Starting phenix.real_space_refine
on Thu Mar 13 04:36:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7eja_31157/03_2025/7eja_31157.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7eja_31157/03_2025/7eja_31157.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7eja_31157/03_2025/7eja_31157.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7eja_31157/03_2025/7eja_31157.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7eja_31157/03_2025/7eja_31157.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7eja_31157/03_2025/7eja_31157.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.007 sd=   0.192
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    5487      2.51       5
     N    1458      2.21       5
     O    1581      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8584
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1632
          Classifications: {'peptide': 210}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'CIS': 7, 'PTRANS': 4, 'TRANS': 198}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 30
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "B"
      Number of atoms: 2541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2541
          Classifications: {'peptide': 331}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 324}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "G"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 418
          Classifications: {'peptide': 54}
          Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 48}
    Chain: "R"
      Number of atoms: 2193
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 269, 2193
          Classifications: {'peptide': 269}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 256}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "H"
      Number of atoms: 1785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1785
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'CZX': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   LYS H 236 " occ=0.00
      ... (7 atoms not shown)
      pdb=" NZ  LYS H 236 " occ=0.00
  Time building chain proxies: 5.49, per 1000 atoms: 0.64
  Number of scatterers: 8584
  At special positions: 0
  Unit cell: (88.4, 120.7, 124.95, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      58     16.00
     O    1581      8.00
     N    1458      7.00
     C    5487      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 121 " - pdb=" SG  CYS R 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 147 " - pdb=" SG  CYS H 217 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.84
  Conformation dependent library (CDL) restraints added in 918.8 milliseconds
  

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2052

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 12 sheets defined
      34.7% alpha, 18.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.682A  pdb=" N   ARG A  10 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 52
      removed outlier: 4.207A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 214
      removed outlier: 4.170A  pdb=" N   TRP A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 217
      No H-bonds generated for 'chain 'A' and resid 215 through 217'
    Processing helix  chain 'A' and resid 245 through 256
      removed outlier: 4.213A  pdb=" N   MET A 249 " --> pdb=" O   HIS A 245 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ASP A 252 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 281
      removed outlier: 4.100A  pdb=" N   LYS A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 307
    Processing helix  chain 'A' and resid 329 through 350
      removed outlier: 4.482A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 25
      removed outlier: 3.591A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 24
      removed outlier: 3.802A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LYS G  20 " --> pdb=" O   VAL G  16 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLU G  22 " --> pdb=" O   GLN G  18 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'R' and resid 47 through 74
    Processing helix  chain 'R' and resid 83 through 108
      removed outlier: 4.473A  pdb=" N   LEU R  87 " --> pdb=" O   GLN R  83 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ILE R 102 " --> pdb=" O   ALA R  98 " (cutoff:3.500A)
      Proline residue:  R 103  - end of helix
    Processing helix  chain 'R' and resid 120 through 151
    Processing helix  chain 'R' and resid 152 through 157
    Processing helix  chain 'R' and resid 158 through 160
      No H-bonds generated for 'chain 'R' and resid 158 through 160'
    Processing helix  chain 'R' and resid 161 through 181
    Processing helix  chain 'R' and resid 208 through 242
      removed outlier: 3.683A  pdb=" N   ILE R 213 " --> pdb=" O   LYS R 209 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   SER R 214 " --> pdb=" O   TRP R 210 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   ALA R 222 " --> pdb=" O   GLY R 218 " (cutoff:3.500A)
      Proline residue:  R 223  - end of helix
    Processing helix  chain 'R' and resid 376 through 411
      removed outlier: 3.698A  pdb=" N   ASN R 382 " --> pdb=" O   ARG R 378 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   PHE R 398 " --> pdb=" O   VAL R 394 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL R 399 " --> pdb=" O   ILE R 395 " (cutoff:3.500A)
      Proline residue:  R 404  - end of helix
    Processing helix  chain 'R' and resid 422 through 443
      removed outlier: 3.775A  pdb=" N   GLY R 430 " --> pdb=" O   PHE R 426 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   TYR R 431 " --> pdb=" O   PHE R 427 " (cutoff:3.500A)
      Proline residue:  R 438  - end of helix
      removed outlier: 3.543A  pdb=" N   TYR R 441 " --> pdb=" O   ASN R 437 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 445 through 457
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.762A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 189
      removed outlier: 3.862A  pdb=" N   VAL A 186 " --> pdb=" O   ASP A 201 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASP A 201 " --> pdb=" O   VAL A 186 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ALA A 221 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.967A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY B 319 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLY B 330 " --> pdb=" O   CYS B 317 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.931A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   SER B  72 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE B  80 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.306A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.615A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.679A  pdb=" N   SER B 191 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.599A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.706A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 277
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6
      removed outlier: 3.804A  pdb=" N   THR H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   THR H  69 " --> pdb=" O   GLN H  82 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 58 through 60
      removed outlier: 5.464A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 134 through 136
      removed outlier: 3.847A  pdb=" N   GLU H 234 " --> pdb=" O   VAL H 135 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   LEU H 162 " --> pdb=" O   TYR H 178 " (cutoff:3.500A)
      removed outlier: 5.239A  pdb=" N   TYR H 178 " --> pdb=" O   LEU H 162 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   TRP H 164 " --> pdb=" O   LEU H 176 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LEU H 176 " --> pdb=" O   TRP H 164 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 143 through 148
      removed outlier: 3.952A  pdb=" N   PHE H 200 " --> pdb=" O   CYS H 147 " (cutoff:3.500A)

    361 hydrogen bonds defined for protein.
    1035 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: 2.28

  Time building geometry restraints manager: 2.57 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1385
        1.31 -     1.44: 2457
        1.44 -     1.56: 4847
        1.56 -     1.69: 0
        1.69 -     1.81: 79
  Bond restraints: 8768
  Sorted by residual:
  bond pdb=" N   ILE R 123 "
       pdb=" CA  ILE R 123 "
    ideal  model  delta    sigma   weight residual
    1.461  1.396  0.065 1.17e-02 7.31e+03 3.07e+01
  bond pdb=" N   ASN A 346 "
       pdb=" CA  ASN A 346 "
    ideal  model  delta    sigma   weight residual
    1.459  1.400  0.060 1.20e-02 6.94e+03 2.47e+01
  bond pdb=" CA  TYR R 156 "
       pdb=" C   TYR R 156 "
    ideal  model  delta    sigma   weight residual
    1.524  1.460  0.064 1.29e-02 6.01e+03 2.45e+01
  bond pdb=" CA  ASN A 346 "
       pdb=" C   ASN A 346 "
    ideal  model  delta    sigma   weight residual
    1.524  1.463  0.060 1.26e-02 6.30e+03 2.30e+01
  bond pdb=" N   PRO R 438 "
       pdb=" CD  PRO R 438 "
    ideal  model  delta    sigma   weight residual
    1.473  1.539 -0.066 1.40e-02 5.10e+03 2.22e+01
  ... (remaining 8763 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.88: 11697
        2.88 -     5.76: 148
        5.76 -     8.64: 27
        8.64 -    11.53: 6
       11.53 -    14.41: 3
  Bond angle restraints: 11881
  Sorted by residual:
  angle pdb=" N   ARG R 378 "
        pdb=" CA  ARG R 378 "
        pdb=" C   ARG R 378 "
      ideal   model   delta    sigma   weight residual
     111.28  121.19   -9.91 1.09e+00 8.42e-01 8.27e+01
  angle pdb=" N   LYS A 211 "
        pdb=" CA  LYS A 211 "
        pdb=" C   LYS A 211 "
      ideal   model   delta    sigma   weight residual
     111.14  119.75   -8.61 1.08e+00 8.57e-01 6.36e+01
  angle pdb=" N   HIS A 214 "
        pdb=" CA  HIS A 214 "
        pdb=" C   HIS A 214 "
      ideal   model   delta    sigma   weight residual
     111.28  119.83   -8.55 1.09e+00 8.42e-01 6.16e+01
  angle pdb=" N   LYS R 159 "
        pdb=" CA  LYS R 159 "
        pdb=" C   LYS R 159 "
      ideal   model   delta    sigma   weight residual
     113.15  122.41   -9.26 1.19e+00 7.06e-01 6.06e+01
  angle pdb=" N   CYS R 121 "
        pdb=" CA  CYS R 121 "
        pdb=" C   CYS R 121 "
      ideal   model   delta    sigma   weight residual
     112.90  103.56    9.34 1.31e+00 5.83e-01 5.08e+01
  ... (remaining 11876 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.99: 5081
       33.99 -    67.98: 90
       67.98 -   101.97: 9
      101.97 -   135.95: 0
      135.95 -   169.94: 2
  Dihedral angle restraints: 5182
    sinusoidal: 2004
      harmonic: 3178
  Sorted by residual:
  dihedral pdb=" N   ILE R 123 "
           pdb=" C   ILE R 123 "
           pdb=" CA  ILE R 123 "
           pdb=" CB  ILE R 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  109.48   13.92     0      2.50e+00 1.60e-01 3.10e+01
  dihedral pdb=" C   PHE A 216 "
           pdb=" N   PHE A 216 "
           pdb=" CA  PHE A 216 "
           pdb=" CB  PHE A 216 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.35   13.75     0      2.50e+00 1.60e-01 3.02e+01
  dihedral pdb=" CA  ILE G  25 "
           pdb=" C   ILE G  25 "
           pdb=" N   ASP G  26 "
           pdb=" CA  ASP G  26 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.22  -23.78     0      5.00e+00 4.00e-02 2.26e+01
  ... (remaining 5179 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.110: 1292
       0.110 -    0.219: 39
       0.219 -    0.329: 12
       0.329 -    0.438: 4
       0.438 -    0.548: 2
  Chirality restraints: 1349
  Sorted by residual:
  chirality pdb=" CA  PHE A 216 "
            pdb=" N   PHE A 216 "
            pdb=" C   PHE A 216 "
            pdb=" CB  PHE A 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.96    0.55 2.00e-01 2.50e+01 7.51e+00
  chirality pdb=" CA  GLU A 217 "
            pdb=" N   GLU A 217 "
            pdb=" C   GLU A 217 "
            pdb=" CB  GLU A 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.46e+00
  chirality pdb=" CA  LYS R 159 "
            pdb=" N   LYS R 159 "
            pdb=" C   LYS R 159 "
            pdb=" CB  LYS R 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.04e+00
  ... (remaining 1346 not shown)

  Planarity restraints: 1496
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 161 "    0.036 5.00e-02 4.00e+02   5.51e-02 4.86e+00
        pdb=" N   PRO R 162 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO R 162 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO R 162 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 183 "    0.010 2.00e-02 2.50e+03   1.97e-02 3.90e+00
        pdb=" C   THR A 183 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   THR A 183 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLY A 184 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 282 "   -0.031 5.00e-02 4.00e+02   4.65e-02 3.45e+00
        pdb=" N   PRO A 283 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 283 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 283 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1493 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 68
        2.49 -     3.10: 6396
        3.10 -     3.70: 13194
        3.70 -     4.30: 17548
        4.30 -     4.90: 28824
  Nonbonded interactions: 66030
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN R  83 "
            pdb=" NH2 ARG R 160 "
     model   vdw
     1.893 3.120
  nonbonded pdb=" O   PHE A 224 "
            pdb=" N   PHE A 268 "
     model   vdw
     1.959 3.120
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASN B 110 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" OG  SER H 192 "
            pdb=" OG1 THR H 203 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.224 3.040
  ... (remaining 66025 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.340
  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:          0.390
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.270
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   8768  Z= 0.292
  Angle     :  0.850  14.408  11881  Z= 0.537
  Chirality :  0.059   0.548   1349
  Planarity :  0.004   0.055   1496
  Dihedral  : 13.816 169.942   3121
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 17.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.75 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    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: 1075
  helix:  1.20 (0.28), residues: 341
  sheet: -0.37 (0.33), residues: 263
  loop : -1.32 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 189 
 PHE   0.022   0.001   PHE R 398 
 TYR   0.013   0.001   TYR R 156 
 ARG   0.005   0.000   ARG R 202 

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 231
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 ARG cc_start: 0.8918 (mmm160) cc_final: 0.8705 (mmm-85)
REVERT: B   36 ASN cc_start: 0.8672 (m-40) cc_final: 0.8362 (p0)
REVERT: B  255 LEU cc_start: 0.9382 (pt) cc_final: 0.9117 (mm)
REVERT: B  261 LEU cc_start: 0.9371 (mt) cc_final: 0.9168 (mt)
REVERT: B  280 LYS cc_start: 0.9349 (tptp) cc_final: 0.9026 (tptp)
REVERT: B  292 PHE cc_start: 0.7801 (m-10) cc_final: 0.7482 (m-10)
REVERT: G   21 MET cc_start: 0.8107 (mmp) cc_final: 0.7295 (mtm)
REVERT: G   32 LYS cc_start: 0.9511 (ptpp) cc_final: 0.9293 (ptmm)
REVERT: G   42 GLU cc_start: 0.8135 (tp30) cc_final: 0.7530 (mt-10)
REVERT: G   58 GLU cc_start: 0.8998 (mp0) cc_final: 0.8428 (mp0)
REVERT: R   53 CYS cc_start: 0.9179 (m) cc_final: 0.8880 (p)
REVERT: R   57 LEU cc_start: 0.9416 (tp) cc_final: 0.9184 (tp)
REVERT: R  109 GLU cc_start: 0.8887 (tp30) cc_final: 0.8314 (tm-30)
REVERT: R  450 ARG cc_start: 0.9489 (mtm110) cc_final: 0.9216 (mtm-85)
REVERT: H   46 GLU cc_start: 0.8579 (pt0) cc_final: 0.8189 (pm20)
REVERT: H   90 ASP cc_start: 0.8059 (m-30) cc_final: 0.7532 (m-30)
REVERT: H  137 VAL cc_start: 0.7359 (m) cc_final: 0.7129 (m)
REVERT: H  180 MET cc_start: 0.8772 (ppp) cc_final: 0.8273 (ppp)
REVERT: H  210 GLU cc_start: 0.8971 (mp0) cc_final: 0.8577 (mp0)
REVERT: H  211 ASP cc_start: 0.7848 (m-30) cc_final: 0.7330 (m-30)
REVERT: H  218 MET cc_start: 0.8712 (tmm) cc_final: 0.8146 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 231
  average time/residue: 0.2381
  time to fit residues: 72.3644
Evaluate side-chains
  152 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    9.9990
   chunk 81 optimal weight:    0.0970
   chunk 45 optimal weight:    8.9990
   chunk 27 optimal weight:    7.9990
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    0.3980
   chunk 84 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 51 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   chunk 98 optimal weight:   50.0000
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
B 266 HIS
R 138 HIS
R 236 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.095551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.071638 restraints weight = 30745.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.073809 restraints weight = 16582.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.075250 restraints weight = 11219.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8768  Z= 0.175
  Angle     :  0.701  10.669  11881  Z= 0.359
  Chirality :  0.045   0.163   1349
  Planarity :  0.004   0.056   1496
  Dihedral  :  7.970 162.677   1193
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 11.94 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    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: 1075
  helix:  1.51 (0.28), residues: 340
  sheet: -0.06 (0.34), residues: 254
  loop : -1.26 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.028   0.001   PHE R 387 
 TYR   0.028   0.001   TYR R 156 
 ARG   0.006   0.000   ARG H 168 

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 187
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8633 (tm-30)
REVERT: A  244 MET cc_start: 0.5329 (mpp) cc_final: 0.4876 (mpp)
REVERT: A  313 ARG cc_start: 0.8872 (mmm160) cc_final: 0.8639 (mmm-85)
REVERT: A  320 TYR cc_start: 0.8406 (m-80) cc_final: 0.8134 (m-80)
REVERT: A  354 TYR cc_start: 0.8578 (p90) cc_final: 0.8332 (p90)
REVERT: B   12 GLU cc_start: 0.9316 (pt0) cc_final: 0.9001 (pm20)
REVERT: B   17 GLN cc_start: 0.7342 (tm-30) cc_final: 0.7073 (pp30)
REVERT: B   59 TYR cc_start: 0.8259 (m-80) cc_final: 0.7909 (m-80)
REVERT: B  292 PHE cc_start: 0.7795 (m-10) cc_final: 0.7529 (m-10)
REVERT: G   21 MET cc_start: 0.8055 (mmp) cc_final: 0.7336 (mtm)
REVERT: G   32 LYS cc_start: 0.9421 (ptpp) cc_final: 0.9211 (ptmm)
REVERT: G   38 MET cc_start: 0.6550 (ptp) cc_final: 0.5674 (ptt)
REVERT: G   42 GLU cc_start: 0.8100 (tp30) cc_final: 0.7464 (mt-10)
REVERT: G   58 GLU cc_start: 0.9041 (mp0) cc_final: 0.8508 (mp0)
REVERT: R   53 CYS cc_start: 0.9081 (m) cc_final: 0.8783 (p)
REVERT: R   94 ASP cc_start: 0.8221 (t70) cc_final: 0.7364 (t70)
REVERT: R   95 ILE cc_start: 0.9697 (mm) cc_final: 0.9465 (mm)
REVERT: R  109 GLU cc_start: 0.8730 (tp30) cc_final: 0.8220 (tm-30)
REVERT: R  381 GLN cc_start: 0.9033 (pt0) cc_final: 0.8515 (pt0)
REVERT: R  446 HIS cc_start: 0.9027 (OUTLIER) cc_final: 0.8738 (t70)
REVERT: R  450 ARG cc_start: 0.9516 (mtm110) cc_final: 0.9312 (mtm110)
REVERT: H   34 MET cc_start: 0.8567 (tpp) cc_final: 0.8342 (tpp)
REVERT: H  180 MET cc_start: 0.8849 (ppp) cc_final: 0.8389 (ppp)
REVERT: H  190 ARG cc_start: 0.6039 (OUTLIER) cc_final: 0.5280 (ptm160)
REVERT: H  211 ASP cc_start: 0.7623 (m-30) cc_final: 0.6706 (m-30)
REVERT: H  218 MET cc_start: 0.8611 (tmm) cc_final: 0.8274 (tmm)
  outliers start: 15
  outliers final: 10
  residues processed: 199
  average time/residue: 0.2150
  time to fit residues: 57.4582
Evaluate side-chains
  169 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 157
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain R residue  127 LEU
Chi-restraints excluded: chain R residue  138 HIS
Chi-restraints excluded: chain R residue  140 CYS
Chi-restraints excluded: chain R residue  216 CYS
Chi-restraints excluded: chain R residue  401 CYS
Chi-restraints excluded: chain R residue  446 HIS
Chi-restraints excluded: chain H residue  190 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 49 optimal weight:    8.9990
   chunk 77 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9980
   chunk 102 optimal weight:    3.9990
   chunk 80 optimal weight:    0.8980
   chunk 81 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 96 optimal weight:   10.0000
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 256 ASN
R 138 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.094505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.070226 restraints weight = 31707.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.072399 restraints weight = 16873.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.073842 restraints weight = 11393.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8768  Z= 0.195
  Angle     :  0.695  12.585  11881  Z= 0.352
  Chirality :  0.043   0.142   1349
  Planarity :  0.004   0.053   1496
  Dihedral  :  7.950 162.557   1193
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 15.91 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.26), residues: 1075
  helix:  1.64 (0.28), residues: 340
  sheet:  0.12 (0.35), residues: 250
  loop : -1.32 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.006   0.001   HIS B 183 
 PHE   0.021   0.001   PHE R 387 
 TYR   0.024   0.001   TYR R 409 
 ARG   0.005   0.000   ARG H 168 

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 164
  time to evaluate  : 1.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8647 (tm-30)
REVERT: A  313 ARG cc_start: 0.8849 (mmm160) cc_final: 0.8345 (mmm-85)
REVERT: A  354 TYR cc_start: 0.8654 (p90) cc_final: 0.8247 (p90)
REVERT: B   12 GLU cc_start: 0.9317 (pt0) cc_final: 0.9009 (pm20)
REVERT: B   17 GLN cc_start: 0.7362 (tm-30) cc_final: 0.7123 (pp30)
REVERT: B   59 TYR cc_start: 0.8332 (m-80) cc_final: 0.8038 (m-80)
REVERT: B  292 PHE cc_start: 0.7937 (m-10) cc_final: 0.7606 (m-10)
REVERT: G   38 MET cc_start: 0.6588 (ptp) cc_final: 0.5782 (ptt)
REVERT: G   42 GLU cc_start: 0.8095 (tp30) cc_final: 0.7470 (mt-10)
REVERT: G   58 GLU cc_start: 0.9051 (mp0) cc_final: 0.8500 (mp0)
REVERT: R   53 CYS cc_start: 0.9111 (m) cc_final: 0.8901 (m)
REVERT: R   94 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7391 (t70)
REVERT: R   95 ILE cc_start: 0.9733 (mm) cc_final: 0.9492 (mm)
REVERT: R  109 GLU cc_start: 0.8719 (tp30) cc_final: 0.8251 (tm-30)
REVERT: H  180 MET cc_start: 0.8814 (ppp) cc_final: 0.8334 (ppp)
REVERT: H  218 MET cc_start: 0.8660 (tmm) cc_final: 0.8442 (tmm)
  outliers start: 24
  outliers final: 16
  residues processed: 180
  average time/residue: 0.2148
  time to fit residues: 52.5990
Evaluate side-chains
  163 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 146
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain R residue   58 LEU
Chi-restraints excluded: chain R residue   89 SER
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue   96 LEU
Chi-restraints excluded: chain R residue  127 LEU
Chi-restraints excluded: chain R residue  140 CYS
Chi-restraints excluded: chain R residue  216 CYS
Chi-restraints excluded: chain R residue  401 CYS
Chi-restraints excluded: chain H residue  190 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 92 optimal weight:   20.0000
   chunk 89 optimal weight:   20.0000
   chunk 49 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 77 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 96 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 87 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0070
   overall best weight:    3.0004

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 333 GLN
R 381 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.091943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.068023 restraints weight = 31689.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.070106 restraints weight = 17057.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.071511 restraints weight = 11569.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8768  Z= 0.261
  Angle     :  0.712  11.024  11881  Z= 0.362
  Chirality :  0.043   0.148   1349
  Planarity :  0.004   0.050   1496
  Dihedral  :  7.987 161.468   1193
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 17.31 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    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: -0.06 (0.26), residues: 1075
  helix:  1.64 (0.28), residues: 339
  sheet: -0.04 (0.33), residues: 263
  loop : -1.30 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.007   0.001   HIS B 225 
 PHE   0.021   0.001   PHE R 387 
 TYR   0.015   0.002   TYR R 156 
 ARG   0.008   0.001   ARG H 190 

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 149
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8602 (tm-30)
REVERT: A  313 ARG cc_start: 0.8933 (mmm160) cc_final: 0.8704 (mmm-85)
REVERT: A  354 TYR cc_start: 0.8724 (p90) cc_final: 0.8325 (p90)
REVERT: B   12 GLU cc_start: 0.9300 (pt0) cc_final: 0.8970 (pm20)
REVERT: B   36 ASN cc_start: 0.8565 (m-40) cc_final: 0.8232 (p0)
REVERT: B   79 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8747 (mm)
REVERT: B  292 PHE cc_start: 0.8174 (m-10) cc_final: 0.7777 (m-10)
REVERT: G   21 MET cc_start: 0.8417 (mmm) cc_final: 0.7458 (mtm)
REVERT: G   38 MET cc_start: 0.6661 (ptp) cc_final: 0.5870 (ptt)
REVERT: G   42 GLU cc_start: 0.8143 (tp30) cc_final: 0.7511 (mt-10)
REVERT: G   58 GLU cc_start: 0.9108 (mp0) cc_final: 0.8551 (mp0)
REVERT: R   49 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7155 (pt)
REVERT: R   53 CYS cc_start: 0.9100 (m) cc_final: 0.8879 (m)
REVERT: R  109 GLU cc_start: 0.8679 (tp30) cc_final: 0.8219 (tm-30)
REVERT: R  204 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8758 (tm-30)
REVERT: H  180 MET cc_start: 0.8833 (ppp) cc_final: 0.8381 (ppp)
REVERT: H  211 ASP cc_start: 0.7999 (m-30) cc_final: 0.7797 (m-30)
  outliers start: 34
  outliers final: 21
  residues processed: 173
  average time/residue: 0.2065
  time to fit residues: 49.2752
Evaluate side-chains
  159 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 136
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain R residue   47 VAL
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue   58 LEU
Chi-restraints excluded: chain R residue   96 LEU
Chi-restraints excluded: chain R residue  127 LEU
Chi-restraints excluded: chain R residue  128 ASP
Chi-restraints excluded: chain R residue  140 CYS
Chi-restraints excluded: chain R residue  216 CYS
Chi-restraints excluded: chain R residue  230 VAL
Chi-restraints excluded: chain R residue  382 ASN
Chi-restraints excluded: chain R residue  401 CYS
Chi-restraints excluded: chain H residue  190 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 73 optimal weight:   20.0000
   chunk 30 optimal weight:    0.0170
   chunk 20 optimal weight:    4.9990
   chunk 58 optimal weight:    9.9990
   chunk 2 optimal weight:    7.9990
   chunk 25 optimal weight:    0.6980
   chunk 49 optimal weight:    8.9990
   chunk 74 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    1.8822

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.093227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.069482 restraints weight = 31513.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.071599 restraints weight = 16890.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.072944 restraints weight = 11438.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8768  Z= 0.208
  Angle     :  0.712  12.930  11881  Z= 0.355
  Chirality :  0.043   0.222   1349
  Planarity :  0.004   0.050   1496
  Dihedral  :  7.975 161.749   1193
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 18.60 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    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: -0.11 (0.26), residues: 1075
  helix:  1.67 (0.29), residues: 336
  sheet: -0.08 (0.33), residues: 253
  loop : -1.35 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.020   0.001   PHE R 387 
 TYR   0.034   0.002   TYR R 409 
 ARG   0.006   0.000   ARG H 190 

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 154
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 ARG cc_start: 0.8902 (mmm160) cc_final: 0.8676 (mmm-85)
REVERT: A  320 TYR cc_start: 0.8292 (m-80) cc_final: 0.7512 (m-80)
REVERT: A  354 TYR cc_start: 0.8737 (p90) cc_final: 0.8346 (p90)
REVERT: B   12 GLU cc_start: 0.9299 (pt0) cc_final: 0.8985 (pm20)
REVERT: B   17 GLN cc_start: 0.7370 (tm-30) cc_final: 0.7095 (pp30)
REVERT: B   36 ASN cc_start: 0.8543 (m-40) cc_final: 0.8177 (p0)
REVERT: B  283 ARG cc_start: 0.7382 (ttt180) cc_final: 0.7049 (ttt180)
REVERT: B  292 PHE cc_start: 0.8162 (m-10) cc_final: 0.7755 (m-10)
REVERT: G   21 MET cc_start: 0.8441 (mmm) cc_final: 0.7649 (mtm)
REVERT: G   24 ASN cc_start: 0.7741 (t0) cc_final: 0.7289 (m-40)
REVERT: G   38 MET cc_start: 0.6725 (ptp) cc_final: 0.6032 (ptt)
REVERT: G   42 GLU cc_start: 0.8115 (tp30) cc_final: 0.7516 (mt-10)
REVERT: G   58 GLU cc_start: 0.9111 (mp0) cc_final: 0.8570 (mp0)
REVERT: R   49 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7223 (pt)
REVERT: R   53 CYS cc_start: 0.9086 (m) cc_final: 0.8852 (m)
REVERT: R   94 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7368 (t70)
REVERT: R   95 ILE cc_start: 0.9728 (mm) cc_final: 0.9510 (mm)
REVERT: R  109 GLU cc_start: 0.8637 (tp30) cc_final: 0.8232 (tm-30)
REVERT: R  448 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8750 (t80)
REVERT: H   34 MET cc_start: 0.8560 (tpp) cc_final: 0.8292 (tpp)
REVERT: H  211 ASP cc_start: 0.8088 (m-30) cc_final: 0.7854 (m-30)
  outliers start: 27
  outliers final: 23
  residues processed: 172
  average time/residue: 0.2155
  time to fit residues: 50.6216
Evaluate side-chains
  162 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 136
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain R residue   47 VAL
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue   58 LEU
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  127 LEU
Chi-restraints excluded: chain R residue  140 CYS
Chi-restraints excluded: chain R residue  216 CYS
Chi-restraints excluded: chain R residue  382 ASN
Chi-restraints excluded: chain R residue  401 CYS
Chi-restraints excluded: chain R residue  448 PHE
Chi-restraints excluded: chain R residue  454 LYS
Chi-restraints excluded: chain H residue  190 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0980
   chunk 23 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9990
   chunk 85 optimal weight:    9.9990
   chunk 88 optimal weight:    8.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    1.6188

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.093571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.069620 restraints weight = 31101.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.071716 restraints weight = 16808.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.073135 restraints weight = 11452.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8768  Z= 0.197
  Angle     :  0.722  12.828  11881  Z= 0.358
  Chirality :  0.043   0.172   1349
  Planarity :  0.004   0.050   1496
  Dihedral  :  7.963 161.972   1193
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 20.22 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    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: 1075
  helix:  1.64 (0.28), residues: 338
  sheet: -0.03 (0.34), residues: 249
  loop : -1.33 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.022   0.001   PHE R 387 
 TYR   0.028   0.001   TYR R 409 
 ARG   0.005   0.000   ARG H 190 

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 153
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 ARG cc_start: 0.8891 (mmm160) cc_final: 0.8665 (mmm-85)
REVERT: A  354 TYR cc_start: 0.8742 (p90) cc_final: 0.8290 (p90)
REVERT: B   12 GLU cc_start: 0.9294 (pt0) cc_final: 0.8970 (pm20)
REVERT: B   17 GLN cc_start: 0.7388 (tm-30) cc_final: 0.7133 (pp30)
REVERT: B   36 ASN cc_start: 0.8591 (m-40) cc_final: 0.8242 (p0)
REVERT: B  130 GLU cc_start: 0.8963 (mp0) cc_final: 0.8710 (mp0)
REVERT: B  283 ARG cc_start: 0.7449 (ttt180) cc_final: 0.7014 (ttt180)
REVERT: B  292 PHE cc_start: 0.8131 (m-10) cc_final: 0.7726 (m-10)
REVERT: G   21 MET cc_start: 0.8532 (mmm) cc_final: 0.7719 (mtm)
REVERT: G   24 ASN cc_start: 0.7792 (t0) cc_final: 0.7282 (m-40)
REVERT: G   38 MET cc_start: 0.6746 (ptp) cc_final: 0.6075 (ptt)
REVERT: G   42 GLU cc_start: 0.8096 (tp30) cc_final: 0.7506 (mt-10)
REVERT: G   58 GLU cc_start: 0.9100 (mp0) cc_final: 0.8573 (mp0)
REVERT: R   53 CYS cc_start: 0.9042 (m) cc_final: 0.8765 (p)
REVERT: R   94 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7284 (t70)
REVERT: R   99 THR cc_start: 0.9199 (t) cc_final: 0.8912 (p)
REVERT: R  109 GLU cc_start: 0.8639 (tp30) cc_final: 0.8250 (tm-30)
REVERT: R  381 GLN cc_start: 0.9016 (pt0) cc_final: 0.8632 (mp10)
REVERT: H  211 ASP cc_start: 0.8159 (m-30) cc_final: 0.7913 (m-30)
REVERT: H  218 MET cc_start: 0.8686 (tmm) cc_final: 0.8453 (ppp)
  outliers start: 28
  outliers final: 22
  residues processed: 173
  average time/residue: 0.2138
  time to fit residues: 50.0257
Evaluate side-chains
  162 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 139
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain R residue   47 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  140 CYS
Chi-restraints excluded: chain R residue  216 CYS
Chi-restraints excluded: chain R residue  230 VAL
Chi-restraints excluded: chain R residue  382 ASN
Chi-restraints excluded: chain R residue  401 CYS
Chi-restraints excluded: chain R residue  439 VAL
Chi-restraints excluded: chain R residue  454 LYS
Chi-restraints excluded: chain H residue  190 ARG
Chi-restraints excluded: chain H residue  212 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 80 optimal weight:    0.3980
   chunk 0 optimal weight:   10.0000
   chunk 60 optimal weight:    3.9990
   chunk 104 optimal weight:   20.0000
   chunk 32 optimal weight:    6.9990
   chunk 58 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 94 optimal weight:   20.0000
   chunk 57 optimal weight:   10.0000
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.092993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.068968 restraints weight = 31548.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.071033 restraints weight = 17051.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.072434 restraints weight = 11611.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.3086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8768  Z= 0.216
  Angle     :  0.738  13.578  11881  Z= 0.364
  Chirality :  0.043   0.183   1349
  Planarity :  0.004   0.049   1496
  Dihedral  :  7.949 161.829   1193
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 21.08 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    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: -0.15 (0.26), residues: 1075
  helix:  1.61 (0.29), residues: 336
  sheet: -0.11 (0.34), residues: 247
  loop : -1.33 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.019   0.001   PHE R 387 
 TYR   0.027   0.001   TYR R 409 
 ARG   0.008   0.000   ARG H  87 

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 148
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 ARG cc_start: 0.8884 (mmm160) cc_final: 0.8659 (mmm-85)
REVERT: A  354 TYR cc_start: 0.8754 (p90) cc_final: 0.8227 (p90)
REVERT: B   12 GLU cc_start: 0.9291 (pt0) cc_final: 0.8975 (pm20)
REVERT: B   36 ASN cc_start: 0.8543 (m-40) cc_final: 0.8228 (p0)
REVERT: B   78 LYS cc_start: 0.9618 (mmmm) cc_final: 0.9211 (mmmm)
REVERT: B  292 PHE cc_start: 0.8176 (m-10) cc_final: 0.7752 (m-10)
REVERT: G   21 MET cc_start: 0.8493 (mmm) cc_final: 0.7540 (mtm)
REVERT: G   38 MET cc_start: 0.6747 (ptp) cc_final: 0.6501 (ptt)
REVERT: G   42 GLU cc_start: 0.8106 (tp30) cc_final: 0.7631 (mt-10)
REVERT: G   58 GLU cc_start: 0.9113 (mp0) cc_final: 0.8585 (mp0)
REVERT: R   94 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7358 (t70)
REVERT: R  109 GLU cc_start: 0.8612 (tp30) cc_final: 0.8226 (tm-30)
REVERT: H   34 MET cc_start: 0.8616 (tpp) cc_final: 0.8298 (tpp)
REVERT: H  211 ASP cc_start: 0.8170 (m-30) cc_final: 0.7714 (m-30)
REVERT: H  218 MET cc_start: 0.8727 (tmm) cc_final: 0.8514 (ppp)
  outliers start: 27
  outliers final: 23
  residues processed: 166
  average time/residue: 0.2185
  time to fit residues: 49.4201
Evaluate side-chains
  163 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 139
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  127 LEU
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  216 CYS
Chi-restraints excluded: chain R residue  230 VAL
Chi-restraints excluded: chain R residue  382 ASN
Chi-restraints excluded: chain R residue  401 CYS
Chi-restraints excluded: chain R residue  439 VAL
Chi-restraints excluded: chain R residue  454 LYS
Chi-restraints excluded: chain H residue  190 ARG
Chi-restraints excluded: chain H residue  212 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 97 optimal weight:    7.9990
   chunk 2 optimal weight:    7.9990
   chunk 81 optimal weight:    8.9990
   chunk 60 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 39 optimal weight:    0.3980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
R 381 GLN
H  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.093916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.069705 restraints weight = 31934.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.071831 restraints weight = 17285.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.073269 restraints weight = 11757.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.3273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8768  Z= 0.200
  Angle     :  0.775  16.058  11881  Z= 0.376
  Chirality :  0.043   0.190   1349
  Planarity :  0.004   0.050   1496
  Dihedral  :  7.898 161.000   1193
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.97 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    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: -0.15 (0.27), residues: 1075
  helix:  1.55 (0.29), residues: 338
  sheet: -0.07 (0.35), residues: 247
  loop : -1.31 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.006   0.001   HIS R 446 
 PHE   0.030   0.001   PHE R 387 
 TYR   0.026   0.001   TYR R 409 
 ARG   0.006   0.000   ARG H  87 

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 158
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 ARG cc_start: 0.8850 (mmm160) cc_final: 0.8626 (mmm-85)
REVERT: B   12 GLU cc_start: 0.9293 (pt0) cc_final: 0.8980 (pm20)
REVERT: B   36 ASN cc_start: 0.8634 (m-40) cc_final: 0.8242 (p0)
REVERT: B   78 LYS cc_start: 0.9590 (mmmm) cc_final: 0.9203 (mmmm)
REVERT: B  292 PHE cc_start: 0.8133 (m-10) cc_final: 0.7736 (m-10)
REVERT: G   21 MET cc_start: 0.8478 (mmm) cc_final: 0.7690 (mtm)
REVERT: G   24 ASN cc_start: 0.7719 (t0) cc_final: 0.7228 (m-40)
REVERT: G   38 MET cc_start: 0.6702 (ptp) cc_final: 0.6047 (ptt)
REVERT: G   42 GLU cc_start: 0.8062 (tp30) cc_final: 0.7486 (mt-10)
REVERT: G   58 GLU cc_start: 0.9085 (mp0) cc_final: 0.8556 (mp0)
REVERT: R   94 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7490 (t70)
REVERT: R  109 GLU cc_start: 0.8630 (tp30) cc_final: 0.8260 (tm-30)
REVERT: R  111 MET cc_start: 0.8596 (mtm) cc_final: 0.8313 (ptp)
REVERT: H   34 MET cc_start: 0.8561 (tpp) cc_final: 0.8282 (tpp)
REVERT: H  218 MET cc_start: 0.8664 (tmm) cc_final: 0.8456 (ppp)
REVERT: H  234 GLU cc_start: 0.6761 (pm20) cc_final: 0.6091 (pp20)
  outliers start: 27
  outliers final: 23
  residues processed: 175
  average time/residue: 0.2316
  time to fit residues: 54.5654
Evaluate side-chains
  174 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 150
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  216 CYS
Chi-restraints excluded: chain R residue  230 VAL
Chi-restraints excluded: chain R residue  382 ASN
Chi-restraints excluded: chain R residue  401 CYS
Chi-restraints excluded: chain R residue  439 VAL
Chi-restraints excluded: chain R residue  454 LYS
Chi-restraints excluded: chain H residue  190 ARG
Chi-restraints excluded: chain H residue  212 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 73 optimal weight:    0.0370
   chunk 37 optimal weight:    6.9990
   chunk 57 optimal weight:    9.9990
   chunk 11 optimal weight:    2.9990
   chunk 76 optimal weight:    0.4980
   chunk 29 optimal weight:    3.9990
   chunk 22 optimal weight:   40.0000
   chunk 92 optimal weight:   20.0000
   chunk 80 optimal weight:    0.9980
   chunk 21 optimal weight:    9.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.5062

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
R 236 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.093713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.069642 restraints weight = 31318.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.071760 restraints weight = 16902.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.073107 restraints weight = 11498.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.3337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8768  Z= 0.208
  Angle     :  0.816  18.138  11881  Z= 0.391
  Chirality :  0.044   0.215   1349
  Planarity :  0.004   0.052   1496
  Dihedral  :  7.883 160.434   1193
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 21.61 %
    Favored  : 75.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    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: -0.17 (0.27), residues: 1075
  helix:  1.52 (0.29), residues: 338
  sheet: -0.09 (0.35), residues: 244
  loop : -1.29 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.007   0.001   HIS B 225 
 PHE   0.033   0.001   PHE R 387 
 TYR   0.025   0.001   TYR R 409 
 ARG   0.006   0.000   ARG H  87 

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 152
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 ARG cc_start: 0.8826 (mmm160) cc_final: 0.8603 (mmm-85)
REVERT: B   12 GLU cc_start: 0.9290 (pt0) cc_final: 0.8984 (pm20)
REVERT: B   36 ASN cc_start: 0.8598 (m-40) cc_final: 0.8236 (p0)
REVERT: B   78 LYS cc_start: 0.9600 (mmmm) cc_final: 0.9180 (mmmm)
REVERT: B  283 ARG cc_start: 0.7480 (ttt180) cc_final: 0.6801 (ttt90)
REVERT: B  292 PHE cc_start: 0.8163 (m-10) cc_final: 0.7738 (m-10)
REVERT: G   21 MET cc_start: 0.8440 (mmm) cc_final: 0.7659 (mtm)
REVERT: G   24 ASN cc_start: 0.7691 (t0) cc_final: 0.7208 (m-40)
REVERT: G   38 MET cc_start: 0.6644 (ptp) cc_final: 0.5934 (ptt)
REVERT: G   42 GLU cc_start: 0.8057 (tp30) cc_final: 0.7485 (mt-10)
REVERT: G   58 GLU cc_start: 0.9093 (mp0) cc_final: 0.8578 (mp0)
REVERT: R   94 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7461 (t70)
REVERT: R  109 GLU cc_start: 0.8629 (tp30) cc_final: 0.8254 (tm-30)
REVERT: R  111 MET cc_start: 0.8599 (mtm) cc_final: 0.8315 (ptp)
REVERT: H  211 ASP cc_start: 0.7949 (m-30) cc_final: 0.7644 (m-30)
REVERT: H  218 MET cc_start: 0.8711 (tmm) cc_final: 0.8510 (ppp)
REVERT: H  232 LYS cc_start: 0.8108 (mppt) cc_final: 0.7751 (pptt)
  outliers start: 26
  outliers final: 24
  residues processed: 168
  average time/residue: 0.2222
  time to fit residues: 50.8463
Evaluate side-chains
  169 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 144
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  127 LEU
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  216 CYS
Chi-restraints excluded: chain R residue  230 VAL
Chi-restraints excluded: chain R residue  382 ASN
Chi-restraints excluded: chain R residue  401 CYS
Chi-restraints excluded: chain R residue  439 VAL
Chi-restraints excluded: chain R residue  454 LYS
Chi-restraints excluded: chain H residue  190 ARG
Chi-restraints excluded: chain H residue  212 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 89 optimal weight:   20.0000
   chunk 8 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 99 optimal weight:   20.0000
   chunk 64 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
B 176 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.093607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.069545 restraints weight = 31321.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.071692 restraints weight = 16996.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.073061 restraints weight = 11533.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.3450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8768  Z= 0.218
  Angle     :  0.817  17.136  11881  Z= 0.392
  Chirality :  0.044   0.206   1349
  Planarity :  0.004   0.052   1496
  Dihedral  :  7.877 159.773   1193
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 21.61 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    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: -0.17 (0.27), residues: 1075
  helix:  1.57 (0.29), residues: 332
  sheet: -0.17 (0.34), residues: 254
  loop : -1.27 (0.28), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.006   0.001   HIS R 446 
 PHE   0.032   0.001   PHE R 387 
 TYR   0.025   0.001   TYR A 354 
 ARG   0.007   0.000   ARG R 450 

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 PHE cc_start: 0.9086 (t80) cc_final: 0.8766 (t80)
REVERT: A  313 ARG cc_start: 0.8830 (mmm160) cc_final: 0.8604 (mmm-85)
REVERT: B   12 GLU cc_start: 0.9278 (pt0) cc_final: 0.8969 (pm20)
REVERT: B   36 ASN cc_start: 0.8603 (m-40) cc_final: 0.8257 (p0)
REVERT: B   78 LYS cc_start: 0.9566 (mmmm) cc_final: 0.9159 (mmmm)
REVERT: B   89 LYS cc_start: 0.9058 (mmtp) cc_final: 0.8375 (mmtp)
REVERT: B  283 ARG cc_start: 0.7559 (ttt180) cc_final: 0.6836 (ttt90)
REVERT: B  292 PHE cc_start: 0.8165 (m-10) cc_final: 0.7744 (m-10)
REVERT: G   21 MET cc_start: 0.8466 (mmm) cc_final: 0.7708 (mtm)
REVERT: G   24 ASN cc_start: 0.7738 (t0) cc_final: 0.7259 (m-40)
REVERT: G   38 MET cc_start: 0.6656 (ptp) cc_final: 0.5945 (ptt)
REVERT: G   42 GLU cc_start: 0.8044 (tp30) cc_final: 0.7482 (mt-10)
REVERT: G   58 GLU cc_start: 0.9105 (mp0) cc_final: 0.8607 (mp0)
REVERT: R   94 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7549 (t70)
REVERT: R  109 GLU cc_start: 0.8651 (tp30) cc_final: 0.8278 (tm-30)
REVERT: R  111 MET cc_start: 0.8621 (mtm) cc_final: 0.8333 (ptp)
REVERT: H   34 MET cc_start: 0.8690 (tpp) cc_final: 0.8343 (tpp)
REVERT: H  218 MET cc_start: 0.8744 (tmm) cc_final: 0.8533 (ppp)
REVERT: H  232 LYS cc_start: 0.8096 (mppt) cc_final: 0.7692 (pptt)
  outliers start: 24
  outliers final: 23
  residues processed: 162
  average time/residue: 0.2282
  time to fit residues: 49.5168
Evaluate side-chains
  168 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 144
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  196 HIS
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  127 LEU
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  216 CYS
Chi-restraints excluded: chain R residue  230 VAL
Chi-restraints excluded: chain R residue  382 ASN
Chi-restraints excluded: chain R residue  401 CYS
Chi-restraints excluded: chain R residue  439 VAL
Chi-restraints excluded: chain R residue  454 LYS
Chi-restraints excluded: chain H residue  190 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 91 optimal weight:   10.0000
   chunk 105 optimal weight:    0.0070
   chunk 11 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.9600

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.094846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.070729 restraints weight = 31582.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.072919 restraints weight = 16992.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.074397 restraints weight = 11489.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.3551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8768  Z= 0.197
  Angle     :  0.809  17.062  11881  Z= 0.388
  Chirality :  0.044   0.204   1349
  Planarity :  0.004   0.054   1496
  Dihedral  :  7.792 158.174   1193
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 22.04 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 1.14 %
    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 (0.27), residues: 1075
  helix:  1.56 (0.30), residues: 332
  sheet: -0.03 (0.34), residues: 253
  loop : -1.27 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.006   0.001   HIS R 446 
 PHE   0.034   0.001   PHE R 387 
 TYR   0.024   0.001   TYR R 409 
 ARG   0.006   0.000   ARG R 450 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3167.04 seconds
wall clock time: 55 minutes 37.00 seconds (3337.00 seconds total)