Starting phenix.real_space_refine
on Fri Jul 25 14:47:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y3x_38906/07_2025/8y3x_38906.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y3x_38906/07_2025/8y3x_38906.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y3x_38906/07_2025/8y3x_38906.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y3x_38906/07_2025/8y3x_38906.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y3x_38906/07_2025/8y3x_38906.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y3x_38906/07_2025/8y3x_38906.cif"
  }
  resolution = 3.11
  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=   0.012
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: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      30      5.16       5
     C    4907      2.51       5
     N    1409      2.21       5
     O    1405      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7757
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1669
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 7, 'TRANS': 210}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "B"
      Number of atoms: 1670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1670
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 7, 'TRANS': 210}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "C"
      Number of atoms: 1918
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 1918
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 108}
          Link IDs: {'PTRANS': 9, 'TRANS': 289}
          Unresolved non-hydrogen bonds: 393
          Unresolved non-hydrogen angles: 505
          Unresolved non-hydrogen dihedrals: 313
          Unresolved non-hydrogen chiralities: 35
          Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 248
    Chain: "D"
      Number of atoms: 1888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 1888
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 117}
          Link IDs: {'PTRANS': 9, 'TRANS': 289}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 425
          Unresolved non-hydrogen angles: 547
          Unresolved non-hydrogen dihedrals: 337
          Unresolved non-hydrogen chiralities: 41
          Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 264
    Chain: "E"
      Number of atoms: 550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 550
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 93}
          Link IDs: {'TRANS': 110}
          Unresolved non-hydrogen bonds: 350
          Unresolved non-hydrogen angles: 437
          Unresolved non-hydrogen dihedrals: 275
          Unresolved non-hydrogen chiralities: 25
          Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 233
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 8.56, per 1000 atoms: 1.10
  Number of scatterers: 7757
  At special positions: 0
  Unit cell: (68.04, 78.96, 197.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P       6     15.00
     O    1405      8.00
     N    1409      7.00
     C    4907      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 2.36
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2100

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 6 sheets defined
      61.6% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 50
    Processing helix  chain 'A' and resid 73 through 80
      removed outlier: 3.608A  pdb=" N   LEU A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 108
      Proline residue:  A 103  - end of helix
    Processing helix  chain 'A' and resid 110 through 125
      removed outlier: 3.857A  pdb=" N   VAL A 125 " --> pdb=" O   ALA A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 131
    Processing helix  chain 'A' and resid 134 through 138
    Processing helix  chain 'A' and resid 139 through 152
    Processing helix  chain 'A' and resid 153 through 155
      No H-bonds generated for 'chain 'A' and resid 153 through 155'
    Processing helix  chain 'A' and resid 169 through 185
    Processing helix  chain 'A' and resid 196 through 201
      removed outlier: 4.217A  pdb=" N   ILE A 200 " --> pdb=" O   ASP A 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 50
    Processing helix  chain 'B' and resid 73 through 77
    Processing helix  chain 'B' and resid 95 through 108
      Proline residue:  B 103  - end of helix
    Processing helix  chain 'B' and resid 110 through 124
    Processing helix  chain 'B' and resid 127 through 131
      removed outlier: 3.505A  pdb=" N   ALA B 131 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 138
      removed outlier: 3.604A  pdb=" N   LEU B 138 " --> pdb=" O   PRO B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 153
    Processing helix  chain 'B' and resid 169 through 185
    Processing helix  chain 'B' and resid 197 through 202
      removed outlier: 3.586A  pdb=" N   ARG B 202 " --> pdb=" O   ASN B 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 79
    Processing helix  chain 'C' and resid 80 through 107
      removed outlier: 3.635A  pdb=" N   VAL C  90 " --> pdb=" O   LEU C  86 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   LEU C  97 " --> pdb=" O   ILE C  93 " (cutoff:3.500A)
      Proline residue:  C  98  - end of helix
      removed outlier: 4.186A  pdb=" N   MET C 103 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   VAL C 104 " --> pdb=" O   VAL C 100 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   TYR C 105 " --> pdb=" O   CYS C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 141
      removed outlier: 3.887A  pdb=" N   ALA C 135 " --> pdb=" O   ASP C 131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 156 through 165
      removed outlier: 3.856A  pdb=" N   GLY C 160 " --> pdb=" O   GLU C 156 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   GLU C 161 " --> pdb=" O   ASP C 157 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   PHE C 162 " --> pdb=" O   ALA C 158 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 189 through 194
      removed outlier: 3.609A  pdb=" N   GLY C 194 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 194 through 207
      removed outlier: 3.632A  pdb=" N   THR C 200 " --> pdb=" O   GLU C 196 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   LEU C 201 " --> pdb=" O   SER C 197 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASP C 203 " --> pdb=" O   ASN C 199 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 225
    Processing helix  chain 'C' and resid 229 through 261
      removed outlier: 3.680A  pdb=" N   SER C 235 " --> pdb=" O   VAL C 231 " (cutoff:3.500A)
      removed outlier: 4.899A  pdb=" N   ALA C 236 " --> pdb=" O   GLY C 232 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   PHE C 247 " --> pdb=" O   VAL C 243 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ARG C 261 " --> pdb=" O   SER C 257 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 270
      removed outlier: 3.668A  pdb=" N   ILE C 265 " --> pdb=" O   ARG C 261 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 279 through 300
      removed outlier: 3.511A  pdb=" N   GLY C 285 " --> pdb=" O   PRO C 281 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LEU C 289 " --> pdb=" O   GLY C 285 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU C 296 " --> pdb=" O   SER C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 320
      removed outlier: 3.925A  pdb=" N   SER C 310 " --> pdb=" O   LEU C 306 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   ALA C 311 " --> pdb=" O   ARG C 307 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   GLN C 317 " --> pdb=" O   ALA C 313 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   VAL C 318 " --> pdb=" O   GLU C 314 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 329 through 355
      removed outlier: 4.134A  pdb=" N   LEU C 335 " --> pdb=" O   ASP C 331 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 64 through 79
    Processing helix  chain 'D' and resid 80 through 116
      removed outlier: 4.159A  pdb=" N   LEU D  97 " --> pdb=" O   ILE D  93 " (cutoff:3.500A)
      Proline residue:  D  98  - end of helix
      removed outlier: 3.641A  pdb=" N   TYR D 116 " --> pdb=" O   ALA D 112 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 130 through 141
    Processing helix  chain 'D' and resid 156 through 164
      removed outlier: 3.573A  pdb=" N   GLY D 160 " --> pdb=" O   GLU D 156 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   GLU D 161 " --> pdb=" O   ASP D 157 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   PHE D 162 " --> pdb=" O   ALA D 158 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 189 through 194
      removed outlier: 3.912A  pdb=" N   GLY D 194 " --> pdb=" O   LEU D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 194 through 207
      removed outlier: 5.036A  pdb=" N   THR D 200 " --> pdb=" O   GLU D 196 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   LEU D 201 " --> pdb=" O   SER D 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 219 through 261
      removed outlier: 4.306A  pdb=" N   SER D 235 " --> pdb=" O   VAL D 231 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 264 through 271
      removed outlier: 4.333A  pdb=" N   GLN D 268 " --> pdb=" O   SER D 264 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ILE D 271 " --> pdb=" O   VAL D 267 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 274 through 319
      removed outlier: 3.512A  pdb=" N   ARG D 280 " --> pdb=" O   GLY D 276 " (cutoff:3.500A)
      Proline residue:  D 281  - end of helix
      removed outlier: 3.789A  pdb=" N   LEU D 289 " --> pdb=" O   GLY D 285 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   SER D 310 " --> pdb=" O   LEU D 306 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   ALA D 311 " --> pdb=" O   ARG D 307 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   VAL D 312 " --> pdb=" O   LEU D 308 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 329 through 359
      removed outlier: 3.548A  pdb=" N   ARG D 357 " --> pdb=" O   VAL D 353 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   HIS D 358 " --> pdb=" O   GLN D 354 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 81 through 123
    Processing helix  chain 'E' and resid 144 through 150
    Processing helix  chain 'E' and resid 152 through 190
    Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 25
      removed outlier: 5.436A  pdb=" N   GLN A  19 " --> pdb=" O   LYS A   9 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   LYS A   9 " --> pdb=" O   GLN A  19 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   PHE A  23 " --> pdb=" O   GLU A   5 " (cutoff:3.500A)
      removed outlier: 5.151A  pdb=" N   GLU A   5 " --> pdb=" O   PHE A  23 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   MET A  25 " --> pdb=" O   ARG A   3 " (cutoff:3.500A)
      removed outlier: 5.354A  pdb=" N   ARG A   3 " --> pdb=" O   MET A  25 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   VAL A   7 " --> pdb=" O   ALA A  56 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ALA A  56 " --> pdb=" O   VAL A   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 84
      removed outlier: 6.465A  pdb=" N   LEU A 159 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   ALA A 193 " --> pdb=" O   LEU A 159 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ALA A 161 " --> pdb=" O   ALA A 193 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   ALA A  31 " --> pdb=" O   MET A 192 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   PHE A  32 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   LEU A 210 " --> pdb=" O   PHE A  32 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   THR A  34 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 15 through 25
      removed outlier: 6.492A  pdb=" N   ALA B  17 " --> pdb=" O   ALA B  10 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   ALA B  10 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   GLN B  19 " --> pdb=" O   SER B   8 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   SER B   8 " --> pdb=" O   GLN B  19 " (cutoff:3.500A)
      removed outlier: 5.415A  pdb=" N   VAL B  21 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   VAL B   7 " --> pdb=" O   ALA B  56 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ALA B  56 " --> pdb=" O   VAL B   7 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 84
      removed outlier: 6.401A  pdb=" N   GLY B  82 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   ASP B 162 " --> pdb=" O   GLY B  82 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   ILE B  84 " --> pdb=" O   ASP B 162 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   LEU B 159 " --> pdb=" O   LEU B 191 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   ALA B 193 " --> pdb=" O   LEU B 159 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ALA B 161 " --> pdb=" O   ALA B 193 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ALA B  31 " --> pdb=" O   VAL B 190 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 150 through 151
    Processing sheet with id=AA6, first strand: chain 'D' and resid 151 through 152

    504 hydrogen bonds defined for protein.
    1467 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: 2.30

  Time building geometry restraints manager: 2.74 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2396
        1.33 -     1.45: 1039
        1.45 -     1.57: 4383
        1.57 -     1.69: 10
        1.69 -     1.81: 52
  Bond restraints: 7880
  Sorted by residual:
  bond pdb=" N   VAL C 185 "
       pdb=" CA  VAL C 185 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.037 1.19e-02 7.06e+03 9.58e+00
  bond pdb=" N   VAL C 186 "
       pdb=" CA  VAL C 186 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.037 1.23e-02 6.61e+03 9.06e+00
  bond pdb=" N   VAL C 183 "
       pdb=" CA  VAL C 183 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.72e+00
  bond pdb=" N   ILE C 121 "
       pdb=" CA  ILE C 121 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 8.02e+00
  bond pdb=" N   ILE C 211 "
       pdb=" CA  ILE C 211 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.96e+00
  ... (remaining 7875 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.48: 10530
        2.48 -     4.95: 208
        4.95 -     7.43: 23
        7.43 -     9.90: 3
        9.90 -    12.38: 2
  Bond angle restraints: 10766
  Sorted by residual:
  angle pdb=" PB  ATP B 301 "
        pdb=" O3B ATP B 301 "
        pdb=" PG  ATP B 301 "
      ideal   model   delta    sigma   weight residual
     139.87  129.08   10.79 1.00e+00 1.00e+00 1.16e+02
  angle pdb=" PB  ATP A 301 "
        pdb=" O3B ATP A 301 "
        pdb=" PG  ATP A 301 "
      ideal   model   delta    sigma   weight residual
     139.87  130.49    9.38 1.00e+00 1.00e+00 8.80e+01
  angle pdb=" N   ALA C 225 "
        pdb=" CA  ALA C 225 "
        pdb=" C   ALA C 225 "
      ideal   model   delta    sigma   weight residual
     114.62  108.03    6.59 1.14e+00 7.69e-01 3.34e+01
  angle pdb=" PA  ATP B 301 "
        pdb=" O3A ATP B 301 "
        pdb=" PB  ATP B 301 "
      ideal   model   delta    sigma   weight residual
     136.83  131.79    5.04 1.00e+00 1.00e+00 2.54e+01
  angle pdb=" N   VAL C 100 "
        pdb=" CA  VAL C 100 "
        pdb=" C   VAL C 100 "
      ideal   model   delta    sigma   weight residual
     112.96  108.55    4.41 1.00e+00 1.00e+00 1.95e+01
  ... (remaining 10761 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.99: 4087
       16.99 -    33.98: 378
       33.98 -    50.97: 158
       50.97 -    67.95: 37
       67.95 -    84.94: 8
  Dihedral angle restraints: 4668
    sinusoidal: 1413
      harmonic: 3255
  Sorted by residual:
  dihedral pdb=" CA  GLU E 114 "
           pdb=" C   GLU E 114 "
           pdb=" N   ARG E 115 "
           pdb=" CA  ARG E 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.16   26.84     0      5.00e+00 4.00e-02 2.88e+01
  dihedral pdb=" CA  HIS A 195 "
           pdb=" C   HIS A 195 "
           pdb=" N   ASP A 196 "
           pdb=" CA  ASP A 196 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.77   22.23     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  SER D 264 "
           pdb=" C   SER D 264 "
           pdb=" N   ILE D 265 "
           pdb=" CA  ILE D 265 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.84   22.16     0      5.00e+00 4.00e-02 1.96e+01
  ... (remaining 4665 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1129
       0.066 -    0.131: 153
       0.131 -    0.197: 28
       0.197 -    0.262: 4
       0.262 -    0.328: 2
  Chirality restraints: 1316
  Sorted by residual:
  chirality pdb=" CB  THR C 360 "
            pdb=" CA  THR C 360 "
            pdb=" OG1 THR C 360 "
            pdb=" CG2 THR C 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.22    0.33 2.00e-01 2.50e+01 2.69e+00
  chirality pdb=" CB  VAL B  96 "
            pdb=" CA  VAL B  96 "
            pdb=" CG1 VAL B  96 "
            pdb=" CG2 VAL B  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CA  LEU C 198 "
            pdb=" N   LEU C 198 "
            pdb=" C   LEU C 198 "
            pdb=" CB  LEU C 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 1313 not shown)

  Planarity restraints: 1396
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS E 110 "    0.022 2.00e-02 2.50e+03   4.44e-02 1.97e+01
        pdb=" C   LYS E 110 "   -0.077 2.00e-02 2.50e+03
        pdb=" O   LYS E 110 "    0.028 2.00e-02 2.50e+03
        pdb=" N   ALA E 111 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG D 280 "    0.060 5.00e-02 4.00e+02   9.00e-02 1.29e+01
        pdb=" N   PRO D 281 "   -0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO D 281 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO D 281 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA E 104 "   -0.015 2.00e-02 2.50e+03   2.97e-02 8.84e+00
        pdb=" C   ALA E 104 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ALA E 104 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LYS E 105 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1393 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 98
        2.64 -     3.21: 7270
        3.21 -     3.77: 11761
        3.77 -     4.34: 15138
        4.34 -     4.90: 25522
  Nonbonded interactions: 59789
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 139 "
            pdb=" OE1 GLU A 142 "
     model   vdw
     2.075 3.040
  nonbonded pdb=" O   ASP A 169 "
            pdb=" OG  SER A 173 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" NH2 ARG A  79 "
            pdb=" O   GLY D 272 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" O   ASP C  76 "
            pdb=" OG  SER C  79 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OH  TYR B  11 "
            pdb=" OG1 THR B  43 "
     model   vdw
     2.244 3.040
  ... (remaining 59784 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 13 through 196 or (resid 197 through 198 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 199 through 218 or  \ 
resid 301))
  selection = (chain 'B' and (resid 1 through 67 or (resid 68 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 69 or (resid 70 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 71 through 218 or resid 301))
}
ncs_group {
  reference = (chain 'C' and ((resid 63 through 65 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 66 through 74 or (resid 75 through 76 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 77 through 220 or (resid 221 thro \ 
ugh 223 and (name N or name CA or name C or name O or name CB )) or resid 224 th \ 
rough 226 or (resid 227 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 228 through 229 or (resid 230 through 231 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 232 or (resid 233 through 234 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 235 through 307 or (resid  \ 
308 through 319 and (name N or name CA or name C or name O or name CB )) or (res \ 
id 320 through 326 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 327 through 331 or (resid 332 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 333 through 353 or (resid 354 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 355 through 359 or (resid 360 through 361 a \ 
nd (name N or name CA or name C or name O or name CB ))))
  selection = (chain 'D' and (resid 63 through 75 or (resid 76 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 77 through 105 or (resid 106 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 107 through 108 or (resid 109  \ 
through 116 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 
7 through 218 or (resid 219 through 223 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 224 through 233 or (resid 234 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 235 through 256 or (resid 257 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 258 through 262 or (re \ 
sid 263 and (name N or name CA or name C or name O or name CB )) or resid 264 th \ 
rough 301 or (resid 302 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 303 through 333 or (resid 334 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 335 through 361))
}

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:             11.270
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     26.380
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
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      :  0.007   0.063   7880  Z= 0.359
  Angle     :  0.839  12.378  10766  Z= 0.508
  Chirality :  0.052   0.328   1316
  Planarity :  0.005   0.090   1396
  Dihedral  : 16.972  84.942   2568
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  1.06 %
    Allowed  : 10.31 %
    Favored  : 88.63 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 27.36 %
    Favored  : 71.17 %
  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: -1.11 (0.25), residues: 1135
  helix:  0.58 (0.21), residues: 637
  sheet: -2.27 (0.51), residues: 68
  loop : -2.53 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D 345 
 HIS   0.006   0.001   HIS A 195 
 PHE   0.018   0.002   PHE B  23 
 TYR   0.008   0.002   TYR C  68 
 ARG   0.004   0.001   ARG C 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17702 (  504)
  hydrogen bonds       : angle       6.68365 ( 1467)
  covalent geometry    : bond        0.00716 ( 7880)
  covalent geometry    : angle       0.83877 (10766)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 132
  time to evaluate  : 0.795 
Fit side-chains
REVERT: A   71 ASN cc_start: 0.8114 (m-40) cc_final: 0.7825 (t0)
REVERT: C  224 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5921 (mt)
REVERT: C  306 LEU cc_start: 0.6683 (mt) cc_final: 0.6349 (pp)
  outliers start: 9
  outliers final: 2
  residues processed: 138
  average time/residue: 0.2959
  time to fit residues: 50.4211
Evaluate side-chains
  104 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  107 ASN
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  224 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 84 optimal weight:   20.0000
   chunk 46 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 56 optimal weight:   20.0000
   chunk 44 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 52 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 100 optimal weight:   10.0000
   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  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  71 HIS
** D 107 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 = 0.4382 r_free = 0.4382 target = 0.206366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.165880 restraints weight = 8650.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 1.85
r_work: 0.3465 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   7880  Z= 0.250
  Angle     :  0.751  13.369  10766  Z= 0.380
  Chirality :  0.045   0.216   1316
  Planarity :  0.005   0.062   1396
  Dihedral  :  9.732  89.827   1273
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  8.55 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  7.33 %
    Allowed  : 21.66 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.25), residues: 1135
  helix:  1.01 (0.21), residues: 635
  sheet: -2.50 (0.52), residues: 77
  loop : -2.51 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP A  60 
 HIS   0.005   0.001   HIS B 214 
 PHE   0.015   0.002   PHE A  23 
 TYR   0.021   0.002   TYR C 105 
 ARG   0.005   0.001   ARG A  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06107 (  504)
  hydrogen bonds       : angle       5.09710 ( 1467)
  covalent geometry    : bond        0.00605 ( 7880)
  covalent geometry    : angle       0.75057 (10766)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 116
  time to evaluate  : 0.884 
Fit side-chains
REVERT: A   71 ASN cc_start: 0.8406 (m-40) cc_final: 0.7774 (t0)
REVERT: A   84 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7765 (pt)
REVERT: B   53 ARG cc_start: 0.8702 (ttm170) cc_final: 0.8414 (mtm180)
REVERT: B   74 VAL cc_start: 0.7797 (OUTLIER) cc_final: 0.7573 (t)
REVERT: B  207 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7162 (tmm)
REVERT: C   68 TYR cc_start: 0.7879 (t80) cc_final: 0.7612 (t80)
REVERT: C  224 LEU cc_start: 0.5879 (OUTLIER) cc_final: 0.5618 (mt)
REVERT: C  319 PHE cc_start: 0.6323 (t80) cc_final: 0.5985 (t80)
REVERT: D  241 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7451 (mp)
REVERT: D  268 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7907 (tt0)
REVERT: D  302 GLU cc_start: 0.6498 (tm-30) cc_final: 0.6215 (tp30)
  outliers start: 45
  outliers final: 20
  residues processed: 153
  average time/residue: 0.2338
  time to fit residues: 46.4964
Evaluate side-chains
  130 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  261 ARG
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain D residue  104 VAL
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  266 ASN
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 36 optimal weight:    0.3980
   chunk 89 optimal weight:    0.8980
   chunk 95 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 96 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0870
   chunk 83 optimal weight:    9.9990
   chunk 24 optimal weight:    0.4980
   chunk 86 optimal weight:   30.0000
   chunk 73 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.207097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.167565 restraints weight = 8815.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3992 rms_B_bonded: 1.75
r_work: 0.3507 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.2997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7880  Z= 0.188
  Angle     :  0.651  11.883  10766  Z= 0.329
  Chirality :  0.042   0.161   1316
  Planarity :  0.004   0.054   1396
  Dihedral  :  9.172  89.452   1271
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  8.11 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  6.68 %
    Allowed  : 21.34 %
    Favored  : 71.99 %
  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: -0.23 (0.26), residues: 1135
  helix:  1.34 (0.21), residues: 645
  sheet: -1.74 (0.54), residues: 68
  loop : -2.33 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 345 
 HIS   0.006   0.001   HIS A 195 
 PHE   0.020   0.002   PHE C 247 
 TYR   0.016   0.001   TYR C 105 
 ARG   0.004   0.001   ARG A  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05028 (  504)
  hydrogen bonds       : angle       4.76449 ( 1467)
  covalent geometry    : bond        0.00443 ( 7880)
  covalent geometry    : angle       0.65144 (10766)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 100
  time to evaluate  : 0.873 
Fit side-chains
REVERT: A   84 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7754 (mp)
REVERT: A   87 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8290 (m-30)
REVERT: A  195 HIS cc_start: 0.8070 (OUTLIER) cc_final: 0.7799 (p-80)
REVERT: A  208 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8334 (mt)
REVERT: B   74 VAL cc_start: 0.7870 (OUTLIER) cc_final: 0.7628 (t)
REVERT: C   68 TYR cc_start: 0.7937 (t80) cc_final: 0.7545 (t80)
REVERT: C  224 LEU cc_start: 0.5225 (OUTLIER) cc_final: 0.4936 (mt)
REVERT: C  319 PHE cc_start: 0.5853 (t80) cc_final: 0.5465 (t80)
REVERT: D  241 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7524 (mp)
REVERT: D  268 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7894 (tt0)
  outliers start: 41
  outliers final: 23
  residues processed: 134
  average time/residue: 0.2352
  time to fit residues: 41.1525
Evaluate side-chains
  125 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 94
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   30 MET
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  261 ARG
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  266 ASN
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  334 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 67 optimal weight:    6.9990
   chunk 109 optimal weight:   20.0000
   chunk 51 optimal weight:   20.0000
   chunk 69 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 77 optimal weight:   30.0000
   chunk 21 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0040
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.206023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.164771 restraints weight = 8687.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 1.70
r_work: 0.3487 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   7880  Z= 0.205
  Angle     :  0.675  11.590  10766  Z= 0.339
  Chirality :  0.043   0.252   1316
  Planarity :  0.004   0.054   1396
  Dihedral  :  9.072  80.514   1271
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  8.19 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  7.65 %
    Allowed  : 21.34 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.26), residues: 1135
  helix:  1.43 (0.21), residues: 648
  sheet: -1.52 (0.54), residues: 78
  loop : -2.34 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 345 
 HIS   0.004   0.001   HIS B 214 
 PHE   0.031   0.002   PHE C 247 
 TYR   0.010   0.001   TYR C 105 
 ARG   0.004   0.000   ARG A  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05198 (  504)
  hydrogen bonds       : angle       4.70369 ( 1467)
  covalent geometry    : bond        0.00496 ( 7880)
  covalent geometry    : angle       0.67486 (10766)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 100
  time to evaluate  : 0.907 
Fit side-chains
REVERT: A   83 MET cc_start: 0.8577 (ptt) cc_final: 0.7809 (ttt)
REVERT: A   84 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7827 (pt)
REVERT: A   87 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8281 (m-30)
REVERT: A  183 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7656 (t80)
REVERT: A  208 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8287 (mt)
REVERT: C   68 TYR cc_start: 0.7940 (t80) cc_final: 0.7613 (t80)
REVERT: C  224 LEU cc_start: 0.5107 (OUTLIER) cc_final: 0.4812 (mt)
REVERT: C  319 PHE cc_start: 0.5770 (t80) cc_final: 0.5358 (t80)
REVERT: D  241 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7359 (mp)
REVERT: D  268 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7851 (tt0)
REVERT: D  302 GLU cc_start: 0.6488 (tp30) cc_final: 0.6228 (tp30)
  outliers start: 47
  outliers final: 30
  residues processed: 139
  average time/residue: 0.2459
  time to fit residues: 45.1026
Evaluate side-chains
  135 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 98
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   84 ILE
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  266 ASN
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 84 optimal weight:    9.9990
   chunk 51 optimal weight:   20.0000
   chunk 22 optimal weight:    0.6980
   chunk 82 optimal weight:   30.0000
   chunk 11 optimal weight:    0.2980
   chunk 5 optimal weight:    0.6980
   chunk 53 optimal weight:   20.0000
   chunk 68 optimal weight:    0.9980
   chunk 55 optimal weight:   50.0000
   chunk 12 optimal weight:    0.0980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.207690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.166055 restraints weight = 8711.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 1.47
r_work: 0.3541 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3365 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7880  Z= 0.163
  Angle     :  0.617  11.726  10766  Z= 0.311
  Chirality :  0.041   0.149   1316
  Planarity :  0.004   0.052   1396
  Dihedral  :  8.760  82.233   1271
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  8.28 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 22.48 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.26), residues: 1135
  helix:  1.64 (0.21), residues: 650
  sheet: -1.82 (0.54), residues: 80
  loop : -2.24 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 345 
 HIS   0.003   0.001   HIS C 358 
 PHE   0.021   0.001   PHE C 247 
 TYR   0.005   0.001   TYR B 205 
 ARG   0.004   0.000   ARG A 115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04481 (  504)
  hydrogen bonds       : angle       4.52418 ( 1467)
  covalent geometry    : bond        0.00384 ( 7880)
  covalent geometry    : angle       0.61745 (10766)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 94
  time to evaluate  : 0.877 
Fit side-chains
REVERT: A   83 MET cc_start: 0.8508 (ptt) cc_final: 0.7792 (ttt)
REVERT: A  183 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7669 (t80)
REVERT: A  208 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8267 (mt)
REVERT: C   68 TYR cc_start: 0.7945 (t80) cc_final: 0.7626 (t80)
REVERT: C  224 LEU cc_start: 0.5161 (OUTLIER) cc_final: 0.4788 (mt)
REVERT: C  342 MET cc_start: 0.8593 (mmm) cc_final: 0.8334 (mmt)
REVERT: D  241 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7403 (mp)
REVERT: D  268 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7877 (tt0)
  outliers start: 40
  outliers final: 26
  residues processed: 128
  average time/residue: 0.2176
  time to fit residues: 36.8154
Evaluate side-chains
  125 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 94
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 47 optimal weight:    9.9990
   chunk 64 optimal weight:    0.5980
   chunk 50 optimal weight:   40.0000
   chunk 2 optimal weight:    0.0270
   chunk 25 optimal weight:    0.7980
   chunk 84 optimal weight:   20.0000
   chunk 104 optimal weight:    0.3980
   chunk 98 optimal weight:    1.9990
   chunk 55 optimal weight:   40.0000
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
C 107 ASN
D 266 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.213192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.174673 restraints weight = 8497.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.4077 rms_B_bonded: 1.36
r_work: 0.3650 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3430 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7880  Z= 0.166
  Angle     :  0.622  11.978  10766  Z= 0.312
  Chirality :  0.041   0.161   1316
  Planarity :  0.004   0.053   1396
  Dihedral  :  8.723  80.815   1271
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  7.93 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  7.33 %
    Allowed  : 21.50 %
    Favored  : 71.17 %
  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:  0.23 (0.26), residues: 1135
  helix:  1.75 (0.21), residues: 650
  sheet: -1.78 (0.54), residues: 81
  loop : -2.18 (0.29), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 345 
 HIS   0.003   0.001   HIS A 195 
 PHE   0.020   0.002   PHE C 247 
 TYR   0.005   0.001   TYR B 205 
 ARG   0.004   0.001   ARG D 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04487 (  504)
  hydrogen bonds       : angle       4.42742 ( 1467)
  covalent geometry    : bond        0.00395 ( 7880)
  covalent geometry    : angle       0.62243 (10766)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 93
  time to evaluate  : 0.802 
Fit side-chains
REVERT: A   83 MET cc_start: 0.8392 (ptt) cc_final: 0.7770 (ttt)
REVERT: A  183 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7668 (t80)
REVERT: A  208 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8332 (mt)
REVERT: B   80 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7827 (mt0)
REVERT: C   68 TYR cc_start: 0.7870 (t80) cc_final: 0.7556 (t80)
REVERT: C   95 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8507 (tt)
REVERT: C  224 LEU cc_start: 0.5213 (OUTLIER) cc_final: 0.4894 (mt)
REVERT: C  306 LEU cc_start: 0.6608 (mt) cc_final: 0.5615 (pp)
REVERT: D  241 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7465 (mp)
REVERT: D  268 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7901 (tt0)
REVERT: D  330 PHE cc_start: 0.4096 (OUTLIER) cc_final: 0.3788 (m-80)
  outliers start: 45
  outliers final: 33
  residues processed: 131
  average time/residue: 0.2207
  time to fit residues: 38.1755
Evaluate side-chains
  129 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 89
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  195 HIS
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  297 SER
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  266 ASN
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  330 PHE
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 83 optimal weight:   20.0000
   chunk 36 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   chunk 32 optimal weight:    0.3980
   chunk 9 optimal weight:    0.0970
   chunk 38 optimal weight:    0.1980
   chunk 5 optimal weight:    0.9990
   chunk 14 optimal weight:    0.1980
   chunk 78 optimal weight:   40.0000
   chunk 100 optimal weight:    8.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.3378

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

Flipped N/Q/H residues before XYZ refinement:
D 266 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.214632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.175188 restraints weight = 8560.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.4073 rms_B_bonded: 1.42
r_work: 0.3658 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3452 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.3900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7880  Z= 0.134
  Angle     :  0.587  12.268  10766  Z= 0.295
  Chirality :  0.040   0.146   1316
  Planarity :  0.004   0.053   1396
  Dihedral  :  8.568  83.822   1271
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  7.49 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 22.80 %
    Favored  : 70.68 %
  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:  0.43 (0.26), residues: 1135
  helix:  1.88 (0.21), residues: 651
  sheet: -1.52 (0.56), residues: 80
  loop : -2.10 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 345 
 HIS   0.003   0.001   HIS C 358 
 PHE   0.017   0.001   PHE C 247 
 TYR   0.004   0.001   TYR C 102 
 ARG   0.005   0.000   ARG D 262 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04081 (  504)
  hydrogen bonds       : angle       4.33974 ( 1467)
  covalent geometry    : bond        0.00300 ( 7880)
  covalent geometry    : angle       0.58731 (10766)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 92
  time to evaluate  : 0.929 
Fit side-chains
REVERT: A  183 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7646 (t80)
REVERT: B   51 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8587 (mm)
REVERT: B   80 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7852 (mt0)
REVERT: C   68 TYR cc_start: 0.7883 (t80) cc_final: 0.7567 (t80)
REVERT: C  224 LEU cc_start: 0.5119 (OUTLIER) cc_final: 0.4786 (mt)
REVERT: C  306 LEU cc_start: 0.6561 (mt) cc_final: 0.5583 (pp)
REVERT: C  342 MET cc_start: 0.8664 (mmm) cc_final: 0.8419 (mmt)
REVERT: D  241 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7509 (mp)
REVERT: D  268 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7839 (tt0)
  outliers start: 40
  outliers final: 29
  residues processed: 125
  average time/residue: 0.2232
  time to fit residues: 36.5487
Evaluate side-chains
  130 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 96
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  195 HIS
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  297 SER
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  266 ASN
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 109 optimal weight:   20.0000
   chunk 47 optimal weight:    6.9990
   chunk 13 optimal weight:    0.2980
   chunk 19 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0020
   chunk 25 optimal weight:    0.6980
   chunk 52 optimal weight:   20.0000
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
D 266 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.213284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.172858 restraints weight = 8577.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 1.40
r_work: 0.3654 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3448 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.3970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7880  Z= 0.170
  Angle     :  0.627  12.241  10766  Z= 0.312
  Chirality :  0.041   0.159   1316
  Planarity :  0.004   0.053   1396
  Dihedral  :  8.698  81.998   1271
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  7.75 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  6.84 %
    Allowed  : 22.96 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.26), residues: 1135
  helix:  1.87 (0.21), residues: 657
  sheet: -1.53 (0.57), residues: 80
  loop : -2.12 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 345 
 HIS   0.003   0.001   HIS D 358 
 PHE   0.016   0.001   PHE C 247 
 TYR   0.005   0.001   TYR B 205 
 ARG   0.005   0.000   ARG A  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04488 (  504)
  hydrogen bonds       : angle       4.32335 ( 1467)
  covalent geometry    : bond        0.00407 ( 7880)
  covalent geometry    : angle       0.62681 (10766)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 96
  time to evaluate  : 1.158 
Fit side-chains
REVERT: A  183 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7694 (t80)
REVERT: B   51 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8599 (mm)
REVERT: B   80 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7850 (mt0)
REVERT: C   68 TYR cc_start: 0.7828 (t80) cc_final: 0.7492 (t80)
REVERT: C  224 LEU cc_start: 0.5054 (OUTLIER) cc_final: 0.4739 (mt)
REVERT: C  342 MET cc_start: 0.8687 (mmm) cc_final: 0.8451 (mmt)
REVERT: D  241 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7351 (mp)
REVERT: D  268 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7879 (tt0)
REVERT: D  330 PHE cc_start: 0.4052 (OUTLIER) cc_final: 0.3780 (m-80)
  outliers start: 42
  outliers final: 30
  residues processed: 131
  average time/residue: 0.3031
  time to fit residues: 57.0224
Evaluate side-chains
  136 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 100
  time to evaluate  : 2.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  195 HIS
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  297 SER
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  330 PHE
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 85 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 104 optimal weight:    0.6980
   chunk 93 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0770
   chunk 95 optimal weight:    2.9990
   chunk 86 optimal weight:    9.9990
   chunk 71 optimal weight:    2.9990
   chunk 48 optimal weight:   40.0000
   chunk 76 optimal weight:    0.0060
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
D 107 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.213125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.175232 restraints weight = 8699.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.4074 rms_B_bonded: 1.33
r_work: 0.3660 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3447 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.4144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7880  Z= 0.173
  Angle     :  0.624  11.633  10766  Z= 0.311
  Chirality :  0.041   0.162   1316
  Planarity :  0.004   0.054   1396
  Dihedral  :  8.725  80.982   1271
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  7.58 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  7.33 %
    Allowed  : 22.64 %
    Favored  : 70.03 %
  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:  0.47 (0.26), residues: 1135
  helix:  1.90 (0.21), residues: 658
  sheet: -1.53 (0.58), residues: 80
  loop : -2.13 (0.29), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 345 
 HIS   0.003   0.001   HIS C 355 
 PHE   0.016   0.002   PHE D  70 
 TYR   0.005   0.001   TYR C 102 
 ARG   0.005   0.000   ARG A  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04513 (  504)
  hydrogen bonds       : angle       4.28419 ( 1467)
  covalent geometry    : bond        0.00416 ( 7880)
  covalent geometry    : angle       0.62404 (10766)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 105
  time to evaluate  : 0.875 
Fit side-chains
REVERT: A  155 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7912 (pttt)
REVERT: A  183 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7626 (t80)
REVERT: B   51 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8600 (mm)
REVERT: B   80 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7861 (mt0)
REVERT: C   68 TYR cc_start: 0.7916 (t80) cc_final: 0.7633 (t80)
REVERT: C  224 LEU cc_start: 0.5206 (OUTLIER) cc_final: 0.4945 (mt)
REVERT: C  342 MET cc_start: 0.8643 (mmm) cc_final: 0.8416 (mmt)
REVERT: D  241 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7401 (mp)
REVERT: D  268 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7980 (tt0)
REVERT: D  330 PHE cc_start: 0.4246 (OUTLIER) cc_final: 0.4030 (m-80)
  outliers start: 45
  outliers final: 32
  residues processed: 143
  average time/residue: 0.2117
  time to fit residues: 40.6130
Evaluate side-chains
  140 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 101
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  155 LYS
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  195 HIS
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  297 SER
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  330 PHE
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 86 optimal weight:    8.9990
   chunk 88 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   chunk 35 optimal weight:    0.4980
   chunk 89 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 2 optimal weight:    0.2980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4471 r_free = 0.4471 target = 0.215030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.174058 restraints weight = 8711.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.4033 rms_B_bonded: 1.41
r_work: 0.3609 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3408 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7880  Z= 0.193
  Angle     :  0.650  11.975  10766  Z= 0.324
  Chirality :  0.042   0.179   1316
  Planarity :  0.004   0.054   1396
  Dihedral  :  8.827  80.734   1271
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  7.58 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  7.00 %
    Allowed  : 23.78 %
    Favored  : 69.22 %
  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:  0.46 (0.26), residues: 1135
  helix:  1.90 (0.21), residues: 656
  sheet: -1.57 (0.55), residues: 90
  loop : -2.12 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 345 
 HIS   0.004   0.001   HIS B 216 
 PHE   0.016   0.002   PHE C 247 
 TYR   0.006   0.001   TYR B 205 
 ARG   0.005   0.001   ARG A  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04727 (  504)
  hydrogen bonds       : angle       4.25819 ( 1467)
  covalent geometry    : bond        0.00470 ( 7880)
  covalent geometry    : angle       0.65005 (10766)

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

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

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2270 Ramachandran restraints generated.
    1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 102
  time to evaluate  : 0.882 
Fit side-chains
REVERT: A  155 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7944 (pttt)
REVERT: A  183 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7693 (t80)
REVERT: B   51 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8598 (mm)
REVERT: B   80 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7853 (mt0)
REVERT: C   68 TYR cc_start: 0.7878 (t80) cc_final: 0.7619 (t80)
REVERT: C  224 LEU cc_start: 0.5165 (OUTLIER) cc_final: 0.4890 (mt)
REVERT: C  342 MET cc_start: 0.8708 (mmm) cc_final: 0.8465 (mmt)
REVERT: C  354 GLN cc_start: 0.7851 (tm-30) cc_final: 0.6614 (mm-40)
REVERT: D  241 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7371 (mp)
REVERT: D  268 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7957 (tt0)
  outliers start: 43
  outliers final: 33
  residues processed: 137
  average time/residue: 0.2229
  time to fit residues: 40.0832
Evaluate side-chains
  141 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 102
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   87 ASP
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  155 LYS
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  183 PHE
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  182 GLU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  195 HIS
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain C residue   93 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  221 PHE
Chi-restraints excluded: chain C residue  224 LEU
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  297 SER
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  312 VAL
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  268 GLN
Chi-restraints excluded: chain D residue  270 LEU
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  334 LEU
Chi-restraints excluded: chain D residue  358 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 106 optimal weight:   10.0000
   chunk 18 optimal weight:    0.7980
   chunk 13 optimal weight:    0.2980
   chunk 82 optimal weight:   10.0000
   chunk 31 optimal weight:    0.2980
   chunk 62 optimal weight:    0.0050
   chunk 52 optimal weight:    7.9990
   chunk 48 optimal weight:   30.0000
   chunk 11 optimal weight:    0.0980
   overall best weight:    0.2994

-------------------------------------------------------------------------------
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 = 0.4482 r_free = 0.4482 target = 0.215456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.173223 restraints weight = 8526.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.4071 rms_B_bonded: 1.62
r_work: 0.3644 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3459 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.4389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7880  Z= 0.127
  Angle     :  0.580  12.162  10766  Z= 0.291
  Chirality :  0.040   0.170   1316
  Planarity :  0.004   0.053   1396
  Dihedral  :  8.436  86.841   1271
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  7.14 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 24.76 %
    Favored  : 69.38 %
  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:  0.69 (0.26), residues: 1135
  helix:  2.10 (0.21), residues: 652
  sheet: -1.34 (0.58), residues: 80
  loop : -2.05 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 345 
 HIS   0.004   0.001   HIS C 358 
 PHE   0.036   0.001   PHE D 247 
 TYR   0.004   0.001   TYR C 102 
 ARG   0.004   0.000   ARG A  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03854 (  504)
  hydrogen bonds       : angle       4.10603 ( 1467)
  covalent geometry    : bond        0.00277 ( 7880)
  covalent geometry    : angle       0.58029 (10766)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6233.14 seconds
wall clock time: 110 minutes 24.58 seconds (6624.58 seconds total)