Starting phenix.real_space_refine
on Fri Dec  8 18:41:53 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wig_32529/12_2023/7wig_32529_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wig_32529/12_2023/7wig_32529.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wig_32529/12_2023/7wig_32529.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wig_32529/12_2023/7wig_32529.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wig_32529/12_2023/7wig_32529_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wig_32529/12_2023/7wig_32529_updated.pdb"
  }
  resolution = 2.7
  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=   0.033
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      67      5.16       5
     C    5697      2.51       5
     N    1507      2.21       5
     O    1660      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: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 8931
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2234
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2234
          Classifications: {'peptide': 283}
          Link IDs: {'PTRANS': 11, 'TRANS': 271}
          Chain breaks: 1
    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: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'9FI': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.53, per 1000 atoms: 0.62
  Number of scatterers: 8931
  At special positions: 0
  Unit cell: (106.47, 126.75, 111.54, 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      67     16.00
     O    1660      8.00
     N    1507      7.00
     C    5697      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 115 " - pdb=" SG  CYS R 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " 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: 3.53
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2126

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      25 helices and 15 sheets defined
      34.9% alpha, 22.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.86
  Creating SS restraints...
    Processing helix  chain 'R' and resid 42 through 68
    Processing helix  chain 'R' and resid 77 through 104
      Proline residue:  R  97  - end of helix
      removed outlier: 4.043A  pdb=" N   ALA R 100 " --> pdb=" O   LEU R  96 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   MET R 101 " --> pdb=" O   PRO R  97 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   GLN R 102 " --> pdb=" O   PHE R  98 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 113 through 144
      removed outlier: 3.891A  pdb=" N   PHE R 127 " --> pdb=" O   GLY R 123 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ILE R 130 " --> pdb=" O   GLN R 126 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE R 131 " --> pdb=" O   PHE R 127 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   CYS R 132 " --> pdb=" O   THR R 128 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 149 through 153
      removed outlier: 4.198A  pdb=" N   TRP R 153 " --> pdb=" O   LYS R 149 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 149 through 153'
    Processing helix  chain 'R' and resid 156 through 180
      removed outlier: 3.888A  pdb=" N   ILE R 174 " --> pdb=" O   SER R 170 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   LEU R 175 " --> pdb=" O   LEU R 171 " (cutoff:3.500A)
      Proline residue:  R 176  - end of helix
    Processing helix  chain 'R' and resid 203 through 242
      removed outlier: 5.273A  pdb=" N   VAL R 219 " --> pdb=" O   LEU R 215 " (cutoff:3.500A)
      Proline residue:  R 220  - end of helix
    Processing helix  chain 'R' and resid 247 through 281
      Proline residue:  R 271  - end of helix
    Processing helix  chain 'R' and resid 288 through 313
      removed outlier: 3.752A  pdb=" N   SER R 305 " --> pdb=" O   THR R 301 " (cutoff:3.500A)
      Proline residue:  R 309  - end of helix
    Processing helix  chain 'R' and resid 317 through 326
      removed outlier: 3.841A  pdb=" N   SER R 322 " --> pdb=" O   ASN R 318 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   ASN R 325 " --> pdb=" O   LYS R 321 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   VAL R 326 " --> pdb=" O   SER R 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 7 through 31
      removed outlier: 3.550A  pdb=" N   GLU A  28 " --> pdb=" O   ARG A  24 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 53
      removed outlier: 3.733A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
      removed outlier: 4.197A  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
      removed outlier: 3.605A  pdb=" N   PHE A 215 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 212 through 215'
    Processing helix  chain 'A' and resid 242 through 254
    Processing helix  chain 'A' and resid 271 through 278
    Processing helix  chain 'A' and resid 283 through 285
      No H-bonds generated for 'chain 'A' and resid 283 through 285'
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 3.761A  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 25
    Processing helix  chain 'B' and resid 30 through 36
      removed outlier: 5.516A  pdb=" N   ASN B  36 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 23
    Processing helix  chain 'G' and resid 30 through 43
    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 sheet with id=  A, first strand: chain 'R' and resid 181 through 183
    Processing sheet with id=  B, first strand: chain 'A' and resid 319 through 323
      removed outlier: 6.580A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.827A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.740A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.942A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.750A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.196A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.583A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.963A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 221 through 223
      removed outlier: 4.365A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.705A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.513A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.736A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=  K, first strand: chain 'S' and resid 10 through 12
    Processing sheet with id=  L, first strand: chain 'S' and resid 95 through 99
      removed outlier: 5.843A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.156A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   ALA S  40 " --> pdb=" O   LEU S  45 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   LEU S  45 " --> pdb=" O   ALA S  40 " (cutoff:3.500A)
    Processing sheet with id=  M, first strand: chain 'S' and resid 146 through 148
      removed outlier: 6.859A  pdb=" N   LYS S 244 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  M
    Processing sheet with id=  N, first strand: chain 'S' and resid 155 through 160
    Processing sheet with id=  O, first strand: chain 'S' and resid 226 through 231
      removed outlier: 3.679A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.579A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)

    410 hydrogen bonds defined for protein.
    1188 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: 2.66

  Time building geometry restraints manager: 3.75 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1444
        1.30 -     1.43: 2413
        1.43 -     1.56: 5163
        1.56 -     1.69: 1
        1.69 -     1.82: 98
  Bond restraints: 9119
  Sorted by residual:
  bond pdb=" C19 9FI R 401 "
       pdb=" N1  9FI R 401 "
    ideal  model  delta    sigma   weight residual
    1.369  1.492 -0.123 2.00e-02 2.50e+03 3.78e+01
  bond pdb=" C11 9FI R 401 "
       pdb=" N1  9FI R 401 "
    ideal  model  delta    sigma   weight residual
    1.455  1.571 -0.116 2.00e-02 2.50e+03 3.37e+01
  bond pdb=" C20 9FI R 401 "
       pdb=" N3  9FI R 401 "
    ideal  model  delta    sigma   weight residual
    1.444  1.334  0.110 2.00e-02 2.50e+03 3.00e+01
  bond pdb=" C12 9FI R 401 "
       pdb=" N1  9FI R 401 "
    ideal  model  delta    sigma   weight residual
    1.456  1.347  0.109 2.00e-02 2.50e+03 2.97e+01
  bond pdb=" C   PHE R 127 "
       pdb=" O   PHE R 127 "
    ideal  model  delta    sigma   weight residual
    1.235  1.168  0.067 1.33e-02 5.65e+03 2.53e+01
  ... (remaining 9114 not shown)

  Histogram of bond angle deviations from ideal:
       86.16 -    95.81: 1
       95.81 -   105.46: 136
      105.46 -   115.11: 5599
      115.11 -   124.77: 6455
      124.77 -   134.42: 159
  Bond angle restraints: 12350
  Sorted by residual:
  angle pdb=" C22 9FI R 401 "
        pdb=" C20 9FI R 401 "
        pdb=" N3  9FI R 401 "
      ideal   model   delta    sigma   weight residual
     110.53   86.16   24.37 3.00e+00 1.11e-01 6.60e+01
  angle pdb=" N   ILE R 124 "
        pdb=" CA  ILE R 124 "
        pdb=" C   ILE R 124 "
      ideal   model   delta    sigma   weight residual
     111.81  105.17    6.64 8.60e-01 1.35e+00 5.96e+01
  angle pdb=" C6  9FI R 401 "
        pdb=" C12 9FI R 401 "
        pdb=" N1  9FI R 401 "
      ideal   model   delta    sigma   weight residual
     111.52  127.12  -15.60 3.00e+00 1.11e-01 2.70e+01
  angle pdb=" N   ALA R 307 "
        pdb=" CA  ALA R 307 "
        pdb=" C   ALA R 307 "
      ideal   model   delta    sigma   weight residual
     111.36  116.61   -5.25 1.09e+00 8.42e-01 2.32e+01
  angle pdb=" C   TYR R 302 "
        pdb=" N   ALA R 303 "
        pdb=" CA  ALA R 303 "
      ideal   model   delta    sigma   weight residual
     120.28  126.19   -5.91 1.34e+00 5.57e-01 1.94e+01
  ... (remaining 12345 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.36: 4880
       16.36 -    32.72: 432
       32.72 -    49.07: 94
       49.07 -    65.43: 16
       65.43 -    81.79: 7
  Dihedral angle restraints: 5429
    sinusoidal: 2132
      harmonic: 3297
  Sorted by residual:
  dihedral pdb=" CA  LEU R 105 "
           pdb=" C   LEU R 105 "
           pdb=" N   VAL R 106 "
           pdb=" CA  VAL R 106 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.70  -18.30     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  GLU B 130 "
           pdb=" C   GLU B 130 "
           pdb=" N   GLY B 131 "
           pdb=" CA  GLY B 131 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.01   17.99     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  TYR S 190 "
           pdb=" C   TYR S 190 "
           pdb=" N   ARG S 191 "
           pdb=" CA  ARG S 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.54   16.46     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 5426 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1231
       0.069 -    0.138: 158
       0.138 -    0.207: 6
       0.207 -    0.275: 7
       0.275 -    0.344: 2
  Chirality restraints: 1404
  Sorted by residual:
  chirality pdb=" CA  ASN R 125 "
            pdb=" N   ASN R 125 "
            pdb=" C   ASN R 125 "
            pdb=" CB  ASN R 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.96e+00
  chirality pdb=" CA  THR R 128 "
            pdb=" N   THR R 128 "
            pdb=" C   THR R 128 "
            pdb=" CB  THR R 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CB  ILE R 174 "
            pdb=" CA  ILE R 174 "
            pdb=" CG1 ILE R 174 "
            pdb=" CG2 ILE R 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 1401 not shown)

  Planarity restraints: 1550
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  9FI R 401 "   -0.007 2.00e-02 2.50e+03   5.42e-01 8.07e+03
        pdb=" C10 9FI R 401 "    0.025 2.00e-02 2.50e+03
        pdb=" C14 9FI R 401 "   -0.004 2.00e-02 2.50e+03
        pdb=" C16 9FI R 401 "    0.010 2.00e-02 2.50e+03
        pdb=" C17 9FI R 401 "   -0.010 2.00e-02 2.50e+03
        pdb=" C18 9FI R 401 "    0.002 2.00e-02 2.50e+03
        pdb=" C21 9FI R 401 "   -0.003 2.00e-02 2.50e+03
        pdb=" C23 9FI R 401 "    0.008 2.00e-02 2.50e+03
        pdb=" C25 9FI R 401 "   -0.015 2.00e-02 2.50e+03
        pdb=" C5  9FI R 401 "   -1.274 2.00e-02 2.50e+03
        pdb=" C6  9FI R 401 "    1.266 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C11 9FI R 401 "   -0.004 2.00e-02 2.50e+03   2.87e-02 1.44e+01
        pdb=" C12 9FI R 401 "   -0.028 2.00e-02 2.50e+03
        pdb=" C19 9FI R 401 "    0.017 2.00e-02 2.50e+03
        pdb=" C20 9FI R 401 "   -0.050 2.00e-02 2.50e+03
        pdb=" N1  9FI R 401 "    0.002 2.00e-02 2.50e+03
        pdb=" N3  9FI R 401 "    0.040 2.00e-02 2.50e+03
        pdb=" O1  9FI R 401 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 127 "    0.035 2.00e-02 2.50e+03   2.61e-02 1.19e+01
        pdb=" CG  PHE R 127 "   -0.051 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 127 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 127 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 127 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 127 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 127 "    0.029 2.00e-02 2.50e+03
  ... (remaining 1547 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 525
        2.73 -     3.27: 8623
        3.27 -     3.82: 14639
        3.82 -     4.36: 17221
        4.36 -     4.90: 30803
  Nonbonded interactions: 71811
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.192 2.440
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 175 "
     model   vdw
     2.244 2.440
  nonbonded pdb=" OG  SER G  57 "
            pdb=" OE1 GLU G  58 "
     model   vdw
     2.252 2.440
  nonbonded pdb=" O   HIS R 146 "
            pdb=" OG  SER R 150 "
     model   vdw
     2.302 2.440
  nonbonded pdb=" NH1 ARG B  48 "
            pdb=" O   ARG G  62 "
     model   vdw
     2.307 2.520
  ... (remaining 71806 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:             0.370
  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:          2.080
  Check model and map are aligned:         0.140
  Set scattering table:                    0.080
  Process input model:                     28.270
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  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:13.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
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   0.123   9119  Z= 0.414
  Angle     :  0.746  24.373  12350  Z= 0.383
  Chirality :  0.048   0.344   1404
  Planarity :  0.014   0.542   1550
  Dihedral  : 13.302  81.791   3294
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.11 (0.26), residues: 1123
  helix:  1.86 (0.27), residues: 398
  sheet:  0.93 (0.32), residues: 282
  loop : -0.39 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP R 108 
   HIS   0.003   0.001   HIS A 188 
   PHE   0.051   0.001   PHE R 127 
   TYR   0.016   0.001   TYR R 211 
   ARG   0.007   0.000   ARG B 251 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 1
  residues processed: 187
  average time/residue: 1.1979
  time to fit residues: 239.1693
Evaluate side-chains
  176 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 0.965 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 1
  residues processed: 1
  average time/residue: 0.1264
  time to fit residues: 1.6458
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 46 optimal weight:    0.3980
   chunk 28 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 87 optimal weight:    0.0010
   chunk 33 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    1.8792

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

Flipped N/Q/H residues before XYZ refinement:
R 125 ASN
A 188 HIS
B 176 GLN
B 220 GLN
B 239 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   9119  Z= 0.387
  Angle     :  0.950  56.980  12350  Z= 0.403
  Chirality :  0.047   0.256   1404
  Planarity :  0.004   0.045   1550
  Dihedral  :  6.253  68.322   1264
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  :  9.72 %
    Favored  : 88.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.01 (0.25), residues: 1123
  helix:  1.85 (0.26), residues: 398
  sheet:  0.76 (0.31), residues: 280
  loop : -0.43 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.002   TRP R 108 
   HIS   0.007   0.001   HIS A 188 
   PHE   0.029   0.002   PHE R  92 
   TYR   0.032   0.002   TYR S 190 
   ARG   0.008   0.000   ARG B 251 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 181
  time to evaluate  : 1.091 
Fit side-chains
  outliers start: 18
  outliers final: 9
  residues processed: 183
  average time/residue: 1.2538
  time to fit residues: 244.8518
Evaluate side-chains
  187 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 178
  time to evaluate  : 1.099 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 2
  residues processed: 8
  average time/residue: 0.2319
  time to fit residues: 3.9397
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 56 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 83 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 100 optimal weight:    0.3980
   chunk 109 optimal weight:    0.8980
   chunk 89 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 99 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 132 ASN
B 155 ASN
B 176 GLN
B 220 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.1274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9119  Z= 0.184
  Angle     :  0.877  56.704  12350  Z= 0.358
  Chirality :  0.042   0.205   1404
  Planarity :  0.003   0.041   1550
  Dihedral  :  5.990  69.896   1264
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.98 %
    Favored  : 86.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.31 (0.25), residues: 1123
  helix:  2.19 (0.26), residues: 398
  sheet:  0.98 (0.31), residues: 273
  loop : -0.38 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.001   TRP B 211 
   HIS   0.002   0.001   HIS S  35 
   PHE   0.017   0.001   PHE R  92 
   TYR   0.024   0.001   TYR S 190 
   ARG   0.015   0.000   ARG B 219 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 182
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
  outliers start: 14
  outliers final: 6
  residues processed: 184
  average time/residue: 1.2835
  time to fit residues: 251.9781
Evaluate side-chains
  183 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 177
  time to evaluate  : 1.084 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 1
  residues processed: 5
  average time/residue: 0.6943
  time to fit residues: 5.2861
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 101 optimal weight:    0.5980
   chunk 107 optimal weight:    2.9990
   chunk 96 optimal weight:    0.3980
   chunk 28 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
B 132 ASN
B 176 GLN
B 220 GLN
B 259 GLN
B 340 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.1486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9119  Z= 0.266
  Angle     :  0.898  57.093  12350  Z= 0.371
  Chirality :  0.043   0.225   1404
  Planarity :  0.004   0.042   1550
  Dihedral  :  5.920  74.651   1264
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.79 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.34 (0.25), residues: 1123
  helix:  2.28 (0.26), residues: 399
  sheet:  0.90 (0.30), residues: 281
  loop : -0.40 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.016   0.001   TRP R 108 
   HIS   0.004   0.001   HIS S  35 
   PHE   0.011   0.001   PHE B 234 
   TYR   0.025   0.001   TYR S 190 
   ARG   0.008   0.000   ARG B 219 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 178
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
  outliers start: 21
  outliers final: 7
  residues processed: 185
  average time/residue: 1.2088
  time to fit residues: 239.2276
Evaluate side-chains
  182 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 175
  time to evaluate  : 1.136 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 2
  residues processed: 5
  average time/residue: 0.6717
  time to fit residues: 5.1569
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 79 optimal weight:    3.9990
   chunk 44 optimal weight:    6.9990
   chunk 91 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 0 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 96 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 36 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
B 220 GLN
B 259 GLN
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.1520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9119  Z= 0.204
  Angle     :  0.882  57.088  12350  Z= 0.359
  Chirality :  0.042   0.204   1404
  Planarity :  0.003   0.042   1550
  Dihedral  :  5.816  77.466   1264
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 13.61 %
    Favored  : 84.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.43 (0.25), residues: 1123
  helix:  2.39 (0.26), residues: 397
  sheet:  1.01 (0.30), residues: 278
  loop : -0.41 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.014   0.001   TRP R 108 
   HIS   0.003   0.001   HIS S  35 
   PHE   0.010   0.001   PHE B 234 
   TYR   0.022   0.001   TYR S 190 
   ARG   0.012   0.000   ARG B 219 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 186
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
  outliers start: 23
  outliers final: 11
  residues processed: 192
  average time/residue: 1.1671
  time to fit residues: 240.0474
Evaluate side-chains
  191 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 180
  time to evaluate  : 1.072 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 2
  residues processed: 9
  average time/residue: 0.5988
  time to fit residues: 7.5377
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 107 optimal weight:    5.9990
   chunk 89 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
B 176 GLN
B 220 GLN
B 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9119  Z= 0.283
  Angle     :  0.910  57.338  12350  Z= 0.377
  Chirality :  0.043   0.223   1404
  Planarity :  0.004   0.043   1550
  Dihedral  :  5.881  81.627   1264
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 13.72 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.31 (0.25), residues: 1123
  helix:  2.30 (0.26), residues: 397
  sheet:  0.88 (0.30), residues: 281
  loop : -0.44 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.001   TRP R 108 
   HIS   0.004   0.001   HIS S  35 
   PHE   0.010   0.001   PHE B 234 
   TYR   0.023   0.002   TYR S 190 
   ARG   0.008   0.000   ARG B 219 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 182
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
  outliers start: 28
  outliers final: 17
  residues processed: 192
  average time/residue: 1.1813
  time to fit residues: 242.2557
Evaluate side-chains
  199 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 182
  time to evaluate  : 0.971 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 5
  residues processed: 12
  average time/residue: 0.5261
  time to fit residues: 8.5194
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 59 optimal weight:    5.9990
   chunk 106 optimal weight:    0.0870
   chunk 66 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 32 optimal weight:   20.0000
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9119  Z= 0.177
  Angle     :  0.882  57.271  12350  Z= 0.359
  Chirality :  0.041   0.193   1404
  Planarity :  0.003   0.042   1550
  Dihedral  :  5.793  83.619   1264
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.94 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.43 (0.26), residues: 1123
  helix:  2.37 (0.26), residues: 398
  sheet:  1.04 (0.30), residues: 278
  loop : -0.42 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP B 169 
   HIS   0.003   0.001   HIS S  35 
   PHE   0.010   0.001   PHE A 274 
   TYR   0.019   0.001   TYR S 190 
   ARG   0.009   0.000   ARG B 219 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 179
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 19
  outliers final: 10
  residues processed: 188
  average time/residue: 1.1754
  time to fit residues: 236.7962
Evaluate side-chains
  191 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 181
  time to evaluate  : 1.101 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 5
  residues processed: 5
  average time/residue: 0.9486
  time to fit residues: 6.6346
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 68 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 52 optimal weight:    0.4980
   chunk 9 optimal weight:    0.5980
   chunk 84 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 102 optimal weight:    9.9990
   chunk 93 optimal weight:    3.9990
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 132 ASN
B 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9119  Z= 0.182
  Angle     :  0.885  57.330  12350  Z= 0.360
  Chirality :  0.042   0.193   1404
  Planarity :  0.003   0.042   1550
  Dihedral  :  5.767  85.772   1264
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.76 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.46 (0.26), residues: 1123
  helix:  2.40 (0.27), residues: 398
  sheet:  1.05 (0.30), residues: 278
  loop : -0.39 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP B 169 
   HIS   0.003   0.001   HIS S  35 
   PHE   0.009   0.001   PHE B 199 
   TYR   0.019   0.001   TYR S 190 
   ARG   0.012   0.000   ARG B 219 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 178
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
  outliers start: 17
  outliers final: 11
  residues processed: 184
  average time/residue: 1.2038
  time to fit residues: 237.2697
Evaluate side-chains
  187 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 176
  time to evaluate  : 1.065 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 5
  residues processed: 6
  average time/residue: 0.8393
  time to fit residues: 7.0309
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 102 optimal weight:    8.9990
   chunk 60 optimal weight:    0.4980
   chunk 43 optimal weight:    0.4980
   chunk 78 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   chunk 94 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 105 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
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      :  0.003   0.037   9119  Z= 0.229
  Angle     :  0.910  57.549  12350  Z= 0.374
  Chirality :  0.043   0.208   1404
  Planarity :  0.003   0.042   1550
  Dihedral  :  5.809  89.816   1264
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 16.38 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.36 (0.26), residues: 1123
  helix:  2.34 (0.27), residues: 398
  sheet:  0.82 (0.30), residues: 287
  loop : -0.36 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.015   0.001   TRP R 269 
   HIS   0.003   0.001   HIS S  35 
   PHE   0.012   0.001   PHE R  92 
   TYR   0.020   0.001   TYR S 190 
   ARG   0.009   0.000   ARG B 219 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 177
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
  outliers start: 12
  outliers final: 8
  residues processed: 184
  average time/residue: 1.1816
  time to fit residues: 232.4930
Evaluate side-chains
  185 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 177
  time to evaluate  : 0.978 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 5
  residues processed: 3
  average time/residue: 0.9905
  time to fit residues: 4.6038
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 110 optimal weight:    2.9990
   chunk 101 optimal weight:   10.0000
   chunk 88 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 68 optimal weight:    0.0470
   chunk 53 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
B 220 GLN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.1729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9119  Z= 0.177
  Angle     :  0.891  57.366  12350  Z= 0.362
  Chirality :  0.042   0.209   1404
  Planarity :  0.003   0.041   1550
  Dihedral  :  5.725  86.792   1264
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 16.99 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.42 (0.26), residues: 1123
  helix:  2.40 (0.27), residues: 397
  sheet:  0.86 (0.30), residues: 287
  loop : -0.36 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP B 169 
   HIS   0.003   0.000   HIS S  35 
   PHE   0.011   0.001   PHE R  92 
   TYR   0.017   0.001   TYR S 190 
   ARG   0.006   0.000   ARG B 251 

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 172
  time to evaluate  : 1.204 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 7
  residues processed: 178
  average time/residue: 1.3358
  time to fit residues: 254.0203
Evaluate side-chains
  175 residues out of total 977 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 168
  time to evaluate  : 1.075 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 5
  residues processed: 2
  average time/residue: 0.7848
  time to fit residues: 3.1992
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 13 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   chunk 36 optimal weight:    0.6980
   chunk 90 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    0.4980
   chunk 77 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
B 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.137935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.118392 restraints weight = 12194.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.87
r_work: 0.3430 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3285 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9119  Z= 0.182
  Angle     :  0.889  57.408  12350  Z= 0.363
  Chirality :  0.042   0.219   1404
  Planarity :  0.004   0.062   1550
  Dihedral  :  5.692  85.045   1264
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 16.99 %
    Favored  : 81.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  1.44 (0.26), residues: 1123
  helix:  2.42 (0.27), residues: 396
  sheet:  0.95 (0.31), residues: 281
  loop : -0.36 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.012   0.001   TRP B 211 
   HIS   0.003   0.000   HIS S  35 
   PHE   0.011   0.001   PHE R  92 
   TYR   0.018   0.001   TYR S 190 
   ARG   0.013   0.000   ARG B 219 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4326.23 seconds
wall clock time: 77 minutes 28.41 seconds (4648.41 seconds total)