70.712   1227
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.23 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 12.50 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.40 (0.24), residues: 1112
  helix:  0.96 (0.27), residues: 376
  sheet: -0.01 (0.29), residues: 282
  loop : -1.46 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.018   0.002   PHE R  25 
 TYR   0.011   0.002   TYR B  85 
 ARG   0.006   0.001   ARG R  68 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8164 (mt-10)
REVERT: A  197 LYS cc_start: 0.8525 (mttm) cc_final: 0.8142 (mttp)
REVERT: A  318 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7615 (mt-10)
REVERT: S   82 GLN cc_start: 0.7804 (tp40) cc_final: 0.6453 (mp10)
  outliers start: 17
  outliers final: 13
  residues processed: 127
  average time/residue: 0.2374
  time to fit residues: 40.9911
Evaluate side-chains
  131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  157 VAL
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  271 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   97 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 110 optimal weight:    7.9990
   chunk 109 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 52 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   chunk 98 optimal weight:    0.9980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 156 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.167384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.126481 restraints weight = 9306.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 3.02
r_work: 0.3054 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8838  Z= 0.233
  Angle     :  0.537   6.109  11992  Z= 0.289
  Chirality :  0.043   0.250   1400
  Planarity :  0.004   0.061   1508
  Dihedral  :  5.359  70.528   1227
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 13.38 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.21 (0.25), residues: 1112
  helix:  1.19 (0.27), residues: 376
  sheet:  0.06 (0.30), residues: 282
  loop : -1.40 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.012   0.001   PHE B 151 
 TYR   0.011   0.001   TYR S 191 
 ARG   0.007   0.000   ARG R  68 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8130 (mt-10)
REVERT: A  197 LYS cc_start: 0.8489 (mttm) cc_final: 0.8121 (mttp)
REVERT: A  318 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7607 (mt-10)
REVERT: B  234 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8751 (m-80)
REVERT: S   82 GLN cc_start: 0.7775 (tp40) cc_final: 0.6462 (mp10)
  outliers start: 21
  outliers final: 12
  residues processed: 127
  average time/residue: 0.2354
  time to fit residues: 40.1531
Evaluate side-chains
  129 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  157 VAL
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  271 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain S residue    6 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 2 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9980
   chunk 95 optimal weight:    2.9990
   chunk 93 optimal weight:    0.7980
   chunk 79 optimal weight:    4.9990
   chunk 34 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    0.8980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 156 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.169502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.129722 restraints weight = 9367.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 2.76
r_work: 0.3035 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8838  Z= 0.211
  Angle     :  0.524   6.122  11992  Z= 0.282
  Chirality :  0.042   0.262   1400
  Planarity :  0.004   0.059   1508
  Dihedral  :  5.266  70.692   1227
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 13.82 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.09 (0.25), residues: 1112
  helix:  1.29 (0.27), residues: 377
  sheet:  0.11 (0.30), residues: 281
  loop : -1.33 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.021   0.001   PHE R  25 
 TYR   0.011   0.001   TYR S 191 
 ARG   0.008   0.000   ARG R  68 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 0.885 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8161 (mt-10)
REVERT: A  197 LYS cc_start: 0.8476 (mttm) cc_final: 0.8165 (mttp)
REVERT: A  318 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7670 (mt-10)
REVERT: B   17 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7390 (pp30)
REVERT: B  217 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8076 (ptm)
REVERT: B  234 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8748 (m-80)
REVERT: S   82 GLN cc_start: 0.7768 (tp40) cc_final: 0.6455 (mp10)
  outliers start: 21
  outliers final: 13
  residues processed: 133
  average time/residue: 0.2351
  time to fit residues: 41.8243
Evaluate side-chains
  133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  157 VAL
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  271 VAL
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   97 VAL
Chi-restraints excluded: chain S residue  113 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0980
   chunk 3 optimal weight:    6.9990
   chunk 106 optimal weight:    9.9990
   chunk 95 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 54 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 51 optimal weight:   10.0000
   chunk 99 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    2.2188

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 156 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.167614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.128024 restraints weight = 9460.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 2.63
r_work: 0.3011 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8838  Z= 0.309
  Angle     :  0.573   6.578  11992  Z= 0.306
  Chirality :  0.044   0.257   1400
  Planarity :  0.004   0.060   1508
  Dihedral  :  5.407  70.982   1227
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 13.71 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.19 (0.25), residues: 1112
  helix:  1.20 (0.27), residues: 376
  sheet:  0.06 (0.29), residues: 283
  loop : -1.38 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.014   0.002   PHE B 151 
 TYR   0.010   0.002   TYR S 191 
 ARG   0.008   0.001   ARG R  68 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.987 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8187 (mt-10)
REVERT: A  197 LYS cc_start: 0.8482 (mttm) cc_final: 0.8178 (mttp)
REVERT: A  318 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7690 (mt-10)
REVERT: B  217 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8090 (ptm)
REVERT: B  234 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8733 (m-80)
REVERT: S   82 GLN cc_start: 0.7787 (tp40) cc_final: 0.6446 (mp10)
  outliers start: 21
  outliers final: 12
  residues processed: 128
  average time/residue: 0.2262
  time to fit residues: 39.3995
Evaluate side-chains
  130 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  157 VAL
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  271 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   97 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 101 optimal weight:    0.9990
   chunk 94 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9990
   chunk 60 optimal weight:    4.9990
   chunk 39 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   chunk 59 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B 156 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.169828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.129700 restraints weight = 9368.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.84
r_work: 0.3028 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8838  Z= 0.194
  Angle     :  0.521   6.720  11992  Z= 0.279
  Chirality :  0.042   0.278   1400
  Planarity :  0.004   0.056   1508
  Dihedral  :  5.235  71.296   1227
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.91 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.02 (0.25), residues: 1112
  helix:  1.40 (0.27), residues: 377
  sheet:  0.11 (0.30), residues: 283
  loop : -1.30 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.023   0.001   PHE R  25 
 TYR   0.011   0.001   TYR S 191 
 ARG   0.008   0.000   ARG R  68 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.911 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8147 (mt-10)
REVERT: A  318 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7606 (mt-10)
REVERT: B  217 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8060 (ptm)
REVERT: B  234 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8743 (m-80)
REVERT: B  258 ASP cc_start: 0.6841 (t70) cc_final: 0.6592 (t70)
REVERT: S   82 GLN cc_start: 0.7757 (tp40) cc_final: 0.6479 (mp10)
  outliers start: 18
  outliers final: 13
  residues processed: 127
  average time/residue: 0.2433
  time to fit residues: 41.3375
Evaluate side-chains
  132 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  137 MET
Chi-restraints excluded: chain R residue  157 VAL
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  271 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   97 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 101 optimal weight:    7.9990
   chunk 12 optimal weight:    9.9990
   chunk 72 optimal weight:    6.9990
   chunk 88 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 83 optimal weight:    0.7980
   chunk 64 optimal weight:    4.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
B  17 GLN
B 156 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.171046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.130631 restraints weight = 9385.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 3.00
r_work: 0.3008 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8838  Z= 0.163
  Angle     :  0.501   7.420  11992  Z= 0.270
  Chirality :  0.042   0.279   1400
  Planarity :  0.004   0.054   1508
  Dihedral  :  5.118  71.836   1227
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 15.79 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.12 (0.25), residues: 1112
  helix:  1.53 (0.28), residues: 378
  sheet:  0.15 (0.30), residues: 284
  loop : -1.22 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.012   0.001   TYR S 191 
 ARG   0.009   0.000   ARG R  68 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8024 (mt-10)
REVERT: A  318 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7585 (mt-10)
REVERT: B  221 THR cc_start: 0.8967 (t) cc_final: 0.8365 (m)
REVERT: B  234 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8693 (m-80)
REVERT: B  258 ASP cc_start: 0.6874 (t70) cc_final: 0.6643 (t70)
REVERT: S   82 GLN cc_start: 0.7713 (tp40) cc_final: 0.6423 (mp10)
  outliers start: 14
  outliers final: 13
  residues processed: 121
  average time/residue: 0.2408
  time to fit residues: 38.9586
Evaluate side-chains
  126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  137 MET
Chi-restraints excluded: chain R residue  157 VAL
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  271 VAL
Chi-restraints excluded: chain B residue   17 GLN
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   97 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   chunk 52 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 3 optimal weight:    4.9990
   chunk 110 optimal weight:    8.9990
   chunk 93 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
B  17 GLN
B 156 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.168991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.128572 restraints weight = 9378.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.80
r_work: 0.3016 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8838  Z= 0.259
  Angle     :  0.544   7.422  11992  Z= 0.291
  Chirality :  0.043   0.257   1400
  Planarity :  0.004   0.058   1508
  Dihedral  :  5.254  72.342   1227
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 15.57 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.02 (0.25), residues: 1112
  helix:  1.40 (0.27), residues: 378
  sheet:  0.17 (0.30), residues: 282
  loop : -1.29 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.013   0.001   PHE B 151 
 TYR   0.010   0.001   TYR S 191 
 ARG   0.009   0.000   ARG R  68 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4229.35 seconds
wall clock time: 76 minutes 13.26 seconds (4573.26 seconds total)