Starting phenix.real_space_refine
on Sat Aug  3 12:04:40 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg8_37505/08_2024/8wg8_37505.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg8_37505/08_2024/8wg8_37505.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg8_37505/08_2024/8wg8_37505.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg8_37505/08_2024/8wg8_37505.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg8_37505/08_2024/8wg8_37505.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wg8_37505/08_2024/8wg8_37505.cif"
  }
  resolution = 2.71
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.017
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      50      5.16       5
     C    5114      2.51       5
     N    1412      2.21       5
     O    1467      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   20": "OE1" <-> "OE2"
    Residue "A ARG   54": "NH1" <-> "NH2"
    Residue "A GLU  207": "OE1" <-> "OE2"
    Residue "A PHE  215": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  223": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  239": "OD1" <-> "OD2"
    Residue "A ARG  247": "NH1" <-> "NH2"
    Residue "A TYR  278": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  279": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  311": "OE1" <-> "OE2"
    Residue "B ARG   48": "NH1" <-> "NH2"
    Residue "B TYR  124": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  235": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  246": "OD1" <-> "OD2"
    Residue "B TYR  264": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  278": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  292": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N TYR   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N ARG   98": "NH1" <-> "NH2"
    Residue "R TYR  145": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R ARG  225": "NH1" <-> "NH2"
    Residue "R TYR  239": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R GLU  290": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
  Total number of atoms: 8043
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1901
          Classifications: {'peptide': 234}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 2577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2577
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "G"
      Number of atoms: 420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 420
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "N"
      Number of atoms: 964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 964
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "R"
      Number of atoms: 2050
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 2050
          Classifications: {'peptide': 263}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 5, 'TRANS': 257}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 82
          Unresolved non-hydrogen angles: 102
          Unresolved non-hydrogen dihedrals: 76
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 58
    Chain: "E"
      Number of atoms: 131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 131
          Classifications: {'peptide': 17}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 13}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 5.20, per 1000 atoms: 0.65
  Number of scatterers: 8043
  At special positions: 0
  Unit cell: (79.254, 93.177, 131.733, 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      50     16.00
     O    1467      8.00
     N    1412      7.00
     C    5114      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 224 " - pdb=" SG  CYS R 294 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.20
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1946

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      39.8% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 33
      removed outlier: 3.587A  pdb=" N   LYS A  27 " --> pdb=" O   LEU A  23 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLN A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   THR A  33 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 50
    Processing helix  chain 'A' and resid 210 through 216
      removed outlier: 3.539A  pdb=" N   GLN A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ASN A 216 " --> pdb=" O   GLN A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 245
    Processing helix  chain 'A' and resid 260 through 270
      removed outlier: 3.740A  pdb=" N   GLU A 266 " --> pdb=" O   ASP A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 279 through 284
    Processing helix  chain 'A' and resid 298 through 319
      removed outlier: 4.211A  pdb=" N   THR A 302 " --> pdb=" O   ASP A 298 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   SER A 319 " --> pdb=" O   ILE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 358
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 4.123A  pdb=" N   ARG B   8 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.767A  pdb=" N   LYS G  14 " --> pdb=" O   ALA G  10 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU G  15 " --> pdb=" O   GLN G  11 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 4.199A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.502A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 28 through 32'
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.657A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 165
      removed outlier: 3.544A  pdb=" N   THR R 146 " --> pdb=" O   GLN R 142 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 202
    Processing helix  chain 'R' and resid 221 through 253
      removed outlier: 3.614A  pdb=" N   VAL R 236 " --> pdb=" O   GLN R 232 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 263 through 272
    Processing helix  chain 'R' and resid 273 through 290
      Proline residue:  R 281  - end of helix
    Processing helix  chain 'R' and resid 304 through 336
      removed outlier: 3.632A  pdb=" N   ARG R 308 " --> pdb=" O   TRP R 304 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   PHE R 309 " --> pdb=" O   TRP R 305 " (cutoff:3.500A)
      Proline residue:  R 310  - end of helix
      removed outlier: 3.746A  pdb=" N   ARG R 336 " --> pdb=" O   LYS R 332 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 343 through 355
      removed outlier: 3.911A  pdb=" N   SER R 350 " --> pdb=" O   ARG R 346 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   THR R 351 " --> pdb=" O   LEU R 347 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 362 through 367
    Processing helix  chain 'R' and resid 375 through 382
    Processing helix  chain 'R' and resid 384 through 402
      removed outlier: 3.503A  pdb=" N   SER R 389 " --> pdb=" O   ASP R 385 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   SER R 390 " --> pdb=" O   LEU R 386 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   GLY R 393 " --> pdb=" O   SER R 389 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   LEU R 394 " --> pdb=" O   SER R 390 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 404 through 419
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191
      removed outlier: 3.663A  pdb=" N   ALA A 220 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.779A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ASN B 340 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.583A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.042A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.817A  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: 6.835A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.220A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.834A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.762A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 3.878A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 5.430A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL N 124 " --> pdb=" O   ALA N  92 " (cutoff:3.500A)

    392 hydrogen bonds defined for protein.
    1113 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: 2.29

  Time building geometry restraints manager: 3.52 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1595
        1.33 -     1.45: 2032
        1.45 -     1.57: 4510
        1.57 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 8207
  Sorted by residual:
  bond pdb=" CA  PHE A 279 "
       pdb=" C   PHE A 279 "
    ideal  model  delta    sigma   weight residual
    1.523  1.565 -0.043 1.00e-02 1.00e+04 1.81e+01
  bond pdb=" C   PHE A 279 "
       pdb=" N   PRO A 280 "
    ideal  model  delta    sigma   weight residual
    1.335  1.379 -0.044 1.19e-02 7.06e+03 1.40e+01
  bond pdb=" CA  ARG A 309 "
       pdb=" C   ARG A 309 "
    ideal  model  delta    sigma   weight residual
    1.524  1.476  0.047 1.27e-02 6.20e+03 1.39e+01
  bond pdb=" CA  CYS N  99 "
       pdb=" C   CYS N  99 "
    ideal  model  delta    sigma   weight residual
    1.522  1.492  0.030 9.10e-03 1.21e+04 1.12e+01
  bond pdb=" CA  PHE A 223 "
       pdb=" C   PHE A 223 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.036 1.17e-02 7.31e+03 9.29e+00
  ... (remaining 8202 not shown)

  Histogram of bond angle deviations from ideal:
       99.25 -   106.20: 148
      106.20 -   113.15: 4451
      113.15 -   120.10: 2823
      120.10 -   127.05: 3613
      127.05 -   134.00: 87
  Bond angle restraints: 11122
  Sorted by residual:
  angle pdb=" N   GLN A  52 "
        pdb=" CA  GLN A  52 "
        pdb=" C   GLN A  52 "
      ideal   model   delta    sigma   weight residual
     111.40  101.42    9.98 1.22e+00 6.72e-01 6.69e+01
  angle pdb=" N   ARG A  54 "
        pdb=" CA  ARG A  54 "
        pdb=" C   ARG A  54 "
      ideal   model   delta    sigma   weight residual
     113.88  106.43    7.45 1.23e+00 6.61e-01 3.67e+01
  angle pdb=" N   GLN A  24 "
        pdb=" CA  GLN A  24 "
        pdb=" C   GLN A  24 "
      ideal   model   delta    sigma   weight residual
     113.12  106.03    7.09 1.25e+00 6.40e-01 3.22e+01
  angle pdb=" N   TYR N 115 "
        pdb=" CA  TYR N 115 "
        pdb=" C   TYR N 115 "
      ideal   model   delta    sigma   weight residual
     109.24  100.38    8.86 1.63e+00 3.76e-01 2.95e+01
  angle pdb=" N   CYS N  99 "
        pdb=" CA  CYS N  99 "
        pdb=" C   CYS N  99 "
      ideal   model   delta    sigma   weight residual
     109.48  100.09    9.39 1.75e+00 3.27e-01 2.88e+01
  ... (remaining 11117 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 4425
       17.84 -    35.67: 349
       35.67 -    53.51: 69
       53.51 -    71.34: 18
       71.34 -    89.18: 8
  Dihedral angle restraints: 4869
    sinusoidal: 1864
      harmonic: 3005
  Sorted by residual:
  dihedral pdb=" CB  CYS R 224 "
           pdb=" SG  CYS R 224 "
           pdb=" SG  CYS R 294 "
           pdb=" CB  CYS R 294 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -172.27   86.27     1      1.00e+01 1.00e-02 8.98e+01
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -137.80   51.80     1      1.00e+01 1.00e-02 3.66e+01
  dihedral pdb=" CA  ASP B 246 "
           pdb=" CB  ASP B 246 "
           pdb=" CG  ASP B 246 "
           pdb=" OD1 ASP B 246 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.60   58.60     1      2.00e+01 2.50e-03 1.15e+01
  ... (remaining 4866 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1060
       0.062 -    0.125: 172
       0.125 -    0.187: 18
       0.187 -    0.249: 10
       0.249 -    0.312: 2
  Chirality restraints: 1262
  Sorted by residual:
  chirality pdb=" CA  MET A  53 "
            pdb=" N   MET A  53 "
            pdb=" C   MET A  53 "
            pdb=" CB  MET A  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.43e+00
  chirality pdb=" CA  TYR N 117 "
            pdb=" N   TYR N 117 "
            pdb=" C   TYR N 117 "
            pdb=" CB  TYR N 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CA  ASP A 310 "
            pdb=" N   ASP A 310 "
            pdb=" C   ASP A 310 "
            pdb=" CB  ASP A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.30e+00
  ... (remaining 1259 not shown)

  Planarity restraints: 1415
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS N  99 "    0.040 5.00e-02 4.00e+02   6.11e-02 5.96e+00
        pdb=" N   PRO N 100 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO N 100 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO N 100 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 306 "    0.011 2.00e-02 2.50e+03   2.24e-02 5.01e+00
        pdb=" C   TYR A 306 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   TYR A 306 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PHE A 307 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 212 "    0.010 2.00e-02 2.50e+03   1.96e-02 3.83e+00
        pdb=" C   ILE A 212 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ILE A 212 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLN A 213 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1412 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 351
        2.72 -     3.26: 7968
        3.26 -     3.81: 13145
        3.81 -     4.35: 16159
        4.35 -     4.90: 27492
  Nonbonded interactions: 65115
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" OD2 ASP A  26 "
            pdb=" NZ  LYS B  78 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.228 3.040
  ... (remaining 65110 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     26.110
  Find NCS groups from input model:        0.090
  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:12.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
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   0.047   8207  Z= 0.297
  Angle     :  0.684   9.979  11122  Z= 0.429
  Chirality :  0.049   0.312   1262
  Planarity :  0.004   0.061   1415
  Dihedral  : 13.928  89.180   2914
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  :  1.89 %
    Favored  : 95.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.27), residues: 1017
  helix:  1.37 (0.28), residues: 387
  sheet: -0.27 (0.33), residues: 221
  loop : -0.92 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A 324 
 PHE   0.027   0.002   PHE A 189 
 TYR   0.021   0.001   TYR B  59 
 ARG   0.003   0.000   ARG A 250 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 166
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
REVERT: B  246 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8349 (t0)
REVERT: N   17 SER cc_start: 0.8150 (m) cc_final: 0.7638 (t)
REVERT: R  287 CYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7433 (t)
REVERT: R  290 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6009 (tm-30)
REVERT: R  293 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.6109 (pp30)
REVERT: R  410 GLU cc_start: 0.8887 (tp30) cc_final: 0.8551 (tp30)
  outliers start: 18
  outliers final: 3
  residues processed: 181
  average time/residue: 1.3231
  time to fit residues: 252.3263
Evaluate side-chains
  133 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 126
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain R residue  226 VAL
Chi-restraints excluded: chain R residue  287 CYS
Chi-restraints excluded: chain R residue  290 GLU
Chi-restraints excluded: chain R residue  293 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 58 optimal weight:   20.0000
   chunk 90 optimal weight:    2.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 246 ASN
A 261 GLN
A 354 HIS
A 357 GLN
B  44 GLN
B 266 HIS
N  35 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072   8207  Z= 0.390
  Angle     :  0.643   8.188  11122  Z= 0.338
  Chirality :  0.044   0.147   1262
  Planarity :  0.005   0.048   1415
  Dihedral  :  6.580  85.296   1136
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 15.70 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.27), residues: 1017
  helix:  1.57 (0.28), residues: 391
  sheet: -0.02 (0.34), residues: 215
  loop : -0.99 (0.29), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP R 282 
 HIS   0.004   0.001   HIS B  62 
 PHE   0.019   0.002   PHE A 185 
 TYR   0.018   0.002   TYR R 145 
 ARG   0.006   0.001   ARG A 250 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 133
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8107 (mm-30)
REVERT: A  311 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7250 (mp0)
REVERT: B  217 MET cc_start: 0.8647 (pmm) cc_final: 0.8322 (pmm)
REVERT: G   21 MET cc_start: 0.7864 (mpp) cc_final: 0.7594 (mpp)
REVERT: N   38 ARG cc_start: 0.8701 (mtm180) cc_final: 0.7764 (mtm180)
REVERT: N   46 GLU cc_start: 0.7881 (pt0) cc_final: 0.7580 (pm20)
REVERT: N   53 GLN cc_start: 0.8180 (mp10) cc_final: 0.7943 (mp10)
REVERT: R  231 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.6952 (ttp)
REVERT: R  290 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.5890 (tm-30)
REVERT: R  293 GLN cc_start: 0.6865 (OUTLIER) cc_final: 0.6623 (pt0)
REVERT: R  408 GLN cc_start: 0.8971 (mt0) cc_final: 0.8688 (mt0)
REVERT: R  410 GLU cc_start: 0.8895 (tp30) cc_final: 0.8548 (tp30)
  outliers start: 27
  outliers final: 13
  residues processed: 145
  average time/residue: 1.2250
  time to fit residues: 187.8647
Evaluate side-chains
  142 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain N residue   45 LEU
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue  138 TYR
Chi-restraints excluded: chain R residue  145 TYR
Chi-restraints excluded: chain R residue  171 CYS
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  226 VAL
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  284 VAL
Chi-restraints excluded: chain R residue  290 GLU
Chi-restraints excluded: chain R residue  293 GLN
Chi-restraints excluded: chain R residue  385 ASP
Chi-restraints excluded: chain E residue   14 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 90 optimal weight:    0.6980
   chunk 98 optimal weight:    0.9980
   chunk 81 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
N  31 ASN
R 177 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8207  Z= 0.211
  Angle     :  0.560  12.760  11122  Z= 0.291
  Chirality :  0.041   0.161   1262
  Planarity :  0.004   0.044   1415
  Dihedral  :  5.838  88.076   1131
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 18.30 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.27), residues: 1017
  helix:  1.78 (0.28), residues: 392
  sheet:  0.04 (0.34), residues: 210
  loop : -0.98 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP R 282 
 HIS   0.003   0.001   HIS R 177 
 PHE   0.012   0.001   PHE A 185 
 TYR   0.015   0.001   TYR R 145 
 ARG   0.005   0.000   ARG N  19 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8058 (mm-30)
REVERT: A  284 ARG cc_start: 0.8390 (ptp90) cc_final: 0.7999 (ptp90)
REVERT: B  217 MET cc_start: 0.8612 (pmm) cc_final: 0.8291 (pmm)
REVERT: G   21 MET cc_start: 0.7967 (mpp) cc_final: 0.7716 (mpp)
REVERT: N   53 GLN cc_start: 0.8239 (mp10) cc_final: 0.7980 (mp10)
REVERT: R  142 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7965 (mm110)
REVERT: R  231 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.6832 (ttp)
REVERT: R  245 GLU cc_start: 0.8382 (tp30) cc_final: 0.8153 (tp30)
REVERT: R  408 GLN cc_start: 0.8970 (mt0) cc_final: 0.8657 (mt0)
REVERT: R  410 GLU cc_start: 0.8839 (tp30) cc_final: 0.8553 (tp30)
  outliers start: 25
  outliers final: 12
  residues processed: 147
  average time/residue: 1.3289
  time to fit residues: 206.8460
Evaluate side-chains
  142 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  138 TYR
Chi-restraints excluded: chain R residue  145 TYR
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  385 ASP
Chi-restraints excluded: chain E residue   14 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 43 optimal weight:    0.1980
   chunk 61 optimal weight:    4.9990
   chunk 91 optimal weight:    0.8980
   chunk 96 optimal weight:    0.7980
   chunk 86 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9980
   chunk 80 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 197 HIS
A 261 GLN
B  44 GLN
N  84 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8207  Z= 0.251
  Angle     :  0.575  12.264  11122  Z= 0.300
  Chirality :  0.041   0.135   1262
  Planarity :  0.004   0.043   1415
  Dihedral  :  4.414  46.379   1124
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 19.01 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.27), residues: 1017
  helix:  1.84 (0.28), residues: 392
  sheet: -0.00 (0.34), residues: 209
  loop : -0.96 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP R 282 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.015   0.001   PHE A 185 
 TYR   0.013   0.001   TYR R 145 
 ARG   0.009   0.000   ARG A 247 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 133
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8060 (mm-30)
REVERT: A  284 ARG cc_start: 0.8432 (ptp90) cc_final: 0.7965 (ptp90)
REVERT: B   32 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8404 (mt0)
REVERT: B   47 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8844 (t)
REVERT: B   59 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.7898 (m-80)
REVERT: B  161 SER cc_start: 0.9290 (OUTLIER) cc_final: 0.9072 (p)
REVERT: B  217 MET cc_start: 0.8634 (pmm) cc_final: 0.8251 (pmm)
REVERT: N   53 GLN cc_start: 0.8282 (mp10) cc_final: 0.8059 (mp10)
REVERT: R  142 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7929 (mm110)
REVERT: R  231 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.6923 (ttp)
REVERT: R  245 GLU cc_start: 0.8333 (tp30) cc_final: 0.8092 (tp30)
REVERT: R  405 LYS cc_start: 0.9251 (tppt) cc_final: 0.9018 (tppt)
REVERT: R  408 GLN cc_start: 0.8926 (mt0) cc_final: 0.8510 (mt0)
REVERT: R  410 GLU cc_start: 0.8835 (tp30) cc_final: 0.8455 (tp30)
  outliers start: 35
  outliers final: 17
  residues processed: 156
  average time/residue: 1.1608
  time to fit residues: 192.5676
Evaluate side-chains
  141 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  206 ASP
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  138 TYR
Chi-restraints excluded: chain R residue  171 CYS
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  284 VAL
Chi-restraints excluded: chain R residue  288 LEU
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  385 ASP
Chi-restraints excluded: chain E residue   14 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 71 optimal weight:    0.4980
   chunk 39 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 49 optimal weight:    0.2980
   chunk 86 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 32 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8207  Z= 0.229
  Angle     :  0.584  11.795  11122  Z= 0.302
  Chirality :  0.041   0.158   1262
  Planarity :  0.003   0.047   1415
  Dihedral  :  4.401  47.278   1124
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 20.66 %
    Favored  : 75.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.27), residues: 1017
  helix:  1.88 (0.28), residues: 394
  sheet:  0.08 (0.34), residues: 209
  loop : -0.97 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP R 282 
 HIS   0.005   0.001   HIS A 197 
 PHE   0.013   0.001   PHE A 185 
 TYR   0.019   0.001   TYR R 145 
 ARG   0.011   0.000   ARG A 247 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 127
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8033 (mm-30)
REVERT: A  284 ARG cc_start: 0.8483 (ptp90) cc_final: 0.8010 (ptp90)
REVERT: B   32 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8432 (mt0)
REVERT: B   47 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8845 (t)
REVERT: B   59 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.7859 (m-80)
REVERT: B  188 MET cc_start: 0.9085 (mmp) cc_final: 0.8584 (mmm)
REVERT: B  217 MET cc_start: 0.8641 (pmm) cc_final: 0.8242 (pmm)
REVERT: G   21 MET cc_start: 0.7977 (mpp) cc_final: 0.7507 (mpp)
REVERT: N   53 GLN cc_start: 0.8310 (mp10) cc_final: 0.8079 (mp10)
REVERT: R  142 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7962 (mm110)
REVERT: R  231 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.6976 (ttp)
REVERT: R  245 GLU cc_start: 0.8317 (tp30) cc_final: 0.8077 (tp30)
REVERT: R  405 LYS cc_start: 0.9216 (tppt) cc_final: 0.8965 (tppt)
REVERT: R  408 GLN cc_start: 0.8963 (mt0) cc_final: 0.8581 (mt0)
REVERT: R  410 GLU cc_start: 0.8735 (tp30) cc_final: 0.8411 (tp30)
  outliers start: 32
  outliers final: 18
  residues processed: 149
  average time/residue: 1.1673
  time to fit residues: 184.6406
Evaluate side-chains
  147 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  138 TYR
Chi-restraints excluded: chain R residue  145 TYR
Chi-restraints excluded: chain R residue  171 CYS
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  288 LEU
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  357 LEU
Chi-restraints excluded: chain R residue  385 ASP
Chi-restraints excluded: chain E residue   14 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    0.1980
   chunk 56 optimal weight:    7.9990
   chunk 23 optimal weight:    0.0170
   chunk 96 optimal weight:    1.9990
   chunk 80 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.4818

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8207  Z= 0.184
  Angle     :  0.579  13.696  11122  Z= 0.298
  Chirality :  0.041   0.151   1262
  Planarity :  0.003   0.056   1415
  Dihedral  :  4.281  46.049   1124
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 21.13 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.27), residues: 1017
  helix:  1.97 (0.28), residues: 394
  sheet:  0.13 (0.34), residues: 209
  loop : -0.94 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP R 282 
 HIS   0.004   0.001   HIS A 197 
 PHE   0.012   0.001   PHE A 185 
 TYR   0.014   0.001   TYR R 145 
 ARG   0.011   0.000   ARG A 247 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 132
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7993 (mm-30)
REVERT: A  239 ASP cc_start: 0.8471 (t0) cc_final: 0.8248 (t0)
REVERT: A  311 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7030 (mp0)
REVERT: B   32 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8466 (mt0)
REVERT: B   47 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8848 (t)
REVERT: B   59 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.7947 (m-80)
REVERT: B  188 MET cc_start: 0.8976 (mmp) cc_final: 0.8529 (mmm)
REVERT: B  217 MET cc_start: 0.8628 (pmm) cc_final: 0.8226 (pmm)
REVERT: G   21 MET cc_start: 0.8077 (mpp) cc_final: 0.7556 (mpp)
REVERT: N   53 GLN cc_start: 0.8287 (mp10) cc_final: 0.8055 (mp10)
REVERT: R  231 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7076 (mtm)
REVERT: R  405 LYS cc_start: 0.9183 (tppt) cc_final: 0.8923 (tppt)
REVERT: R  408 GLN cc_start: 0.8970 (mt0) cc_final: 0.8514 (mt0)
REVERT: R  410 GLU cc_start: 0.8700 (tp30) cc_final: 0.8500 (tp30)
  outliers start: 32
  outliers final: 14
  residues processed: 152
  average time/residue: 1.1581
  time to fit residues: 186.8532
Evaluate side-chains
  141 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue  138 TYR
Chi-restraints excluded: chain R residue  171 CYS
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  284 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain E residue   14 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 54 optimal weight:    0.5980
   chunk 81 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 57 optimal weight:    5.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN
B  44 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8207  Z= 0.216
  Angle     :  0.601  13.708  11122  Z= 0.309
  Chirality :  0.041   0.176   1262
  Planarity :  0.003   0.052   1415
  Dihedral  :  4.307  47.398   1124
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 22.43 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.27), residues: 1017
  helix:  2.10 (0.28), residues: 386
  sheet:  0.14 (0.34), residues: 209
  loop : -0.92 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP R 282 
 HIS   0.004   0.001   HIS A 197 
 PHE   0.013   0.001   PHE A 185 
 TYR   0.018   0.001   TYR R 145 
 ARG   0.011   0.000   ARG A 247 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7965 (mm-30)
REVERT: A  239 ASP cc_start: 0.8472 (t0) cc_final: 0.8252 (t0)
REVERT: A  284 ARG cc_start: 0.8699 (ptp-110) cc_final: 0.8495 (ptp90)
REVERT: B   32 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8520 (mt0)
REVERT: B   47 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8856 (t)
REVERT: B   59 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.7959 (m-80)
REVERT: B  188 MET cc_start: 0.8971 (mmp) cc_final: 0.8463 (mmm)
REVERT: B  217 MET cc_start: 0.8622 (pmm) cc_final: 0.8306 (pmm)
REVERT: G   21 MET cc_start: 0.8066 (mpp) cc_final: 0.7840 (mpp)
REVERT: G   47 GLU cc_start: 0.8095 (mp0) cc_final: 0.7872 (mp0)
REVERT: N   53 GLN cc_start: 0.8324 (mp10) cc_final: 0.8072 (mp10)
REVERT: R  231 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7100 (mtm)
REVERT: R  405 LYS cc_start: 0.9191 (tppt) cc_final: 0.8922 (tppt)
REVERT: R  408 GLN cc_start: 0.8973 (mt0) cc_final: 0.8562 (mt0)
  outliers start: 28
  outliers final: 15
  residues processed: 152
  average time/residue: 1.2044
  time to fit residues: 193.9462
Evaluate side-chains
  149 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   65 LYS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue  138 TYR
Chi-restraints excluded: chain R residue  171 CYS
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  284 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain E residue   14 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 61 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0070
   chunk 47 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9990
   chunk 87 optimal weight:   10.0000
   chunk 92 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 89 optimal weight:    0.6980
   overall best weight:    0.6200

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
N  84 ASN
R 318 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8207  Z= 0.205
  Angle     :  0.609  14.585  11122  Z= 0.313
  Chirality :  0.041   0.173   1262
  Planarity :  0.004   0.057   1415
  Dihedral  :  4.291  47.480   1124
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 22.90 %
    Favored  : 73.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.27), residues: 1017
  helix:  2.15 (0.28), residues: 386
  sheet:  0.10 (0.34), residues: 211
  loop : -0.89 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP R 282 
 HIS   0.004   0.001   HIS A 197 
 PHE   0.014   0.001   PHE E   5 
 TYR   0.012   0.001   TYR R 145 
 ARG   0.012   0.000   ARG A 247 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8209 (tm-30) cc_final: 0.8002 (pp20)
REVERT: A   20 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7961 (mm-30)
REVERT: A  239 ASP cc_start: 0.8467 (t0) cc_final: 0.8238 (t0)
REVERT: B   32 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8520 (mt0)
REVERT: B   47 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8835 (t)
REVERT: B   59 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.7963 (m-80)
REVERT: B  188 MET cc_start: 0.8939 (mmp) cc_final: 0.8450 (mmm)
REVERT: B  217 MET cc_start: 0.8621 (pmm) cc_final: 0.8270 (pmm)
REVERT: G   21 MET cc_start: 0.7980 (tpp) cc_final: 0.7743 (mpp)
REVERT: G   47 GLU cc_start: 0.8022 (mp0) cc_final: 0.7773 (mp0)
REVERT: N   53 GLN cc_start: 0.8318 (mp10) cc_final: 0.8103 (mp10)
REVERT: N   87 LYS cc_start: 0.8551 (mttm) cc_final: 0.8280 (mttm)
REVERT: R  142 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7902 (mm110)
REVERT: R  195 ASP cc_start: 0.9178 (t0) cc_final: 0.8818 (t0)
REVERT: R  231 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7120 (mtm)
REVERT: R  405 LYS cc_start: 0.9194 (tppt) cc_final: 0.8863 (tppt)
REVERT: R  408 GLN cc_start: 0.8930 (mt0) cc_final: 0.8502 (mt0)
  outliers start: 27
  outliers final: 16
  residues processed: 151
  average time/residue: 1.1959
  time to fit residues: 191.2972
Evaluate side-chains
  148 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   65 LYS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue  171 CYS
Chi-restraints excluded: chain R residue  230 PHE
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  284 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  385 ASP
Chi-restraints excluded: chain E residue   14 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 27 optimal weight:    0.2980
   chunk 81 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 89 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 94 optimal weight:    0.5980
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
N  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.2550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8207  Z= 0.212
  Angle     :  0.621  14.233  11122  Z= 0.319
  Chirality :  0.041   0.180   1262
  Planarity :  0.004   0.058   1415
  Dihedral  :  4.285  47.831   1124
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 23.61 %
    Favored  : 73.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.27), residues: 1017
  helix:  2.18 (0.28), residues: 386
  sheet:  0.11 (0.34), residues: 211
  loop : -0.86 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP R 282 
 HIS   0.004   0.001   HIS A 197 
 PHE   0.015   0.001   PHE E   5 
 TYR   0.017   0.001   TYR R 145 
 ARG   0.014   0.000   ARG A 247 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8227 (tm-30) cc_final: 0.8005 (pp20)
REVERT: A   20 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7963 (mm-30)
REVERT: A  239 ASP cc_start: 0.8469 (t0) cc_final: 0.8257 (t0)
REVERT: B   32 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8536 (mt0)
REVERT: B   47 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8839 (t)
REVERT: B   59 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.7976 (m-80)
REVERT: B  188 MET cc_start: 0.8934 (mmp) cc_final: 0.8460 (mmm)
REVERT: B  217 MET cc_start: 0.8634 (pmm) cc_final: 0.8289 (pmm)
REVERT: G   21 MET cc_start: 0.8057 (tpp) cc_final: 0.7525 (mpp)
REVERT: N   53 GLN cc_start: 0.8309 (mp10) cc_final: 0.8079 (mp10)
REVERT: N   70 ILE cc_start: 0.8819 (tt) cc_final: 0.8501 (pp)
REVERT: N   87 LYS cc_start: 0.8539 (mttm) cc_final: 0.8256 (mttm)
REVERT: R  195 ASP cc_start: 0.9194 (t0) cc_final: 0.8718 (t0)
REVERT: R  231 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.7036 (mtm)
REVERT: R  405 LYS cc_start: 0.9196 (tppt) cc_final: 0.8866 (tppt)
REVERT: R  408 GLN cc_start: 0.8930 (mt0) cc_final: 0.8514 (mt0)
  outliers start: 24
  outliers final: 15
  residues processed: 149
  average time/residue: 1.2336
  time to fit residues: 195.1163
Evaluate side-chains
  152 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   65 LYS
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue  138 TYR
Chi-restraints excluded: chain R residue  145 TYR
Chi-restraints excluded: chain R residue  171 CYS
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  284 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain E residue   14 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 99 optimal weight:    0.0670
   chunk 91 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.6720

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  84 ASN
R 232 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8207  Z= 0.220
  Angle     :  0.641  13.614  11122  Z= 0.328
  Chirality :  0.041   0.183   1262
  Planarity :  0.004   0.062   1415
  Dihedral  :  4.333  48.135   1124
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 24.32 %
    Favored  : 73.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.27), residues: 1017
  helix:  2.20 (0.28), residues: 386
  sheet:  0.12 (0.34), residues: 211
  loop : -0.89 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP R 282 
 HIS   0.004   0.001   HIS A 197 
 PHE   0.016   0.001   PHE E   5 
 TYR   0.013   0.001   TYR R 138 
 ARG   0.014   0.000   ARG A 247 

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7971 (mm-30)
REVERT: A  239 ASP cc_start: 0.8450 (t0) cc_final: 0.8207 (t0)
REVERT: A  284 ARG cc_start: 0.8562 (mpp80) cc_final: 0.8206 (ptp90)
REVERT: B   32 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8600 (mt0)
REVERT: B   47 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8854 (t)
REVERT: B   59 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.7976 (m-80)
REVERT: B  188 MET cc_start: 0.8944 (mmp) cc_final: 0.8478 (mmm)
REVERT: B  217 MET cc_start: 0.8628 (pmm) cc_final: 0.8285 (pmm)
REVERT: G   21 MET cc_start: 0.7991 (tpp) cc_final: 0.7502 (mpp)
REVERT: N   53 GLN cc_start: 0.8329 (mp10) cc_final: 0.8095 (mp10)
REVERT: N   70 ILE cc_start: 0.8807 (tt) cc_final: 0.8495 (pp)
REVERT: N   87 LYS cc_start: 0.8583 (mttm) cc_final: 0.8297 (mttm)
REVERT: R  166 LEU cc_start: 0.7426 (mm) cc_final: 0.7190 (mt)
REVERT: R  231 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7037 (mtm)
REVERT: R  405 LYS cc_start: 0.9199 (tppt) cc_final: 0.8862 (tppt)
REVERT: R  408 GLN cc_start: 0.8920 (mt0) cc_final: 0.8502 (mt0)
  outliers start: 20
  outliers final: 16
  residues processed: 143
  average time/residue: 1.1678
  time to fit residues: 177.4538
Evaluate side-chains
  151 residues out of total 884 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   65 LYS
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue  138 TYR
Chi-restraints excluded: chain R residue  145 TYR
Chi-restraints excluded: chain R residue  171 CYS
Chi-restraints excluded: chain R residue  194 ILE
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  284 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain E residue   14 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    7.9990
   chunk 11 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 57 optimal weight:    5.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  84 ASN
N 120 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.115477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.083883 restraints weight = 14066.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 3.14
r_work: 0.3037 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8207  Z= 0.231
  Angle     :  0.654  13.701  11122  Z= 0.334
  Chirality :  0.042   0.182   1262
  Planarity :  0.004   0.060   1415
  Dihedral  :  4.407  48.879   1124
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 24.20 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.27), residues: 1017
  helix:  2.20 (0.28), residues: 386
  sheet:  0.20 (0.34), residues: 208
  loop : -0.91 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP R 282 
 HIS   0.004   0.001   HIS A 197 
 PHE   0.021   0.001   PHE E   5 
 TYR   0.014   0.001   TYR R 138 
 ARG   0.014   0.000   ARG A 247 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3535.76 seconds
wall clock time: 62 minutes 31.61 seconds (3751.61 seconds total)