Starting phenix.real_space_refine
on Fri Dec  8 21:02:23 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6r_36012/12_2023/8j6r_36012_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6r_36012/12_2023/8j6r_36012.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6r_36012/12_2023/8j6r_36012.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6r_36012/12_2023/8j6r_36012.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6r_36012/12_2023/8j6r_36012_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6r_36012/12_2023/8j6r_36012_updated.pdb"
  }
  resolution = 2.76
  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=   0.002 sd=   0.034
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      69      5.16       5
     C    5811      2.51       5
     N    1554      2.21       5
     O    1686      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "S TYR  190": "CD1" <-> "CD2" "CE1" <-> "CE2"
  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: 9120
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1811
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "S"
      Number of atoms: 1795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1795
          Classifications: {'peptide': 234}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2420
          Classifications: {'peptide': 295}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 284}
    Chain: "R"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 43
          Unusual residues: {'FI7': 1, 'NAG': 1}
          Classifications: {'undetermined': 2, 'water': 1}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.51, per 1000 atoms: 0.60
  Number of scatterers: 9120
  At special positions: 0
  Unit cell: (108.498, 122.694, 112.554, 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      69     16.00
     O    1686      8.00
     N    1554      7.00
     C    5811      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  18 " - pdb=" SG  CYS R 183 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  19 " - pdb=" SG  CYS R 266 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 100 " - pdb=" SG  CYS R 177 " 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
  Links applied
    NAG-ASN
      " NAG R 402 " - " ASN R  17 "
  Time building additional restraints: 3.28
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2156

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      27 helices and 13 sheets defined
      33.4% alpha, 22.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 4.297A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 53
      removed outlier: 3.805A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 210
      No H-bonds generated for 'chain 'A' and resid 208 through 210'
    Processing helix  chain 'A' and resid 212 through 215
    Processing helix  chain 'A' and resid 242 through 254
    Processing helix  chain 'A' and resid 271 through 277
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 4.003A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
    Processing helix  chain 'B' and resid 4 through 24
      removed outlier: 4.512A  pdb=" N   ALA B  11 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 34
    Processing helix  chain 'G' and resid 8 through 23
    Processing helix  chain 'G' and resid 30 through 43
    Processing helix  chain 'G' and resid 45 through 47
      No H-bonds generated for 'chain 'G' and resid 45 through 47'
    Processing helix  chain 'G' and resid 56 through 58
      No H-bonds generated for 'chain 'G' and resid 56 through 58'
    Processing helix  chain 'S' and resid 29 through 31
      No H-bonds generated for 'chain 'S' and resid 29 through 31'
    Processing helix  chain 'S' and resid 88 through 90
      No H-bonds generated for 'chain 'S' and resid 88 through 90'
    Processing helix  chain 'S' and resid 221 through 223
      No H-bonds generated for 'chain 'S' and resid 221 through 223'
    Processing helix  chain 'R' and resid 24 through 54
      Proline residue:  R  31  - end of helix
    Processing helix  chain 'R' and resid 61 through 89
      removed outlier: 4.304A  pdb=" N   CYS R  79 " --> pdb=" O   LEU R  75 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   LEU R  80 " --> pdb=" O   LEU R  76 " (cutoff:3.500A)
      Proline residue:  R  81  - end of helix
      removed outlier: 3.825A  pdb=" N   ARG R  89 " --> pdb=" O   ASP R  85 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 97 through 129
    Processing helix  chain 'R' and resid 135 through 138
    Processing helix  chain 'R' and resid 141 through 162
      removed outlier: 5.183A  pdb=" N   HIS R 161 " --> pdb=" O   GLY R 157 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   LEU R 162 " --> pdb=" O   LEU R 158 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 188 through 217
      removed outlier: 3.798A  pdb=" N   LEU R 194 " --> pdb=" O   GLU R 190 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   PHE R 197 " --> pdb=" O   PHE R 193 " (cutoff:3.500A)
      Proline residue:  R 200  - end of helix
    Processing helix  chain 'R' and resid 220 through 222
      No H-bonds generated for 'chain 'R' and resid 220 through 222'
    Processing helix  chain 'R' and resid 224 through 260
      Proline residue:  R 246  - end of helix
    Processing helix  chain 'R' and resid 266 through 268
      No H-bonds generated for 'chain 'R' and resid 266 through 268'
    Processing helix  chain 'R' and resid 270 through 294
      removed outlier: 3.812A  pdb=" N   PHE R 277 " --> pdb=" O   ASP R 273 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER R 287 " --> pdb=" O   THR R 283 " (cutoff:3.500A)
      Proline residue:  R 291  - end of helix
    Processing sheet with id=  A, first strand: chain 'A' and resid 319 through 323
      removed outlier: 6.760A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 8.087A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.970A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.057A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.017A  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: 7.104A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.897A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.147A  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: 6.649A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.241A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.678A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.084A  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: 6.850A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.470A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.400A  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: 6.667A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.884A  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: 6.470A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.357A  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: 6.569A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=  J, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.213A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.351A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   ALA S  40 " --> pdb=" O   LEU S  45 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   LEU S  45 " --> pdb=" O   ALA S  40 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'S' and resid 146 through 148
      removed outlier: 6.498A  pdb=" N   LYS S 244 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  K
    Processing sheet with id=  L, first strand: chain 'S' and resid 155 through 160
      removed outlier: 3.786A  pdb=" N   ALA S 211 " --> pdb=" O   SER S 208 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'S' and resid 225 through 231
      removed outlier: 3.693A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)

    393 hydrogen bonds defined for protein.
    1137 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: 2.68

  Time building geometry restraints manager: 3.59 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2928
        1.34 -     1.46: 2278
        1.46 -     1.58: 4012
        1.58 -     1.71: 1
        1.71 -     1.83: 100
  Bond restraints: 9319
  Sorted by residual:
  bond pdb=" C20 FI7 R 401 "
       pdb=" N19 FI7 R 401 "
    ideal  model  delta    sigma   weight residual
    1.396  1.486 -0.090 2.00e-02 2.50e+03 2.01e+01
  bond pdb=" C07 FI7 R 401 "
       pdb=" C08 FI7 R 401 "
    ideal  model  delta    sigma   weight residual
    1.466  1.546 -0.080 2.00e-02 2.50e+03 1.61e+01
  bond pdb=" C04 FI7 R 401 "
       pdb=" C05 FI7 R 401 "
    ideal  model  delta    sigma   weight residual
    1.483  1.563 -0.080 2.00e-02 2.50e+03 1.61e+01
  bond pdb=" C05 FI7 R 401 "
       pdb=" O16 FI7 R 401 "
    ideal  model  delta    sigma   weight residual
    1.330  1.406 -0.076 2.00e-02 2.50e+03 1.44e+01
  bond pdb=" C17 FI7 R 401 "
       pdb=" N19 FI7 R 401 "
    ideal  model  delta    sigma   weight residual
    1.348  1.420 -0.072 2.00e-02 2.50e+03 1.30e+01
  ... (remaining 9314 not shown)

  Histogram of bond angle deviations from ideal:
       99.53 -   107.00: 207
      107.00 -   114.46: 5464
      114.46 -   121.93: 4923
      121.93 -   129.40: 1939
      129.40 -   136.86: 77
  Bond angle restraints: 12610
  Sorted by residual:
  angle pdb=" C   MET R 167 "
        pdb=" N   PRO R 168 "
        pdb=" CA  PRO R 168 "
      ideal   model   delta    sigma   weight residual
     127.00  136.86   -9.86 2.40e+00 1.74e-01 1.69e+01
  angle pdb=" C   ASP R  14 "
        pdb=" N   LYS R  15 "
        pdb=" CA  LYS R  15 "
      ideal   model   delta    sigma   weight residual
     121.54  129.12   -7.58 1.91e+00 2.74e-01 1.57e+01
  angle pdb=" C   MET R 167 "
        pdb=" N   PRO R 168 "
        pdb=" CD  PRO R 168 "
      ideal   model   delta    sigma   weight residual
     120.60  112.67    7.93 2.20e+00 2.07e-01 1.30e+01
  angle pdb=" C02 FI7 R 401 "
        pdb=" C17 FI7 R 401 "
        pdb=" N19 FI7 R 401 "
      ideal   model   delta    sigma   weight residual
     113.44  123.58  -10.14 3.00e+00 1.11e-01 1.14e+01
  angle pdb=" N   HIS R 184 "
        pdb=" CA  HIS R 184 "
        pdb=" C   HIS R 184 "
      ideal   model   delta    sigma   weight residual
     111.30  115.76   -4.46 1.36e+00 5.41e-01 1.08e+01
  ... (remaining 12605 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.57: 4976
       16.57 -    33.13: 451
       33.13 -    49.70: 102
       49.70 -    66.26: 17
       66.26 -    82.83: 7
  Dihedral angle restraints: 5553
    sinusoidal: 2218
      harmonic: 3335
  Sorted by residual:
  dihedral pdb=" CB  CYS R 100 "
           pdb=" SG  CYS R 100 "
           pdb=" SG  CYS R 177 "
           pdb=" CB  CYS R 177 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.69  -45.69     1      1.00e+01 1.00e-02 2.89e+01
  dihedral pdb=" CB  CYS R  18 "
           pdb=" SG  CYS R  18 "
           pdb=" SG  CYS R 183 "
           pdb=" CB  CYS R 183 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.83   39.17     1      1.00e+01 1.00e-02 2.16e+01
  dihedral pdb=" CA  PHE A 323 "
           pdb=" C   PHE A 323 "
           pdb=" N   THR A 324 "
           pdb=" CA  THR A 324 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.03  -19.97     0      5.00e+00 4.00e-02 1.59e+01
  ... (remaining 5550 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.244: 1411
       0.244 -    0.489: 0
       0.489 -    0.733: 0
       0.733 -    0.977: 0
       0.977 -    1.222: 1
  Chirality restraints: 1412
  Sorted by residual:
  chirality pdb=" C1  NAG R 402 "
            pdb=" ND2 ASN R  17 "
            pdb=" C2  NAG R 402 "
            pdb=" O5  NAG R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.18   -1.22 2.00e-01 2.50e+01 3.73e+01
  chirality pdb=" CA  TRP R  59 "
            pdb=" N   TRP R  59 "
            pdb=" C   TRP R  59 "
            pdb=" CB  TRP R  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CA  TYR S 190 "
            pdb=" N   TYR S 190 "
            pdb=" C   TYR S 190 "
            pdb=" CB  TYR S 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 1409 not shown)

  Planarity restraints: 1595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG R 402 "    0.350 2.00e-02 2.50e+03   3.00e-01 1.13e+03
        pdb=" C7  NAG R 402 "   -0.087 2.00e-02 2.50e+03
        pdb=" C8  NAG R 402 "    0.154 2.00e-02 2.50e+03
        pdb=" N2  NAG R 402 "   -0.533 2.00e-02 2.50e+03
        pdb=" O7  NAG R 402 "    0.115 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP S  74 "   -0.059 5.00e-02 4.00e+02   8.91e-02 1.27e+01
        pdb=" N   PRO S  75 "    0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO S  75 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO S  75 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN R  17 "    0.026 2.00e-02 2.50e+03   2.89e-02 1.05e+01
        pdb=" CG  ASN R  17 "   -0.005 2.00e-02 2.50e+03
        pdb=" OD1 ASN R  17 "   -0.009 2.00e-02 2.50e+03
        pdb=" ND2 ASN R  17 "   -0.047 2.00e-02 2.50e+03
        pdb=" C1  NAG R 402 "    0.035 2.00e-02 2.50e+03
  ... (remaining 1592 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 137
        2.67 -     3.23: 8098
        3.23 -     3.79: 13952
        3.79 -     4.34: 18785
        4.34 -     4.90: 32054
  Nonbonded interactions: 73026
  Sorted by model distance:
  nonbonded pdb=" O   GLU R 196 "
            pdb=" CG  PRO R 200 "
     model   vdw
     2.116 3.440
  nonbonded pdb=" O   GLU R 196 "
            pdb=" CD  PRO R 200 "
     model   vdw
     2.125 3.440
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.208 2.440
  nonbonded pdb=" O   LYS R  60 "
            pdb=" N   ARG R  63 "
     model   vdw
     2.228 2.520
  nonbonded pdb=" O   LEU B  30 "
            pdb=" OG1 THR B  34 "
     model   vdw
     2.280 2.440
  ... (remaining 73021 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:             0.330
  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:          1.980
  Check model and map are aligned:         0.150
  Set scattering table:                    0.090
  Process input model:                     28.060
  Find NCS groups from input model:        0.270
  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:12.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
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      :  0.004   0.090   9319  Z= 0.282
  Angle     :  0.625  10.140  12610  Z= 0.325
  Chirality :  0.055   1.222   1412
  Planarity :  0.009   0.300   1594
  Dihedral  : 13.554  82.831   3382
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.52 (0.25), residues: 1137
  helix:  1.31 (0.27), residues: 387
  sheet:  0.50 (0.31), residues: 295
  loop : -0.53 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP R  59 
   HIS   0.004   0.001   HIS R 161 
   PHE   0.015   0.001   PHE R  52 
   TYR   0.016   0.001   TYR S 190 
   ARG   0.004   0.000   ARG R 253 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 1.052 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 1.1800
  time to fit residues: 258.7212
Evaluate side-chains
  190 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 1.051 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4627
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0570
   chunk 57 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 53 optimal weight:    0.3980
   chunk 65 optimal weight:    0.4980
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
B 176 GLN
S  82 GLN
S 186 GLN
** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.0827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9319  Z= 0.156
  Angle     :  0.493   6.390  12610  Z= 0.263
  Chirality :  0.041   0.173   1412
  Planarity :  0.004   0.068   1594
  Dihedral  :  5.081  40.000   1290
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  9.95 %
    Favored  : 88.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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 (0.25), residues: 1137
  helix:  1.58 (0.27), residues: 387
  sheet:  0.65 (0.31), residues: 284
  loop : -0.53 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.001   TRP R  59 
   HIS   0.005   0.001   HIS R 161 
   PHE   0.009   0.001   PHE B 199 
   TYR   0.022   0.001   TYR S 190 
   ARG   0.008   0.000   ARG R 270 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 194
  time to evaluate  : 0.963 
Fit side-chains
  outliers start: 18
  outliers final: 9
  residues processed: 200
  average time/residue: 1.2833
  time to fit residues: 273.0738
Evaluate side-chains
  199 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 190
  time to evaluate  : 1.086 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 4
  residues processed: 5
  average time/residue: 1.0148
  time to fit residues: 7.0145
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 28 optimal weight:    0.3980
   chunk 101 optimal weight:    0.5980
   chunk 110 optimal weight:    0.5980
   chunk 90 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
B 340 ASN
S  82 GLN
R 110 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
moved from start:          0.1058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9319  Z= 0.167
  Angle     :  0.479   6.232  12610  Z= 0.257
  Chirality :  0.041   0.176   1412
  Planarity :  0.004   0.063   1594
  Dihedral  :  4.985  45.162   1290
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 12.56 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.76 (0.25), residues: 1137
  helix:  1.65 (0.27), residues: 388
  sheet:  0.63 (0.31), residues: 285
  loop : -0.51 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP R  59 
   HIS   0.004   0.001   HIS A 188 
   PHE   0.009   0.001   PHE R 117 
   TYR   0.022   0.001   TYR S 190 
   ARG   0.009   0.000   ARG R 270 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 192
  time to evaluate  : 1.101 
Fit side-chains
  outliers start: 17
  outliers final: 7
  residues processed: 199
  average time/residue: 1.3093
  time to fit residues: 278.2778
Evaluate side-chains
  200 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 193
  time to evaluate  : 1.007 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 4
  residues processed: 3
  average time/residue: 1.0098
  time to fit residues: 4.6814
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0170
   chunk 48 optimal weight:    4.9990
   chunk 68 optimal weight:    0.6980
   chunk 102 optimal weight:    0.9980
   chunk 108 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 96 optimal weight:    0.4980
   chunk 29 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   overall best weight:    0.8420

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN
S 186 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9319  Z= 0.197
  Angle     :  0.491   6.212  12610  Z= 0.261
  Chirality :  0.041   0.190   1412
  Planarity :  0.004   0.062   1594
  Dihedral  :  5.042  47.190   1290
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.97 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.25), residues: 1137
  helix:  1.62 (0.27), residues: 389
  sheet:  0.69 (0.30), residues: 292
  loop : -0.59 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP B  82 
   HIS   0.005   0.001   HIS A 188 
   PHE   0.011   0.001   PHE R 117 
   TYR   0.022   0.001   TYR S 190 
   ARG   0.008   0.000   ARG R 270 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 191
  time to evaluate  : 1.170 
Fit side-chains
  outliers start: 17
  outliers final: 12
  residues processed: 200
  average time/residue: 1.2374
  time to fit residues: 263.9356
Evaluate side-chains
  199 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 187
  time to evaluate  : 1.036 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 5
  residues processed: 7
  average time/residue: 0.4796
  time to fit residues: 5.3423
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 92 optimal weight:    0.4980
   chunk 74 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 97 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN
S 186 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9319  Z= 0.264
  Angle     :  0.528   7.739  12610  Z= 0.280
  Chirality :  0.043   0.209   1412
  Planarity :  0.004   0.062   1594
  Dihedral  :  5.245  48.685   1290
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 15.98 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.61 (0.25), residues: 1137
  helix:  1.49 (0.27), residues: 388
  sheet:  0.62 (0.30), residues: 292
  loop : -0.63 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.002   TRP B  82 
   HIS   0.005   0.001   HIS A 188 
   PHE   0.015   0.002   PHE R 117 
   TYR   0.023   0.002   TYR S 190 
   ARG   0.009   0.001   ARG R 270 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 186
  time to evaluate  : 1.157 
Fit side-chains
  outliers start: 21
  outliers final: 10
  residues processed: 197
  average time/residue: 1.3601
  time to fit residues: 284.5563
Evaluate side-chains
  194 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 184
  time to evaluate  : 0.911 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 5
  residues processed: 5
  average time/residue: 0.6360
  time to fit residues: 4.9463
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 104 optimal weight:    3.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9319  Z= 0.225
  Angle     :  0.517   6.918  12610  Z= 0.275
  Chirality :  0.042   0.198   1412
  Planarity :  0.004   0.062   1594
  Dihedral  :  5.250  49.109   1290
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.58 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.60 (0.25), residues: 1137
  helix:  1.49 (0.27), residues: 387
  sheet:  0.60 (0.30), residues: 292
  loop : -0.64 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP B  82 
   HIS   0.004   0.001   HIS A 188 
   PHE   0.011   0.001   PHE R 276 
   TYR   0.023   0.001   TYR S 190 
   ARG   0.011   0.000   ARG R 270 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 186
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
  outliers start: 21
  outliers final: 11
  residues processed: 199
  average time/residue: 1.2910
  time to fit residues: 273.5784
Evaluate side-chains
  195 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 184
  time to evaluate  : 1.046 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 7
  residues processed: 4
  average time/residue: 0.3308
  time to fit residues: 3.0725
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0070
   chunk 79 optimal weight:    0.9980
   chunk 91 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 107 optimal weight:    0.7980
   chunk 67 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0170
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN
S 186 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9319  Z= 0.150
  Angle     :  0.481   6.549  12610  Z= 0.259
  Chirality :  0.041   0.171   1412
  Planarity :  0.004   0.060   1594
  Dihedral  :  5.017  47.498   1290
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.39 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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 (0.25), residues: 1137
  helix:  1.57 (0.27), residues: 389
  sheet:  0.64 (0.30), residues: 292
  loop : -0.57 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP B  82 
   HIS   0.003   0.001   HIS A 188 
   PHE   0.008   0.001   PHE B 199 
   TYR   0.020   0.001   TYR S 190 
   ARG   0.012   0.000   ARG R 270 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 1.001 
Fit side-chains
  outliers start: 20
  outliers final: 13
  residues processed: 193
  average time/residue: 1.2775
  time to fit residues: 262.6221
Evaluate side-chains
  189 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 176
  time to evaluate  : 0.934 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 10
  residues processed: 3
  average time/residue: 1.5965
  time to fit residues: 6.5320
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 73 optimal weight:    8.9990
   chunk 53 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0270
   chunk 84 optimal weight:    0.9990
   chunk 98 optimal weight:    0.0870
   chunk 103 optimal weight:    0.8980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9319  Z= 0.161
  Angle     :  0.487   7.839  12610  Z= 0.261
  Chirality :  0.041   0.177   1412
  Planarity :  0.004   0.059   1594
  Dihedral  :  4.990  47.821   1290
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 17.19 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.71 (0.25), residues: 1137
  helix:  1.57 (0.27), residues: 389
  sheet:  0.60 (0.30), residues: 296
  loop : -0.53 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP B  82 
   HIS   0.003   0.001   HIS A 188 
   PHE   0.008   0.001   PHE R 276 
   TYR   0.021   0.001   TYR S 190 
   ARG   0.012   0.000   ARG R 270 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 179
  time to evaluate  : 0.995 
Fit side-chains
  outliers start: 24
  outliers final: 11
  residues processed: 195
  average time/residue: 1.2214
  time to fit residues: 254.4527
Evaluate side-chains
  192 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 181
  time to evaluate  : 1.036 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 9
  residues processed: 2
  average time/residue: 0.0844
  time to fit residues: 1.7623
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.6980
   chunk 100 optimal weight:    3.9990
   chunk 103 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 78 optimal weight:    0.0770
   chunk 30 optimal weight:    0.9990
   chunk 90 optimal weight:    0.7980
   chunk 95 optimal weight:    0.5980
   chunk 66 optimal weight:    0.0670
   chunk 106 optimal weight:    0.7980
   overall best weight:    0.4276

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 186 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.1626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   9319  Z= 0.149
  Angle     :  0.485   8.317  12610  Z= 0.261
  Chirality :  0.041   0.166   1412
  Planarity :  0.004   0.059   1594
  Dihedral  :  4.884  47.059   1290
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 18.29 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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 (0.25), residues: 1137
  helix:  1.60 (0.27), residues: 389
  sheet:  0.63 (0.30), residues: 301
  loop : -0.49 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP R 188 
   HIS   0.003   0.001   HIS A 188 
   PHE   0.008   0.001   PHE B 199 
   TYR   0.019   0.001   TYR S 190 
   ARG   0.007   0.000   ARG R 270 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 176
  time to evaluate  : 1.005 
Fit side-chains
  outliers start: 15
  outliers final: 8
  residues processed: 190
  average time/residue: 1.2816
  time to fit residues: 259.7001
Evaluate side-chains
  181 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 173
  time to evaluate  : 1.038 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 8
  residues processed: 0
  time to fit residues: 1.4629
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 111 optimal weight:    0.0670
   chunk 102 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 68 optimal weight:    0.3980
   chunk 54 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 94 optimal weight:    0.5980
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9319  Z= 0.171
  Angle     :  0.498   8.629  12610  Z= 0.268
  Chirality :  0.041   0.177   1412
  Planarity :  0.004   0.059   1594
  Dihedral  :  4.934  47.674   1290
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 19.10 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.25), residues: 1137
  helix:  1.61 (0.27), residues: 390
  sheet:  0.57 (0.30), residues: 301
  loop : -0.49 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP R 188 
   HIS   0.003   0.001   HIS A 188 
   PHE   0.008   0.001   PHE R 117 
   TYR   0.020   0.001   TYR S 190 
   ARG   0.014   0.000   ARG R 270 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 178
  time to evaluate  : 1.039 
Fit side-chains
  outliers start: 10
  outliers final: 8
  residues processed: 188
  average time/residue: 1.2618
  time to fit residues: 253.2425
Evaluate side-chains
  186 residues out of total 995 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 178
  time to evaluate  : 1.108 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 8
  residues processed: 0
  time to fit residues: 1.3936
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:   10.0000
   chunk 88 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 78 optimal weight:    5.9990
   chunk 5 optimal weight:    0.4980
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 186 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.145651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.123933 restraints weight = 11974.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 1.97
r_work: 0.3482 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   9319  Z= 0.305
  Angle     :  0.571   8.124  12610  Z= 0.303
  Chirality :  0.044   0.216   1412
  Planarity :  0.004   0.060   1594
  Dihedral  :  5.333  51.644   1290
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 18.69 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.54 (0.25), residues: 1137
  helix:  1.40 (0.27), residues: 388
  sheet:  0.53 (0.30), residues: 297
  loop : -0.62 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.002   TRP B  82 
   HIS   0.005   0.001   HIS A 188 
   PHE   0.016   0.002   PHE R 117 
   TYR   0.023   0.002   TYR S 190 
   ARG   0.017   0.001   ARG R 270 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4539.36 seconds
wall clock time: 81 minutes 8.85 seconds (4868.85 seconds total)