Starting phenix.real_space_refine
on Fri Dec  8 11:26:32 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/12_2023/8w89_37349_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/12_2023/8w89_37349.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/12_2023/8w89_37349.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/12_2023/8w89_37349.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/12_2023/8w89_37349_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/12_2023/8w89_37349_updated.pdb"
  }
  resolution = 3.0
  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=   0.026
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      61      5.16       5
     C    5229      2.51       5
     N    1419      2.21       5
     O    1521      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   61": "NH1" <-> "NH2"
    Residue "A PHE   70": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  100": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  125": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  174": "OE1" <-> "OE2"
    Residue "B GLU  138": "OE1" <-> "OE2"
    Residue "B PHE  241": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G GLU   17": "OE1" <-> "OE2"
    Residue "G GLU   58": "OE1" <-> "OE2"
    Residue "N TYR   80": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R GLU  169": "OE1" <-> "OE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 8230
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1934
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "R"
      Number of atoms: 2283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2283
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 11, 'TRANS': 273}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 31
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 21
    Chain: "R"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 10
          Unusual residues: {'PEA': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 4.87, per 1000 atoms: 0.59
  Number of scatterers: 8230
  At special positions: 0
  Unit cell: (81.536, 100.672, 132.288, 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      61     16.00
     O    1521      8.00
     N    1419      7.00
     C    5229      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  96 " - pdb=" SG  CYS R 182 " 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: 3.49
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1964

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      37.5% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 34
    Processing helix  chain 'A' and resid 53 through 55
      No H-bonds generated for 'chain 'A' and resid 53 through 55'
    Processing helix  chain 'A' and resid 99 through 101
      No H-bonds generated for 'chain 'A' and resid 99 through 101'
    Processing helix  chain 'A' and resid 118 through 130
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 160 through 163
      No H-bonds generated for 'chain 'A' and resid 160 through 163'
    Processing helix  chain 'A' and resid 165 through 169
    Processing helix  chain 'A' and resid 184 through 203
      removed outlier: 3.650A  pdb=" N   ILE A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 242
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 30 through 33
      No H-bonds generated for 'chain 'B' and resid 30 through 33'
    Processing helix  chain 'G' and resid 7 through 23
    Processing helix  chain 'G' and resid 30 through 43
    Processing helix  chain 'N' and resid 88 through 90
      No H-bonds generated for 'chain 'N' and resid 88 through 90'
    Processing helix  chain 'R' and resid 20 through 51
    Processing helix  chain 'R' and resid 57 through 75
      removed outlier: 3.607A  pdb=" N   LEU R  61 " --> pdb=" O   PRO R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 77 through 84
    Processing helix  chain 'R' and resid 93 through 126
    Processing helix  chain 'R' and resid 131 through 134
      No H-bonds generated for 'chain 'R' and resid 131 through 134'
    Processing helix  chain 'R' and resid 137 through 160
      Proline residue:  R 151  - end of helix
    Processing helix  chain 'R' and resid 169 through 179
    Processing helix  chain 'R' and resid 188 through 198
    Processing helix  chain 'R' and resid 200 through 230
    Processing helix  chain 'R' and resid 248 through 274
      Proline residue:  R 266  - end of helix
    Processing helix  chain 'R' and resid 283 through 305
      removed outlier: 3.619A  pdb=" N   TRP R 291 " --> pdb=" O   ASP R 287 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   SER R 297 " --> pdb=" O   GLY R 293 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 309 through 315
    Processing sheet with id=  A, first strand: chain 'A' and resid 211 through 215
      removed outlier: 7.378A  pdb=" N   VAL A 139 " --> pdb=" O   TYR A 212 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   HIS A 214 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   LEU A 141 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ALA A 105 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   ASN A  80 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 7.891A  pdb=" N   LEU A  43 " --> pdb=" O   ASN A  80 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   HIS A  82 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   LEU A  45 " --> pdb=" O   HIS A  82 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   PHE A  84 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   PHE A  70 " --> pdb=" O   ASP A  85 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.732A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.886A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.194A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.397A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.787A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.145A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.881A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.507A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.918A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.518A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.740A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'N' and resid 3 through 6
      removed outlier: 3.503A  pdb=" N   LEU N  18 " --> pdb=" O   MET N  83 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.136A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.491A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 7.575A  pdb=" N   ALA N  40 " --> pdb=" O   LEU N  45 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   LEU N  45 " --> pdb=" O   ALA N  40 " (cutoff:3.500A)

    386 hydrogen bonds defined for protein.
    1128 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: 2.34

  Time building geometry restraints manager: 3.74 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1806
        1.33 -     1.46: 2217
        1.46 -     1.58: 4297
        1.58 -     1.71: 0
        1.71 -     1.84: 88
  Bond restraints: 8408
  Sorted by residual:
  bond pdb=" CA  TYR R 122 "
       pdb=" C   TYR R 122 "
    ideal  model  delta    sigma   weight residual
    1.524  1.471  0.053 1.27e-02 6.20e+03 1.75e+01
  bond pdb=" CA  ARG N  98 "
       pdb=" C   ARG N  98 "
    ideal  model  delta    sigma   weight residual
    1.526  1.474  0.052 1.37e-02 5.33e+03 1.43e+01
  bond pdb=" CA  THR A 216 "
       pdb=" C   THR A 216 "
    ideal  model  delta    sigma   weight residual
    1.523  1.481  0.042 1.21e-02 6.83e+03 1.18e+01
  bond pdb=" CA  TRP B 297 "
       pdb=" C   TRP B 297 "
    ideal  model  delta    sigma   weight residual
    1.523  1.485  0.039 1.18e-02 7.18e+03 1.07e+01
  bond pdb=" CA  ASN R 296 "
       pdb=" C   ASN R 296 "
    ideal  model  delta    sigma   weight residual
    1.524  1.482  0.041 1.29e-02 6.01e+03 1.02e+01
  ... (remaining 8403 not shown)

  Histogram of bond angle deviations from ideal:
      100.17 -   106.98: 221
      106.98 -   113.80: 4620
      113.80 -   120.62: 3572
      120.62 -   127.44: 2886
      127.44 -   134.25: 89
  Bond angle restraints: 11388
  Sorted by residual:
  angle pdb=" N   GLN R  53 "
        pdb=" CA  GLN R  53 "
        pdb=" C   GLN R  53 "
      ideal   model   delta    sigma   weight residual
     113.38  104.99    8.39 1.23e+00 6.61e-01 4.65e+01
  angle pdb=" N   HIS R  50 "
        pdb=" CA  HIS R  50 "
        pdb=" C   HIS R  50 "
      ideal   model   delta    sigma   weight residual
     111.36  118.67   -7.31 1.09e+00 8.42e-01 4.50e+01
  angle pdb=" N   ARG R  23 "
        pdb=" CA  ARG R  23 "
        pdb=" C   ARG R  23 "
      ideal   model   delta    sigma   weight residual
     111.28  104.39    6.89 1.09e+00 8.42e-01 3.99e+01
  angle pdb=" N   GLN B 259 "
        pdb=" CA  GLN B 259 "
        pdb=" C   GLN B 259 "
      ideal   model   delta    sigma   weight residual
     109.14  117.78   -8.64 1.49e+00 4.50e-01 3.36e+01
  angle pdb=" N   ASP B 228 "
        pdb=" CA  ASP B 228 "
        pdb=" C   ASP B 228 "
      ideal   model   delta    sigma   weight residual
     110.24  117.28   -7.04 1.47e+00 4.63e-01 2.29e+01
  ... (remaining 11383 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 4545
       17.55 -    35.10: 367
       35.10 -    52.65: 68
       52.65 -    70.20: 12
       70.20 -    87.75: 5
  Dihedral angle restraints: 4997
    sinusoidal: 1957
      harmonic: 3040
  Sorted by residual:
  dihedral pdb=" N   ASP B 258 "
           pdb=" C   ASP B 258 "
           pdb=" CA  ASP B 258 "
           pdb=" CB  ASP B 258 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.20   -9.40     0      2.50e+00 1.60e-01 1.41e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   62.27   30.73     1      1.00e+01 1.00e-02 1.35e+01
  dihedral pdb=" C   VAL R 288 "
           pdb=" N   VAL R 288 "
           pdb=" CA  VAL R 288 "
           pdb=" CB  VAL R 288 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.56    8.56     0      2.50e+00 1.60e-01 1.17e+01
  ... (remaining 4994 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 1083
       0.076 -    0.152: 146
       0.152 -    0.229: 29
       0.229 -    0.305: 11
       0.305 -    0.381: 3
  Chirality restraints: 1272
  Sorted by residual:
  chirality pdb=" CA  ASP B 258 "
            pdb=" N   ASP B 258 "
            pdb=" C   ASP B 258 "
            pdb=" CB  ASP B 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.63e+00
  chirality pdb=" CA  PHE R 268 "
            pdb=" N   PHE R 268 "
            pdb=" C   PHE R 268 "
            pdb=" CB  PHE R 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.03e+00
  chirality pdb=" CA  TRP A  96 "
            pdb=" N   TRP A  96 "
            pdb=" C   TRP A  96 "
            pdb=" CB  TRP A  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.85e+00
  ... (remaining 1269 not shown)

  Planarity restraints: 1452
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R  94 "    0.016 2.00e-02 2.50e+03   3.13e-02 9.82e+00
        pdb=" C   VAL R  94 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   VAL R  94 "    0.021 2.00e-02 2.50e+03
        pdb=" N   PHE R  95 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R  48 "   -0.015 2.00e-02 2.50e+03   3.04e-02 9.23e+00
        pdb=" C   ILE R  48 "    0.053 2.00e-02 2.50e+03
        pdb=" O   ILE R  48 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   SER R  49 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS R 265 "    0.044 5.00e-02 4.00e+02   6.70e-02 7.18e+00
        pdb=" N   PRO R 266 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO R 266 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO R 266 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1449 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 2858
        2.85 -     3.36: 7764
        3.36 -     3.87: 13973
        3.87 -     4.39: 16331
        4.39 -     4.90: 28041
  Nonbonded interactions: 68967
  Sorted by model distance:
  nonbonded pdb=" O   SER B  67 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.334 2.440
  nonbonded pdb=" OG1 THR R  37 "
            pdb=" OG1 THR R 298 "
     model   vdw
     2.368 2.440
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.382 2.440
  nonbonded pdb=" O   SER R 115 "
            pdb=" OG  SER R 118 "
     model   vdw
     2.407 2.440
  nonbonded pdb=" ND1 HIS B 311 "
            pdb=" OG  SER B 331 "
     model   vdw
     2.430 2.520
  ... (remaining 68962 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             1.430
  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:          6.030
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     26.840
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
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      :  0.006   0.053   8408  Z= 0.392
  Angle     :  0.826  10.489  11388  Z= 0.525
  Chirality :  0.063   0.381   1272
  Planarity :  0.005   0.067   1452
  Dihedral  : 13.331  87.748   3024
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  2.24 %
    Favored  : 96.86 %
  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:  0.85 (0.26), residues: 1031
  helix:  2.05 (0.26), residues: 392
  sheet:  0.11 (0.36), residues: 216
  loop : -0.58 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.027   0.002   TRP A  96 
   HIS   0.002   0.001   HIS R  63 
   PHE   0.023   0.002   PHE B 235 
   TYR   0.021   0.001   TYR A 210 
   ARG   0.005   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 156
  time to evaluate  : 0.921 
Fit side-chains
  outliers start: 8
  outliers final: 0
  residues processed: 163
  average time/residue: 1.1475
  time to fit residues: 199.1289
Evaluate side-chains
  129 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.924 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3237
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 76 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 51 optimal weight:    0.5980
   chunk 40 optimal weight:    0.4980
   chunk 79 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 58 optimal weight:    8.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
A 223 ASN
B  88 ASN
B 220 GLN
B 259 GLN
R  53 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.1246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8408  Z= 0.185
  Angle     :  0.528   6.390  11388  Z= 0.283
  Chirality :  0.043   0.339   1272
  Planarity :  0.004   0.045   1452
  Dihedral  :  4.136  38.086   1141
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 12.23 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.26), residues: 1031
  helix:  2.33 (0.26), residues: 394
  sheet:  0.19 (0.35), residues: 199
  loop : -0.61 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.002   TRP B  82 
   HIS   0.003   0.001   HIS R  63 
   PHE   0.018   0.001   PHE A  70 
   TYR   0.016   0.001   TYR A 210 
   ARG   0.005   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
  outliers start: 12
  outliers final: 5
  residues processed: 138
  average time/residue: 1.1257
  time to fit residues: 166.1371
Evaluate side-chains
  129 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 124
  time to evaluate  : 0.924 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 2
  residues processed: 3
  average time/residue: 1.0967
  time to fit residues: 4.7088
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   chunk 76 optimal weight:    7.9990
   chunk 62 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0170
   chunk 91 optimal weight:    0.9980
   chunk 99 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.9220

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B  88 ASN
B 259 GLN
** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 175 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8408  Z= 0.207
  Angle     :  0.519   6.596  11388  Z= 0.273
  Chirality :  0.042   0.286   1272
  Planarity :  0.004   0.039   1452
  Dihedral  :  4.109  35.350   1141
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 13.92 %
    Favored  : 83.73 %
  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:  0.95 (0.26), residues: 1031
  helix:  2.17 (0.26), residues: 400
  sheet:  0.20 (0.35), residues: 198
  loop : -0.62 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.002   TRP B  82 
   HIS   0.003   0.001   HIS A 209 
   PHE   0.040   0.002   PHE A  70 
   TYR   0.016   0.001   TYR A 210 
   ARG   0.008   0.000   ARG G  27 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.943 
Fit side-chains
  outliers start: 21
  outliers final: 8
  residues processed: 143
  average time/residue: 1.1800
  time to fit residues: 179.9678
Evaluate side-chains
  135 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 127
  time to evaluate  : 1.013 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 3
  residues processed: 5
  average time/residue: 0.7249
  time to fit residues: 5.3510
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 92 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 26 optimal weight:    0.1980
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 131 ASN
A 146 GLN
B  75 GLN
B  88 ASN
B 259 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.1753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8408  Z= 0.182
  Angle     :  0.501   6.780  11388  Z= 0.263
  Chirality :  0.042   0.334   1272
  Planarity :  0.003   0.036   1452
  Dihedral  :  4.019  32.824   1141
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 14.81 %
    Favored  : 81.82 %
  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:  0.99 (0.26), residues: 1031
  helix:  2.16 (0.26), residues: 400
  sheet:  0.29 (0.36), residues: 196
  loop : -0.58 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP B  82 
   HIS   0.003   0.001   HIS A 209 
   PHE   0.041   0.001   PHE A  70 
   TYR   0.021   0.001   TYR R 172 
   ARG   0.004   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 141
  time to evaluate  : 0.928 
Fit side-chains
  outliers start: 30
  outliers final: 8
  residues processed: 153
  average time/residue: 1.1418
  time to fit residues: 186.3133
Evaluate side-chains
  140 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 132
  time to evaluate  : 0.854 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 6
  residues processed: 2
  average time/residue: 0.0736
  time to fit residues: 1.5034
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0670
   chunk 83 optimal weight:    0.6980
   chunk 67 optimal weight:    5.9990
   chunk 0 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    0.7320

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 144 ASN
A 146 GLN
B  88 ASN
B 259 GLN
** N  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8408  Z= 0.185
  Angle     :  0.512   8.431  11388  Z= 0.271
  Chirality :  0.042   0.346   1272
  Planarity :  0.003   0.037   1452
  Dihedral  :  4.007  31.334   1141
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 16.84 %
    Favored  : 80.47 %
  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:  0.90 (0.26), residues: 1031
  helix:  2.06 (0.26), residues: 401
  sheet:  0.30 (0.37), residues: 179
  loop : -0.60 (0.28), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.002   TRP B  82 
   HIS   0.005   0.001   HIS A  82 
   PHE   0.035   0.001   PHE A  70 
   TYR   0.016   0.001   TYR R 172 
   ARG   0.003   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.926 
Fit side-chains
  outliers start: 24
  outliers final: 6
  residues processed: 145
  average time/residue: 1.3101
  time to fit residues: 202.5482
Evaluate side-chains
  138 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 132
  time to evaluate  : 0.867 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 6
  residues processed: 0
  time to fit residues: 1.2824
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0470
   chunk 57 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 45 optimal weight:    5.9990
   chunk 8 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.8280

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
B  88 ASN
B 119 ASN
B 259 GLN
B 293 ASN
** N  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.2108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8408  Z= 0.195
  Angle     :  0.510   7.348  11388  Z= 0.273
  Chirality :  0.041   0.207   1272
  Planarity :  0.003   0.039   1452
  Dihedral  :  4.039  30.609   1141
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 17.62 %
    Favored  : 79.57 %
  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:  0.86 (0.26), residues: 1031
  helix:  2.06 (0.26), residues: 401
  sheet:  0.15 (0.36), residues: 182
  loop : -0.60 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.002   TRP B  82 
   HIS   0.003   0.001   HIS R  63 
   PHE   0.046   0.001   PHE A  70 
   TYR   0.015   0.001   TYR A 210 
   ARG   0.007   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 1.037 
Fit side-chains
  outliers start: 25
  outliers final: 7
  residues processed: 143
  average time/residue: 1.1600
  time to fit residues: 176.8683
Evaluate side-chains
  134 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 127
  time to evaluate  : 0.904 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 4
  residues processed: 3
  average time/residue: 0.4305
  time to fit residues: 2.7316
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 55 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
A 146 GLN
B  75 GLN
B 259 GLN
** N  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8408  Z= 0.200
  Angle     :  0.528  10.629  11388  Z= 0.278
  Chirality :  0.043   0.378   1272
  Planarity :  0.003   0.041   1452
  Dihedral  :  4.061  30.147   1141
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 18.74 %
    Favored  : 79.35 %
  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:  0.80 (0.26), residues: 1031
  helix:  2.02 (0.26), residues: 401
  sheet:  0.07 (0.35), residues: 184
  loop : -0.62 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.002   TRP R 310 
   HIS   0.003   0.001   HIS A 209 
   PHE   0.040   0.001   PHE A  70 
   TYR   0.015   0.001   TYR A 210 
   ARG   0.005   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.966 
Fit side-chains
  outliers start: 17
  outliers final: 6
  residues processed: 136
  average time/residue: 1.2071
  time to fit residues: 174.7052
Evaluate side-chains
  133 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 127
  time to evaluate  : 0.965 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 5
  residues processed: 1
  average time/residue: 0.0717
  time to fit residues: 1.2991
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:    0.3980
   chunk 19 optimal weight:    0.0670
   chunk 18 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 76 optimal weight:    7.9990
   chunk 88 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.5920

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8408  Z= 0.175
  Angle     :  0.537  11.133  11388  Z= 0.278
  Chirality :  0.043   0.352   1272
  Planarity :  0.003   0.041   1452
  Dihedral  :  3.966  27.085   1141
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 19.64 %
    Favored  : 78.79 %
  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 (0.26), residues: 1031
  helix:  1.98 (0.26), residues: 401
  sheet:  0.14 (0.35), residues: 177
  loop : -0.66 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.025   0.002   TRP R 310 
   HIS   0.003   0.001   HIS A 209 
   PHE   0.037   0.001   PHE A  70 
   TYR   0.016   0.001   TYR N  60 
   ARG   0.006   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.975 
Fit side-chains
  outliers start: 14
  outliers final: 6
  residues processed: 141
  average time/residue: 1.1680
  time to fit residues: 175.7211
Evaluate side-chains
  134 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 128
  time to evaluate  : 0.951 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 5
  residues processed: 1
  average time/residue: 0.0768
  time to fit residues: 1.4429
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 93 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 71 optimal weight:    7.9990
   chunk 27 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 95 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
B  75 GLN
B  88 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8408  Z= 0.203
  Angle     :  0.533   9.551  11388  Z= 0.281
  Chirality :  0.042   0.339   1272
  Planarity :  0.003   0.043   1452
  Dihedral  :  4.035  31.596   1141
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 20.43 %
    Favored  : 78.00 %
  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:  0.79 (0.26), residues: 1031
  helix:  1.99 (0.26), residues: 401
  sheet:  0.04 (0.35), residues: 184
  loop : -0.60 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.030   0.002   TRP R 310 
   HIS   0.003   0.001   HIS A 209 
   PHE   0.046   0.001   PHE A  70 
   TYR   0.018   0.001   TYR N  60 
   ARG   0.007   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.986 
Fit side-chains
  outliers start: 14
  outliers final: 8
  residues processed: 139
  average time/residue: 1.2680
  time to fit residues: 187.4196
Evaluate side-chains
  134 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 126
  time to evaluate  : 0.963 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 7
  residues processed: 1
  average time/residue: 1.8386
  time to fit residues: 3.1929
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   chunk 100 optimal weight:    0.8980
   chunk 92 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B  88 ASN
** N  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   8408  Z= 0.235
  Angle     :  0.557  12.957  11388  Z= 0.292
  Chirality :  0.043   0.438   1272
  Planarity :  0.003   0.043   1452
  Dihedral  :  4.125  33.778   1141
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 20.65 %
    Favored  : 78.11 %
  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:  0.72 (0.26), residues: 1031
  helix:  1.91 (0.26), residues: 401
  sheet: -0.05 (0.35), residues: 187
  loop : -0.59 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.037   0.002   TRP R 310 
   HIS   0.004   0.001   HIS R  63 
   PHE   0.045   0.002   PHE A  70 
   TYR   0.018   0.001   TYR A 210 
   ARG   0.007   0.000   ARG N  19 

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.945 
Fit side-chains
  outliers start: 11
  outliers final: 9
  residues processed: 138
  average time/residue: 1.2452
  time to fit residues: 182.9062
Evaluate side-chains
  135 residues out of total 898 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 126
  time to evaluate  : 0.957 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 8
  residues processed: 1
  average time/residue: 0.0773
  time to fit residues: 1.4732
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0770
   chunk 22 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 82 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 70 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0070
   chunk 57 optimal weight:    7.9990
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.161043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.127659 restraints weight = 10350.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.41
r_work: 0.3406 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.054   8408  Z= 0.162
  Angle     :  0.526  13.525  11388  Z= 0.274
  Chirality :  0.042   0.438   1272
  Planarity :  0.003   0.043   1452
  Dihedral  :  3.949  29.646   1141
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 21.10 %
    Favored  : 77.33 %
  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 (0.26), residues: 1031
  helix:  2.00 (0.26), residues: 401
  sheet:  0.05 (0.35), residues: 180
  loop : -0.64 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.040   0.002   TRP R 310 
   HIS   0.003   0.001   HIS A 209 
   PHE   0.043   0.001   PHE A  70 
   TYR   0.019   0.001   TYR N  60 
   ARG   0.007   0.000   ARG N  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3387.29 seconds
wall clock time: 60 minutes 49.83 seconds (3649.83 seconds total)