Starting phenix.real_space_refine
on Thu Feb 13 02:57:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7eja_31157/02_2025/7eja_31157.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7eja_31157/02_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_31157/02_2025/7eja_31157.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7eja_31157/02_2025/7eja_31157.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7eja_31157/02_2025/7eja_31157.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7eja_31157/02_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-5592/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: 5.29, per 1000 atoms: 0.62
  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: 2.90
  Conformation dependent library (CDL) restraints added in 984.3 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: 0.89
  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: 2.50

  Time building geometry restraints manager: 2.49 seconds

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

  Histogram of bond lengths:
        1.19 -     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:             0.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     21.970
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.030
-------------------------------------------------------------------------------
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  : 0.953 
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: 0.2557
  time to fit residues: 78.0025
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  : 0.978 
-------------------------------------------------------------------------------
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 = 48)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.071646 restraints weight = 30746.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.073805 restraints weight = 16560.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.075174 restraints weight = 11227.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
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  : 1.036 
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: 0.5325 (mpp) cc_final: 0.4873 (mpp)
REVERT: A  313 ARG cc_start: 0.8874 (mmm160) cc_final: 0.8640 (mmm-85)
REVERT: A  320 TYR cc_start: 0.8412 (m-80) cc_final: 0.8138 (m-80)
REVERT: A  354 TYR cc_start: 0.8584 (p90) cc_final: 0.8337 (p90)
REVERT: B   12 GLU cc_start: 0.9315 (pt0) cc_final: 0.9007 (pm20)
REVERT: B   17 GLN cc_start: 0.7326 (tm-30) cc_final: 0.7065 (pp30)
REVERT: B   59 TYR cc_start: 0.8260 (m-80) cc_final: 0.7910 (m-80)
REVERT: B  292 PHE cc_start: 0.7808 (m-10) cc_final: 0.7542 (m-10)
REVERT: G   21 MET cc_start: 0.8044 (mmp) cc_final: 0.7332 (mtm)
REVERT: G   32 LYS cc_start: 0.9419 (ptpp) cc_final: 0.9209 (ptmm)
REVERT: G   38 MET cc_start: 0.6541 (ptp) cc_final: 0.5660 (ptt)
REVERT: G   42 GLU cc_start: 0.8102 (tp30) cc_final: 0.7461 (mt-10)
REVERT: G   58 GLU cc_start: 0.9044 (mp0) cc_final: 0.8513 (mp0)
REVERT: R   53 CYS cc_start: 0.9088 (m) cc_final: 0.8789 (p)
REVERT: R   94 ASP cc_start: 0.8228 (t70) cc_final: 0.7369 (t70)
REVERT: R   95 ILE cc_start: 0.9700 (mm) cc_final: 0.9467 (mm)
REVERT: R  109 GLU cc_start: 0.8738 (tp30) cc_final: 0.8223 (tm-30)
REVERT: R  381 GLN cc_start: 0.9030 (pt0) cc_final: 0.8512 (pt0)
REVERT: R  446 HIS cc_start: 0.9031 (OUTLIER) cc_final: 0.8738 (t70)
REVERT: R  450 ARG cc_start: 0.9518 (mtm110) cc_final: 0.9311 (mtm110)
REVERT: H   34 MET cc_start: 0.8571 (tpp) cc_final: 0.8345 (tpp)
REVERT: H  180 MET cc_start: 0.8860 (ppp) cc_final: 0.8399 (ppp)
REVERT: H  190 ARG cc_start: 0.6039 (OUTLIER) cc_final: 0.5296 (ptm160)
REVERT: H  211 ASP cc_start: 0.7593 (m-30) cc_final: 0.6691 (m-30)
REVERT: H  218 MET cc_start: 0.8615 (tmm) cc_final: 0.8269 (tmm)
  outliers start: 15
  outliers final: 10
  residues processed: 199
  average time/residue: 0.2252
  time to fit residues: 59.9866
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  : 0.961 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 49 optimal weight:    8.9990
   chunk 77 optimal weight:    7.9990
   chunk 25 optimal weight:    0.0270
   chunk 102 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 96 optimal weight:    8.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.3444

-------------------------------------------------------------------------------
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 = 0.3792 r_free = 0.3792 target = 0.094878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.070593 restraints weight = 31620.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.072783 restraints weight = 16871.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.074239 restraints weight = 11390.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8768  Z= 0.187
  Angle     :  0.695  12.331  11881  Z= 0.351
  Chirality :  0.043   0.144   1349
  Planarity :  0.004   0.053   1496
  Dihedral  :  7.946 162.636   1193
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.02 %
    Favored  : 81.40 %
  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: 341
  sheet:  0.12 (0.35), residues: 250
  loop : -1.33 (0.28), residues: 484

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   0.022   0.001   PHE R 387 
 TYR   0.024   0.001   TYR R 409 
 ARG   0.004   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
  190 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 166
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8649 (tm-30)
REVERT: A  313 ARG cc_start: 0.8863 (mmm160) cc_final: 0.8422 (mmm-85)
REVERT: A  354 TYR cc_start: 0.8667 (p90) cc_final: 0.8263 (p90)
REVERT: B   12 GLU cc_start: 0.9318 (pt0) cc_final: 0.9010 (pm20)
REVERT: B   17 GLN cc_start: 0.7351 (tm-30) cc_final: 0.7117 (pp30)
REVERT: B   59 TYR cc_start: 0.8320 (m-80) cc_final: 0.8011 (m-80)
REVERT: B  292 PHE cc_start: 0.7939 (m-10) cc_final: 0.7604 (m-10)
REVERT: G   21 MET cc_start: 0.8035 (mmp) cc_final: 0.7374 (mtm)
REVERT: G   38 MET cc_start: 0.6556 (ptp) cc_final: 0.5743 (ptt)
REVERT: G   42 GLU cc_start: 0.8094 (tp30) cc_final: 0.7463 (mt-10)
REVERT: G   58 GLU cc_start: 0.9056 (mp0) cc_final: 0.8511 (mp0)
REVERT: R   53 CYS cc_start: 0.9123 (m) cc_final: 0.8910 (m)
REVERT: R   94 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7395 (t70)
REVERT: R   95 ILE cc_start: 0.9736 (mm) cc_final: 0.9491 (mm)
REVERT: R  109 GLU cc_start: 0.8740 (tp30) cc_final: 0.8269 (tm-30)
REVERT: R  446 HIS cc_start: 0.8894 (OUTLIER) cc_final: 0.8687 (t70)
REVERT: H  180 MET cc_start: 0.8841 (ppp) cc_final: 0.8357 (ppp)
REVERT: H  218 MET cc_start: 0.8652 (tmm) cc_final: 0.8425 (tmm)
  outliers start: 24
  outliers final: 15
  residues processed: 182
  average time/residue: 0.2200
  time to fit residues: 53.8249
Evaluate side-chains
  162 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 145
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
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  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 R residue  446 HIS
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:   10.0000
   chunk 89 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   chunk 77 optimal weight:    9.9990
   chunk 8 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 29 optimal weight:    4.9990
   chunk 87 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    2.9988

-------------------------------------------------------------------------------
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 = 0.3741 r_free = 0.3741 target = 0.091496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.067413 restraints weight = 31557.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.069473 restraints weight = 16928.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.070847 restraints weight = 11468.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8768  Z= 0.266
  Angle     :  0.718  11.175  11881  Z= 0.366
  Chirality :  0.044   0.149   1349
  Planarity :  0.004   0.050   1496
  Dihedral  :  7.991 161.597   1193
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 16.67 %
    Favored  : 79.35 %
  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: -0.05 (0.26), residues: 1075
  helix:  1.66 (0.28), residues: 339
  sheet: -0.04 (0.33), residues: 263
  loop : -1.29 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.008   0.001   HIS B 225 
 PHE   0.022   0.001   PHE R 387 
 TYR   0.015   0.002   TYR A 320 
 ARG   0.007   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
  186 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 149
  time to evaluate  : 0.998 
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: 0.8942 (mmm160) cc_final: 0.8707 (mmm-85)
REVERT: A  354 TYR cc_start: 0.8742 (p90) cc_final: 0.8326 (p90)
REVERT: B   12 GLU cc_start: 0.9304 (pt0) cc_final: 0.8973 (pm20)
REVERT: B   36 ASN cc_start: 0.8579 (m-40) cc_final: 0.8244 (p0)
REVERT: B   79 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8740 (mm)
REVERT: B  292 PHE cc_start: 0.8210 (m-10) cc_final: 0.7814 (m-10)
REVERT: G   38 MET cc_start: 0.6655 (ptp) cc_final: 0.5858 (ptt)
REVERT: G   42 GLU cc_start: 0.8154 (tp30) cc_final: 0.7517 (mt-10)
REVERT: G   58 GLU cc_start: 0.9103 (mp0) cc_final: 0.8554 (mp0)
REVERT: R   49 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7177 (pt)
REVERT: R   53 CYS cc_start: 0.9114 (m) cc_final: 0.8890 (m)
REVERT: R  109 GLU cc_start: 0.8732 (tp30) cc_final: 0.8255 (tm-30)
REVERT: R  204 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8766 (tm-30)
REVERT: R  446 HIS cc_start: 0.8982 (OUTLIER) cc_final: 0.8709 (t70)
REVERT: H  180 MET cc_start: 0.8845 (ppp) cc_final: 0.8389 (ppp)
REVERT: H  211 ASP cc_start: 0.7968 (m-30) cc_final: 0.7756 (m-30)
  outliers start: 37
  outliers final: 22
  residues processed: 174
  average time/residue: 0.2131
  time to fit residues: 51.0686
Evaluate side-chains
  161 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
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   94 ASP
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 R residue  446 HIS
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:    8.9990
   chunk 73 optimal weight:   20.0000
   chunk 30 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 58 optimal weight:   20.0000
   chunk 2 optimal weight:   20.0000
   chunk 25 optimal weight:    6.9990
   chunk 49 optimal weight:    9.9990
   chunk 74 optimal weight:    0.6980
   chunk 89 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0050
   overall best weight:    2.4598

-------------------------------------------------------------------------------
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 = 0.3754 r_free = 0.3754 target = 0.092174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.068308 restraints weight = 31412.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.070343 restraints weight = 17032.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.071652 restraints weight = 11612.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8768  Z= 0.234
  Angle     :  0.719  12.572  11881  Z= 0.361
  Chirality :  0.044   0.233   1349
  Planarity :  0.004   0.049   1496
  Dihedral  :  8.009 161.887   1193
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.82 %
    Favored  : 78.17 %
  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:  1.65 (0.28), residues: 336
  sheet: -0.07 (0.34), residues: 247
  loop : -1.34 (0.28), residues: 492

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   0.020   0.001   PHE R 387 
 TYR   0.033   0.002   TYR R 409 
 ARG   0.007   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
  180 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 ARG cc_start: 0.8952 (mmm160) cc_final: 0.8727 (mmm-85)
REVERT: A  354 TYR cc_start: 0.8755 (p90) cc_final: 0.8346 (p90)
REVERT: B   12 GLU cc_start: 0.9298 (pt0) cc_final: 0.8983 (pm20)
REVERT: B   17 GLN cc_start: 0.7360 (tm-30) cc_final: 0.7060 (pp30)
REVERT: B   36 ASN cc_start: 0.8539 (m-40) cc_final: 0.8178 (p0)
REVERT: B  283 ARG cc_start: 0.7396 (ttt180) cc_final: 0.7142 (ttt180)
REVERT: B  292 PHE cc_start: 0.8221 (m-10) cc_final: 0.7781 (m-10)
REVERT: G   21 MET cc_start: 0.8376 (mmm) cc_final: 0.7337 (mtm)
REVERT: G   38 MET cc_start: 0.6774 (ptp) cc_final: 0.6073 (ptt)
REVERT: G   42 GLU cc_start: 0.8136 (tp30) cc_final: 0.7526 (mt-10)
REVERT: G   58 GLU cc_start: 0.9111 (mp0) cc_final: 0.8571 (mp0)
REVERT: R   49 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7177 (pt)
REVERT: R   53 CYS cc_start: 0.9079 (m) cc_final: 0.8845 (m)
REVERT: R   94 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7346 (t70)
REVERT: R   95 ILE cc_start: 0.9727 (mm) cc_final: 0.9515 (mm)
REVERT: R  109 GLU cc_start: 0.8666 (tp30) cc_final: 0.8227 (tm-30)
REVERT: H   34 MET cc_start: 0.8573 (tpp) cc_final: 0.8292 (tpp)
REVERT: H  180 MET cc_start: 0.8864 (ppp) cc_final: 0.8390 (ppp)
REVERT: H  211 ASP cc_start: 0.7922 (m-30) cc_final: 0.7648 (m-30)
  outliers start: 28
  outliers final: 22
  residues processed: 171
  average time/residue: 0.2166
  time to fit residues: 50.4912
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  : 1.060 
-------------------------------------------------------------------------------
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  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    9 ILE
Chi-restraints excluded: chain R residue   48 THR
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  439 VAL
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:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 28 optimal weight:    7.9990
   chunk 23 optimal weight:    8.9990
   chunk 31 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 85 optimal weight:   10.0000
   chunk 88 optimal weight:    9.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    1.5384

-------------------------------------------------------------------------------
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 = 0.3772 r_free = 0.3772 target = 0.093487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.069573 restraints weight = 31452.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.071683 restraints weight = 16911.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.073044 restraints weight = 11500.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.2999

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= 0.195
  Angle     :  0.719  13.190  11881  Z= 0.355
  Chirality :  0.043   0.173   1349
  Planarity :  0.004   0.050   1496
  Dihedral  :  7.972 161.965   1193
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 20.54 %
    Favored  : 76.45 %
  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: -0.06 (0.26), residues: 1075
  helix:  1.66 (0.29), residues: 336
  sheet: -0.03 (0.34), residues: 256
  loop : -1.28 (0.28), residues: 483

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   0.029   0.001   TYR R 409 
 ARG   0.006   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
  184 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 156
  time to evaluate  : 1.017 
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: 0.8663 (mmm-85)
REVERT: A  354 TYR cc_start: 0.8757 (p90) cc_final: 0.8297 (p90)
REVERT: B   12 GLU cc_start: 0.9296 (pt0) cc_final: 0.8979 (pm20)
REVERT: B   17 GLN cc_start: 0.7383 (tm-30) cc_final: 0.7132 (pp30)
REVERT: B   36 ASN cc_start: 0.8575 (m-40) cc_final: 0.8225 (p0)
REVERT: B   78 LYS cc_start: 0.9614 (mmmm) cc_final: 0.9228 (mmmm)
REVERT: B  130 GLU cc_start: 0.8959 (mp0) cc_final: 0.8704 (mp0)
REVERT: B  292 PHE cc_start: 0.8139 (m-10) cc_final: 0.7699 (m-10)
REVERT: G   21 MET cc_start: 0.8453 (mmm) cc_final: 0.7608 (mtm)
REVERT: G   24 ASN cc_start: 0.7712 (t0) cc_final: 0.7219 (m-40)
REVERT: G   38 MET cc_start: 0.6744 (ptp) cc_final: 0.6074 (ptt)
REVERT: G   42 GLU cc_start: 0.8111 (tp30) cc_final: 0.7527 (mt-10)
REVERT: G   58 GLU cc_start: 0.9106 (mp0) cc_final: 0.8572 (mp0)
REVERT: R   49 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7209 (pt)
REVERT: R   53 CYS cc_start: 0.9031 (m) cc_final: 0.8789 (m)
REVERT: R   94 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7239 (t70)
REVERT: R   95 ILE cc_start: 0.9710 (mm) cc_final: 0.9487 (mm)
REVERT: R  109 GLU cc_start: 0.8642 (tp30) cc_final: 0.8250 (tm-30)
REVERT: R  381 GLN cc_start: 0.9022 (pt0) cc_final: 0.8634 (mp10)
REVERT: H  211 ASP cc_start: 0.8056 (m-30) cc_final: 0.7672 (m-30)
REVERT: H  218 MET cc_start: 0.8693 (tmm) cc_final: 0.8459 (ppp)
REVERT: H  234 GLU cc_start: 0.6815 (pm20) cc_final: 0.6232 (pp20)
  outliers start: 28
  outliers final: 22
  residues processed: 175
  average time/residue: 0.2305
  time to fit residues: 54.5191
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  : 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  299 ASP
Chi-restraints excluded: chain B residue   58 ILE
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   48 THR
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  140 CYS
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  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:    6.9990
   chunk 80 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 60 optimal weight:    3.9990
   chunk 104 optimal weight:   20.0000
   chunk 32 optimal weight:    7.9990
   chunk 58 optimal weight:   30.0000
   chunk 71 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0670
   chunk 94 optimal weight:   20.0000
   chunk 57 optimal weight:    5.9990
   overall best weight:    2.8124

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
H   3 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 = 0.3741 r_free = 0.3741 target = 0.091693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.067709 restraints weight = 31960.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.069746 restraints weight = 17323.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.071119 restraints weight = 11862.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8768  Z= 0.254
  Angle     :  0.743  13.003  11881  Z= 0.370
  Chirality :  0.043   0.162   1349
  Planarity :  0.004   0.048   1496
  Dihedral  :  7.999 162.072   1193
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 20.86 %
    Favored  : 75.91 %
  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: -0.13 (0.26), residues: 1075
  helix:  1.55 (0.28), residues: 342
  sheet: -0.14 (0.33), residues: 267
  loop : -1.30 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.018   0.001   PHE R 387 
 TYR   0.027   0.002   TYR R 409 
 ARG   0.010   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
  180 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 150
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 ARG cc_start: 0.8937 (mmm160) cc_final: 0.8715 (mmm-85)
REVERT: A  320 TYR cc_start: 0.8260 (m-80) cc_final: 0.7774 (m-80)
REVERT: A  354 TYR cc_start: 0.8770 (p90) cc_final: 0.8295 (p90)
REVERT: B   12 GLU cc_start: 0.9288 (pt0) cc_final: 0.8975 (pm20)
REVERT: B   36 ASN cc_start: 0.8559 (m-40) cc_final: 0.8250 (p0)
REVERT: B  130 GLU cc_start: 0.8957 (mp0) cc_final: 0.8671 (mp0)
REVERT: B  292 PHE cc_start: 0.8268 (m-10) cc_final: 0.7821 (m-80)
REVERT: G   21 MET cc_start: 0.8505 (mmm) cc_final: 0.7668 (mtm)
REVERT: G   24 ASN cc_start: 0.7719 (t0) cc_final: 0.7219 (m-40)
REVERT: G   38 MET cc_start: 0.6619 (ptp) cc_final: 0.6359 (ptt)
REVERT: G   42 GLU cc_start: 0.8126 (tp30) cc_final: 0.7642 (mt-10)
REVERT: G   58 GLU cc_start: 0.9125 (mp0) cc_final: 0.8599 (mp0)
REVERT: R   49 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7165 (pt)
REVERT: R   53 CYS cc_start: 0.9057 (m) cc_final: 0.8822 (m)
REVERT: R  109 GLU cc_start: 0.8645 (tp30) cc_final: 0.8218 (tm-30)
REVERT: H   34 MET cc_start: 0.8593 (tpp) cc_final: 0.8286 (tpp)
REVERT: H  211 ASP cc_start: 0.7987 (m-30) cc_final: 0.7656 (m-30)
REVERT: H  218 MET cc_start: 0.8769 (tmm) cc_final: 0.8556 (ppp)
  outliers start: 30
  outliers final: 22
  residues processed: 173
  average time/residue: 0.2197
  time to fit residues: 51.4788
Evaluate side-chains
  163 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
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  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   49 LEU
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  140 CYS
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 44 optimal weight:   20.0000
   chunk 97 optimal weight:    9.9990
   chunk 2 optimal weight:    9.9990
   chunk 81 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 34 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.091098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.066994 restraints weight = 32261.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.069033 restraints weight = 17547.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.070403 restraints weight = 11987.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
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      :  0.004   0.043   8768  Z= 0.281
  Angle     :  0.779  14.347  11881  Z= 0.388
  Chirality :  0.044   0.217   1349
  Planarity :  0.004   0.047   1496
  Dihedral  :  8.058 161.810   1193
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 21.18 %
    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: -0.24 (0.26), residues: 1075
  helix:  1.41 (0.28), residues: 344
  sheet: -0.09 (0.34), residues: 249
  loop : -1.36 (0.28), residues: 482

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   0.030   0.001   PHE R 387 
 TYR   0.028   0.002   TYR R 409 
 ARG   0.010   0.001   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
  174 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 146
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 LEU cc_start: 0.3816 (OUTLIER) cc_final: 0.3533 (pp)
REVERT: A  313 ARG cc_start: 0.8965 (mmm160) cc_final: 0.8745 (mmm-85)
REVERT: A  320 TYR cc_start: 0.8355 (m-80) cc_final: 0.7905 (m-80)
REVERT: A  354 TYR cc_start: 0.8723 (p90) cc_final: 0.8300 (p90)
REVERT: B   12 GLU cc_start: 0.9285 (pt0) cc_final: 0.8970 (pm20)
REVERT: B   36 ASN cc_start: 0.8595 (m-40) cc_final: 0.8269 (p0)
REVERT: B   78 LYS cc_start: 0.9640 (mmmm) cc_final: 0.9217 (mmmm)
REVERT: B  226 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8937 (mt-10)
REVERT: B  292 PHE cc_start: 0.8366 (m-10) cc_final: 0.8024 (m-80)
REVERT: G   21 MET cc_start: 0.8507 (mmm) cc_final: 0.7681 (mtm)
REVERT: G   24 ASN cc_start: 0.7688 (t0) cc_final: 0.7185 (m-40)
REVERT: G   38 MET cc_start: 0.6622 (ptp) cc_final: 0.6196 (ptt)
REVERT: G   42 GLU cc_start: 0.8095 (tp30) cc_final: 0.7574 (mt-10)
REVERT: G   58 GLU cc_start: 0.9135 (mp0) cc_final: 0.8464 (mp0)
REVERT: R   49 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7182 (pt)
REVERT: R   53 CYS cc_start: 0.9049 (m) cc_final: 0.8808 (m)
REVERT: R   94 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7386 (t70)
REVERT: R  109 GLU cc_start: 0.8648 (tp30) cc_final: 0.8179 (tm-30)
REVERT: H  218 MET cc_start: 0.8775 (tmm) cc_final: 0.8573 (ppp)
  outliers start: 28
  outliers final: 25
  residues processed: 166
  average time/residue: 0.2189
  time to fit residues: 49.5929
Evaluate side-chains
  174 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 146
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
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  228 LEU
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   47 VAL
Chi-restraints excluded: chain R residue   49 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  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:    0.0000
   chunk 37 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0980
   chunk 22 optimal weight:   40.0000
   chunk 92 optimal weight:    8.9990
   chunk 80 optimal weight:    0.8980
   chunk 21 optimal weight:    8.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.7586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.094429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.070427 restraints weight = 31254.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.072564 restraints weight = 16857.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.074050 restraints weight = 11378.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.3390

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= 0.190
  Angle     :  0.785  14.830  11881  Z= 0.379
  Chirality :  0.044   0.189   1349
  Planarity :  0.004   0.050   1496
  Dihedral  :  7.864 159.238   1193
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 21.51 %
    Favored  : 75.70 %
  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: -0.21 (0.27), residues: 1075
  helix:  1.47 (0.29), residues: 338
  sheet: -0.07 (0.35), residues: 241
  loop : -1.34 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 148 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.034   0.001   PHE R 387 
 TYR   0.026   0.001   TYR R 409 
 ARG   0.009   0.001   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
  191 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 165
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 LEU cc_start: 0.3733 (OUTLIER) cc_final: 0.3494 (pp)
REVERT: A  244 MET cc_start: 0.5991 (mpp) cc_final: 0.5610 (mpp)
REVERT: A  313 ARG cc_start: 0.8879 (mmm160) cc_final: 0.8646 (mmm-85)
REVERT: A  320 TYR cc_start: 0.8302 (m-80) cc_final: 0.7772 (m-80)
REVERT: A  354 TYR cc_start: 0.8692 (p90) cc_final: 0.8284 (p90)
REVERT: B   12 GLU cc_start: 0.9290 (pt0) cc_final: 0.8973 (pm20)
REVERT: B   36 ASN cc_start: 0.8590 (m-40) cc_final: 0.8249 (p0)
REVERT: B   59 TYR cc_start: 0.8627 (m-80) cc_final: 0.8003 (m-80)
REVERT: B   78 LYS cc_start: 0.9594 (mmmm) cc_final: 0.9170 (mmmm)
REVERT: B   89 LYS cc_start: 0.9045 (mmtp) cc_final: 0.8521 (mmtm)
REVERT: B  283 ARG cc_start: 0.7520 (ttt180) cc_final: 0.6837 (ttt90)
REVERT: B  292 PHE cc_start: 0.8141 (m-10) cc_final: 0.7730 (m-10)
REVERT: G   21 MET cc_start: 0.8488 (mmm) cc_final: 0.7670 (mtm)
REVERT: G   24 ASN cc_start: 0.7720 (t0) cc_final: 0.7215 (m-40)
REVERT: G   38 MET cc_start: 0.6650 (ptp) cc_final: 0.6239 (ptt)
REVERT: G   42 GLU cc_start: 0.8024 (tp30) cc_final: 0.7525 (mt-10)
REVERT: G   58 GLU cc_start: 0.9120 (mp0) cc_final: 0.8603 (mp0)
REVERT: R   53 CYS cc_start: 0.9025 (m) cc_final: 0.8737 (p)
REVERT: R   94 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7451 (t70)
REVERT: R  109 GLU cc_start: 0.8618 (tp30) cc_final: 0.8208 (tm-30)
REVERT: R  111 MET cc_start: 0.8563 (mtm) cc_final: 0.8297 (ptp)
REVERT: H   34 MET cc_start: 0.8702 (tpp) cc_final: 0.8350 (tpp)
REVERT: H  218 MET cc_start: 0.8689 (tmm) cc_final: 0.8485 (ppp)
REVERT: H  232 LYS cc_start: 0.8093 (mppt) cc_final: 0.7695 (pptt)
REVERT: H  234 GLU cc_start: 0.6870 (pm20) cc_final: 0.6301 (pp20)
  outliers start: 26
  outliers final: 21
  residues processed: 182
  average time/residue: 0.2263
  time to fit residues: 55.5053
Evaluate side-chains
  180 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 157
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
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  228 LEU
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 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   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  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:    3.9990
   chunk 76 optimal weight:    0.0370
   chunk 32 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 99 optimal weight:   20.0000
   chunk 64 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.1662

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.093783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.069781 restraints weight = 31314.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.071927 restraints weight = 16863.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.073379 restraints weight = 11417.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.3517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8768  Z= 0.205
  Angle     :  0.817  17.960  11881  Z= 0.390
  Chirality :  0.044   0.217   1349
  Planarity :  0.004   0.051   1496
  Dihedral  :  7.813 158.638   1193
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 22.37 %
    Favored  : 74.84 %
  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: -0.19 (0.26), residues: 1075
  helix:  1.49 (0.29), residues: 338
  sheet: -0.14 (0.34), residues: 250
  loop : -1.29 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.036   0.001   PHE R 387 
 TYR   0.026   0.001   TYR R 409 
 ARG   0.009   0.000   ARG H  87 

********************** 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
  186 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 160
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8640 (tm-30)
REVERT: A  228 LEU cc_start: 0.3609 (OUTLIER) cc_final: 0.3331 (pp)
REVERT: A  313 ARG cc_start: 0.8839 (mmm160) cc_final: 0.8622 (mmm-85)
REVERT: A  320 TYR cc_start: 0.8276 (m-80) cc_final: 0.7873 (m-80)
REVERT: A  354 TYR cc_start: 0.8671 (p90) cc_final: 0.8215 (p90)
REVERT: B   12 GLU cc_start: 0.9285 (pt0) cc_final: 0.8967 (pm20)
REVERT: B   36 ASN cc_start: 0.8618 (m-40) cc_final: 0.8257 (p0)
REVERT: B   59 TYR cc_start: 0.8578 (m-80) cc_final: 0.8216 (m-80)
REVERT: B   78 LYS cc_start: 0.9560 (mmmm) cc_final: 0.9141 (mmmm)
REVERT: B   89 LYS cc_start: 0.9045 (mmtp) cc_final: 0.8374 (mmtp)
REVERT: B  283 ARG cc_start: 0.7522 (ttt180) cc_final: 0.6801 (ttt90)
REVERT: B  292 PHE cc_start: 0.8197 (m-10) cc_final: 0.7757 (m-10)
REVERT: G   21 MET cc_start: 0.8484 (mmm) cc_final: 0.7668 (mtm)
REVERT: G   24 ASN cc_start: 0.7656 (t0) cc_final: 0.7166 (m-40)
REVERT: G   38 MET cc_start: 0.6645 (ptp) cc_final: 0.6359 (ptt)
REVERT: G   42 GLU cc_start: 0.8045 (tp30) cc_final: 0.7574 (mt-10)
REVERT: G   58 GLU cc_start: 0.9110 (mp0) cc_final: 0.8620 (mp0)
REVERT: R   53 CYS cc_start: 0.9020 (m) cc_final: 0.8737 (p)
REVERT: R   94 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7523 (t70)
REVERT: R  109 GLU cc_start: 0.8649 (tp30) cc_final: 0.8275 (tm-30)
REVERT: R  111 MET cc_start: 0.8590 (mtm) cc_final: 0.8296 (ptp)
REVERT: H   34 MET cc_start: 0.8719 (tpp) cc_final: 0.8362 (tpp)
REVERT: H  160 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8192 (p)
REVERT: H  211 ASP cc_start: 0.7911 (m-30) cc_final: 0.7633 (m-30)
REVERT: H  218 MET cc_start: 0.8704 (tmm) cc_final: 0.8498 (ppp)
REVERT: H  232 LYS cc_start: 0.8067 (mppt) cc_final: 0.7689 (pptt)
  outliers start: 26
  outliers final: 21
  residues processed: 177
  average time/residue: 0.2322
  time to fit residues: 54.7289
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  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   36 LEU
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  228 LEU
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 B residue  225 HIS
Chi-restraints excluded: chain G residue   37 LEU
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  439 VAL
Chi-restraints excluded: chain R residue  454 LYS
Chi-restraints excluded: chain H residue  160 THR
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 6 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 91 optimal weight:    9.9990
   chunk 105 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 84 optimal weight:    0.4980
   chunk 70 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3799 r_free = 0.3799 target = 0.094704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.070606 restraints weight = 31663.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.072788 restraints weight = 16995.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.074252 restraints weight = 11477.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.3626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8768  Z= 0.198
  Angle     :  0.821  17.382  11881  Z= 0.391
  Chirality :  0.044   0.206   1349
  Planarity :  0.004   0.052   1496
  Dihedral  :  7.753 157.644   1193
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 22.58 %
    Favored  : 74.52 %
  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: -0.14 (0.27), residues: 1075
  helix:  1.46 (0.29), residues: 338
  sheet: -0.03 (0.34), residues: 250
  loop : -1.25 (0.28), residues: 487

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   0.031   0.001   PHE R 387 
 TYR   0.025   0.001   TYR R 409 
 ARG   0.008   0.000   ARG H  87 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3122.28 seconds
wall clock time: 56 minutes 41.67 seconds (3401.67 seconds total)