Starting phenix.real_space_refine
on Wed Feb 14 07:01:37 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb0_20284/02_2024/6pb0_20284_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb0_20284/02_2024/6pb0_20284.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb0_20284/02_2024/6pb0_20284.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb0_20284/02_2024/6pb0_20284.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb0_20284/02_2024/6pb0_20284_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pb0_20284/02_2024/6pb0_20284_updated.pdb"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    5685      2.51       5
     N    1509      2.21       5
     O    1583      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "R ARG  143": "NH1" <-> "NH2"
    Residue "R ARG  151": "NH1" <-> "NH2"
    Residue "R PHE  203": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R ARG  225": "NH1" <-> "NH2"
    Residue "R TYR  272": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R ARG  299": "NH1" <-> "NH2"
    Residue "R ARG  341": "NH1" <-> "NH2"
    Residue "R ARG  371": "NH1" <-> "NH2"
    Residue "U ARG   27": "NH1" <-> "NH2"
    Residue "A ARG   38": "NH1" <-> "NH2"
    Residue "A ARG  317": "NH1" <-> "NH2"
    Residue "A ARG  336": "NH1" <-> "NH2"
    Residue "A ARG  356": "NH1" <-> "NH2"
    Residue "A ARG  373": "NH1" <-> "NH2"
    Residue "B ARG   96": "NH1" <-> "NH2"
    Residue "B ARG  134": "NH1" <-> "NH2"
    Residue "B ARG  137": "NH1" <-> "NH2"
    Residue "B ARG  256": "NH1" <-> "NH2"
    Residue "B ARG  314": "NH1" <-> "NH2"
    Residue "N PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N PHE   68": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 8827
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "R"
      Number of atoms: 2349
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2349
          Classifications: {'peptide': 281}
          Link IDs: {'PTRANS': 7, 'TRANS': 273}
    Chain: "U"
      Number of atoms: 322
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 322
          Classifications: {'peptide': 39}
          Link IDs: {'PTRANS': 1, 'TRANS': 37}
    Chain: "A"
      Number of atoms: 1892
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1892
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 220}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "R"
      Number of atoms: 266
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 266
          Unusual residues: {'CLR': 5, 'PLM': 7}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
  Time building chain proxies: 5.32, per 1000 atoms: 0.60
  Number of scatterers: 8827
  At special positions: 0
  Unit cell: (102.414, 98.358, 142.974, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1583      8.00
     N    1509      7.00
     C    5685      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 188 " - pdb=" SG  CYS R 258 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " 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: 3.17
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2014

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      37.8% alpha, 18.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.58
  Creating SS restraints...
    Processing helix  chain 'R' and resid 113 through 143
      removed outlier: 3.606A  pdb=" N   HIS R 117 " --> pdb=" O   LYS R 113 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   VAL R 118 " --> pdb=" O   VAL R 114 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   HIS R 127 " --> pdb=" O   ASN R 123 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   CYS R 128 " --> pdb=" O   TYR R 124 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   VAL R 136 " --> pdb=" O   VAL R 132 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 150 through 174
    Processing helix  chain 'R' and resid 178 through 182
    Processing helix  chain 'R' and resid 186 through 217
    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 228 through 235
    Processing helix  chain 'R' and resid 238 through 252
      removed outlier: 3.906A  pdb=" N   ILE R 242 " --> pdb=" O   VAL R 238 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 257 through 259
      No H-bonds generated for 'chain 'R' and resid 257 through 259'
    Processing helix  chain 'R' and resid 269 through 301
      removed outlier: 4.708A  pdb=" N   GLY R 274 " --> pdb=" O   ILE R 271 " (cutoff:3.500A)
      Proline residue:  R 275  - end of helix
      removed outlier: 4.967A  pdb=" N   PHE R 286 " --> pdb=" O   ASN R 283 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   ARG R 299 " --> pdb=" O   THR R 296 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 305 through 323
      Proline residue:  R 321  - end of helix
    Processing helix  chain 'R' and resid 340 through 364
      removed outlier: 5.186A  pdb=" N   GLY R 356 " --> pdb=" O   GLU R 352 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   PHE R 357 " --> pdb=" O   SER R 353 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 368 through 385
    Processing helix  chain 'U' and resid 9 through 39
    Processing helix  chain 'A' and resid 12 through 37
    Processing helix  chain 'A' and resid 53 through 59
    Processing helix  chain 'A' and resid 265 through 277
    Processing helix  chain 'A' and resid 295 through 300
    Processing helix  chain 'A' and resid 308 through 311
      No H-bonds generated for 'chain 'A' and resid 308 through 311'
    Processing helix  chain 'A' and resid 332 through 349
      removed outlier: 4.062A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 390
    Processing helix  chain 'B' and resid 4 through 24
    Processing helix  chain 'B' and resid 30 through 33
      No H-bonds generated for 'chain 'B' and resid 30 through 33'
    Processing helix  chain 'G' and resid 9 through 23
    Processing helix  chain 'G' and resid 30 through 45
      removed outlier: 3.509A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ALA G  45 " --> pdb=" O   CYS G  41 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 29 through 31
      No H-bonds generated for 'chain 'N' and resid 29 through 31'
    Processing helix  chain 'N' and resid 62 through 64
      No H-bonds generated for 'chain 'N' and resid 62 through 64'
    Processing sheet with id=  A, first strand: chain 'A' and resid 286 through 291
      removed outlier: 4.185A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 7.238A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.088A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.403A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.973A  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: 7.016A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.045A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.817A  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: 6.861A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.345A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.784A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.851A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.452A  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: 6.853A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.269A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 5.903A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.886A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 275 through 278
      removed outlier: 4.032A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.697A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=  J, first strand: chain 'N' and resid 122 through 124
      removed outlier: 5.992A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   ALA N  40 " --> pdb=" O   LEU N  45 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   LEU N  45 " --> pdb=" O   ALA N  40 " (cutoff:3.500A)

    407 hydrogen bonds defined for protein.
    1107 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: 2.27

  Time building geometry restraints manager: 3.41 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: 2734
        1.34 -     1.46: 1951
        1.46 -     1.58: 4264
        1.58 -     1.70: 0
        1.70 -     1.82: 70
  Bond restraints: 9019
  Sorted by residual:
  bond pdb=" C10 CLR R 402 "
       pdb=" C9  CLR R 402 "
    ideal  model  delta    sigma   weight residual
    1.551  1.518  0.033 2.00e-02 2.50e+03 2.65e+00
  bond pdb=" C5  CLR R 406 "
       pdb=" C6  CLR R 406 "
    ideal  model  delta    sigma   weight residual
    1.332  1.300  0.032 2.00e-02 2.50e+03 2.49e+00
  bond pdb=" C10 CLR R 404 "
       pdb=" C9  CLR R 404 "
    ideal  model  delta    sigma   weight residual
    1.551  1.520  0.031 2.00e-02 2.50e+03 2.39e+00
  bond pdb=" C5  CLR R 404 "
       pdb=" C6  CLR R 404 "
    ideal  model  delta    sigma   weight residual
    1.332  1.301  0.031 2.00e-02 2.50e+03 2.34e+00
  bond pdb=" C10 CLR R 401 "
       pdb=" C9  CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.551  1.521  0.030 2.00e-02 2.50e+03 2.25e+00
  ... (remaining 9014 not shown)

  Histogram of bond angle deviations from ideal:
       99.31 -   106.27: 198
      106.27 -   113.23: 4931
      113.23 -   120.18: 3324
      120.18 -   127.14: 3648
      127.14 -   134.10: 95
  Bond angle restraints: 12196
  Sorted by residual:
  angle pdb=" C   THR B  86 "
        pdb=" N   THR B  87 "
        pdb=" CA  THR B  87 "
      ideal   model   delta    sigma   weight residual
     121.54  129.56   -8.02 1.91e+00 2.74e-01 1.76e+01
  angle pdb=" CA  THR B  87 "
        pdb=" CB  THR B  87 "
        pdb=" CG2 THR B  87 "
      ideal   model   delta    sigma   weight residual
     110.50  115.65   -5.15 1.70e+00 3.46e-01 9.18e+00
  angle pdb=" CA  TYR R 272 "
        pdb=" CB  TYR R 272 "
        pdb=" CG  TYR R 272 "
      ideal   model   delta    sigma   weight residual
     113.90  118.83   -4.93 1.80e+00 3.09e-01 7.51e+00
  angle pdb=" C   ILE R 271 "
        pdb=" N   TYR R 272 "
        pdb=" CA  TYR R 272 "
      ideal   model   delta    sigma   weight residual
     122.26  117.60    4.66 1.73e+00 3.34e-01 7.24e+00
  angle pdb=" CA  LEU R 320 "
        pdb=" C   LEU R 320 "
        pdb=" N   PRO R 321 "
      ideal   model   delta    sigma   weight residual
     118.44  122.69   -4.25 1.59e+00 3.96e-01 7.14e+00
  ... (remaining 12191 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.93: 5339
       14.93 -    29.85: 198
       29.85 -    44.78: 60
       44.78 -    59.70: 16
       59.70 -    74.63: 3
  Dihedral angle restraints: 5616
    sinusoidal: 2505
      harmonic: 3111
  Sorted by residual:
  dihedral pdb=" CA  ALA R 133 "
           pdb=" C   ALA R 133 "
           pdb=" N   LEU R 134 "
           pdb=" CA  LEU R 134 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.33  -29.67     0      5.00e+00 4.00e-02 3.52e+01
  dihedral pdb=" CA  PHE R 284 "
           pdb=" C   PHE R 284 "
           pdb=" N   ILE R 285 "
           pdb=" CA  ILE R 285 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.45  -21.55     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CA  HIS R 115 "
           pdb=" C   HIS R 115 "
           pdb=" N   TYR R 116 "
           pdb=" CA  TYR R 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.31  -19.69     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 5613 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 1195
       0.085 -    0.169: 134
       0.169 -    0.254: 14
       0.254 -    0.338: 3
       0.338 -    0.423: 8
  Chirality restraints: 1354
  Sorted by residual:
  chirality pdb=" C14 CLR R 404 "
            pdb=" C13 CLR R 404 "
            pdb=" C15 CLR R 404 "
            pdb=" C8  CLR R 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.74    0.42 2.00e-01 2.50e+01 4.46e+00
  chirality pdb=" C14 CLR R 401 "
            pdb=" C13 CLR R 401 "
            pdb=" C15 CLR R 401 "
            pdb=" C8  CLR R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.73    0.41 2.00e-01 2.50e+01 4.27e+00
  chirality pdb=" C14 CLR R 403 "
            pdb=" C13 CLR R 403 "
            pdb=" C15 CLR R 403 "
            pdb=" C8  CLR R 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.72    0.41 2.00e-01 2.50e+01 4.12e+00
  ... (remaining 1351 not shown)

  Planarity restraints: 1517
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET R 295 "   -0.012 2.00e-02 2.50e+03   2.35e-02 5.51e+00
        pdb=" C   MET R 295 "    0.041 2.00e-02 2.50e+03
        pdb=" O   MET R 295 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   THR R 296 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 291 "   -0.012 2.00e-02 2.50e+03   2.34e-02 5.46e+00
        pdb=" C   VAL R 291 "    0.040 2.00e-02 2.50e+03
        pdb=" O   VAL R 291 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ARG R 292 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 288 "   -0.012 2.00e-02 2.50e+03   2.32e-02 5.37e+00
        pdb=" C   PHE R 288 "    0.040 2.00e-02 2.50e+03
        pdb=" O   PHE R 288 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ASN R 289 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1514 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2126
        2.80 -     3.33: 7318
        3.33 -     3.85: 13708
        3.85 -     4.38: 15880
        4.38 -     4.90: 28190
  Nonbonded interactions: 67222
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.277 2.440
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.299 2.440
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.308 2.440
  nonbonded pdb=" NE2 HIS B 225 "
            pdb=" OG1 THR B 243 "
     model   vdw
     2.343 2.520
  nonbonded pdb=" O   ARG N  98 "
            pdb=" OH  TYR N 115 "
     model   vdw
     2.401 2.440
  ... (remaining 67217 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:             0.550
  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:          2.710
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     25.980
  Find NCS groups from input model:        0.240
  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:12.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
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   0.046   9019  Z= 0.239
  Angle     :  0.824   8.517  12196  Z= 0.432
  Chirality :  0.063   0.423   1354
  Planarity :  0.006   0.056   1517
  Dihedral  :  9.455  74.628   3593
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  1.29 %
    Favored  : 98.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.20), residues: 1050
  helix: -1.43 (0.18), residues: 424
  sheet: -1.35 (0.31), residues: 226
  loop : -2.57 (0.24), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP R 156 
 HIS   0.010   0.001   HIS A 220 
 PHE   0.024   0.002   PHE R 203 
 TYR   0.022   0.002   TYR N  94 
 ARG   0.008   0.001   ARG N 118 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 256
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  377 ARG cc_start: 0.7354 (mtp85) cc_final: 0.6727 (tmt170)
REVERT: U   24 GLN cc_start: 0.8159 (tp40) cc_final: 0.7800 (mt0)
REVERT: A  218 ASN cc_start: 0.7579 (m-40) cc_final: 0.7345 (m110)
REVERT: A  220 HIS cc_start: 0.6201 (t-90) cc_final: 0.5542 (t-90)
REVERT: A  284 THR cc_start: 0.8125 (m) cc_final: 0.7844 (p)
REVERT: B  189 SER cc_start: 0.8732 (p) cc_final: 0.8384 (m)
REVERT: B  258 ASP cc_start: 0.7241 (t70) cc_final: 0.6486 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 258
  average time/residue: 1.0854
  time to fit residues: 299.6950
Evaluate side-chains
  159 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 41 optimal weight:    0.2980
   chunk 80 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9990
   chunk 93 optimal weight:    7.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
R 181 HIS
R 182 GLN
R 255 ASN
R 308 GLN
A  23 ASN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 387 HIS
B  75 GLN
B 295 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9019  Z= 0.194
  Angle     :  0.489   5.022  12196  Z= 0.260
  Chirality :  0.041   0.131   1354
  Planarity :  0.004   0.042   1517
  Dihedral  :  7.503  59.952   1597
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 14.46 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.24), residues: 1050
  helix:  0.89 (0.24), residues: 418
  sheet: -1.19 (0.30), residues: 238
  loop : -1.91 (0.27), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R 156 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.014   0.002   PHE A 376 
 TYR   0.014   0.001   TYR N  60 
 ARG   0.011   0.001   ARG B 256 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 173
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 TYR cc_start: 0.7384 (m-80) cc_final: 0.6509 (m-80)
REVERT: R  377 ARG cc_start: 0.7351 (mtp85) cc_final: 0.6677 (tmt170)
REVERT: A  218 ASN cc_start: 0.7594 (m-40) cc_final: 0.7362 (m110)
REVERT: A  222 PHE cc_start: 0.7748 (m-80) cc_final: 0.7423 (m-80)
REVERT: A  278 ASN cc_start: 0.8948 (m-40) cc_final: 0.8444 (m110)
REVERT: B  188 MET cc_start: 0.7541 (mmm) cc_final: 0.7233 (mmm)
REVERT: B  189 SER cc_start: 0.8650 (p) cc_final: 0.8312 (m)
REVERT: B  258 ASP cc_start: 0.7657 (t70) cc_final: 0.7119 (t0)
REVERT: N   20 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8087 (mt)
REVERT: N   72 ARG cc_start: 0.8249 (ptp-170) cc_final: 0.8008 (ptp-170)
  outliers start: 38
  outliers final: 20
  residues processed: 189
  average time/residue: 1.0158
  time to fit residues: 207.7932
Evaluate side-chains
  178 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 157
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  118 VAL
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  292 ARG
Chi-restraints excluded: chain R residue  317 LEU
Chi-restraints excluded: chain R residue  360 SER
Chi-restraints excluded: chain R residue  379 HIS
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain B residue   27 ASP
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   90 ASP
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   chunk 63 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 93 optimal weight:    0.7980
   chunk 101 optimal weight:    0.7980
   chunk 83 optimal weight:    7.9990
   chunk 92 optimal weight:    6.9990
   chunk 31 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
R 182 GLN
** R 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  24 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
B   6 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9019  Z= 0.197
  Angle     :  0.486   6.736  12196  Z= 0.259
  Chirality :  0.041   0.130   1354
  Planarity :  0.004   0.037   1517
  Dihedral  :  7.130  59.891   1597
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 14.67 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.25), residues: 1050
  helix:  1.74 (0.25), residues: 412
  sheet: -0.85 (0.31), residues: 221
  loop : -1.57 (0.27), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP R 156 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.011   0.001   TYR N  94 
 ARG   0.006   0.000   ARG A 280 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 48
    poor density    : 166
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
REVERT: R  309 TYR cc_start: 0.7503 (m-80) cc_final: 0.7010 (m-80)
REVERT: R  377 ARG cc_start: 0.7318 (mtp85) cc_final: 0.6655 (tmt170)
REVERT: A   29 GLN cc_start: 0.7835 (tp40) cc_final: 0.6832 (tt0)
REVERT: A  222 PHE cc_start: 0.7809 (m-80) cc_final: 0.7586 (m-80)
REVERT: A  278 ASN cc_start: 0.9061 (m-40) cc_final: 0.8568 (m110)
REVERT: A  284 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8173 (p)
REVERT: B   42 ARG cc_start: 0.7564 (tpt90) cc_final: 0.7160 (ttt-90)
REVERT: B  189 SER cc_start: 0.8670 (p) cc_final: 0.8414 (m)
REVERT: B  258 ASP cc_start: 0.7769 (t70) cc_final: 0.6952 (t0)
REVERT: N   72 ARG cc_start: 0.8253 (ptp-170) cc_final: 0.7974 (ptp-170)
  outliers start: 48
  outliers final: 29
  residues processed: 193
  average time/residue: 0.9596
  time to fit residues: 200.3069
Evaluate side-chains
  177 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 147
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  112 SER
Chi-restraints excluded: chain R residue  118 VAL
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  139 VAL
Chi-restraints excluded: chain R residue  163 ILE
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain R residue  303 THR
Chi-restraints excluded: chain R residue  339 VAL
Chi-restraints excluded: chain R residue  360 SER
Chi-restraints excluded: chain R residue  361 VAL
Chi-restraints excluded: chain R residue  379 HIS
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain B residue   27 ASP
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 92 optimal weight:    8.9990
   chunk 70 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 94 optimal weight:    7.9990
   chunk 99 optimal weight:    0.1980
   chunk 49 optimal weight:    8.9990
   chunk 89 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0670
   overall best weight:    1.1720

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

Flipped N/Q/H residues before XYZ refinement:
R 182 GLN
** R 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
N 120 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.3318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9019  Z= 0.183
  Angle     :  0.465   5.048  12196  Z= 0.248
  Chirality :  0.040   0.130   1354
  Planarity :  0.003   0.035   1517
  Dihedral  :  6.775  59.439   1597
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 16.29 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.26), residues: 1050
  helix:  1.96 (0.25), residues: 416
  sheet: -0.70 (0.31), residues: 225
  loop : -1.41 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 156 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.006   0.000   ARG A 280 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 47
    poor density    : 159
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
REVERT: R  309 TYR cc_start: 0.7372 (m-80) cc_final: 0.6859 (m-80)
REVERT: R  377 ARG cc_start: 0.7298 (mtp85) cc_final: 0.6684 (tmt170)
REVERT: A  222 PHE cc_start: 0.7903 (m-80) cc_final: 0.7663 (m-10)
REVERT: A  278 ASN cc_start: 0.9127 (m-40) cc_final: 0.8694 (m110)
REVERT: A  284 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8210 (p)
REVERT: B   42 ARG cc_start: 0.7611 (tpt90) cc_final: 0.7015 (ttt90)
REVERT: B   59 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7517 (m-80)
REVERT: B  189 SER cc_start: 0.8690 (p) cc_final: 0.8436 (m)
REVERT: B  258 ASP cc_start: 0.7817 (t70) cc_final: 0.7032 (t0)
REVERT: N   72 ARG cc_start: 0.8231 (ptp-170) cc_final: 0.8021 (ptp-170)
REVERT: N  120 GLN cc_start: 0.7468 (mm110) cc_final: 0.6989 (mt0)
  outliers start: 47
  outliers final: 27
  residues processed: 182
  average time/residue: 0.9427
  time to fit residues: 185.5153
Evaluate side-chains
  173 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 144
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  112 SER
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain R residue  303 THR
Chi-restraints excluded: chain R residue  339 VAL
Chi-restraints excluded: chain R residue  360 SER
Chi-restraints excluded: chain R residue  361 VAL
Chi-restraints excluded: chain R residue  379 HIS
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain B residue   27 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 1 optimal weight:    0.8980
   chunk 74 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 68 optimal weight:    0.4980
   chunk 0 optimal weight:    9.9990
   chunk 50 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
** R 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 HIS
B 295 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.3708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9019  Z= 0.265
  Angle     :  0.532   8.265  12196  Z= 0.280
  Chirality :  0.042   0.180   1354
  Planarity :  0.004   0.034   1517
  Dihedral  :  7.058  58.647   1597
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 17.26 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.26), residues: 1050
  helix:  1.88 (0.25), residues: 417
  sheet: -0.68 (0.32), residues: 216
  loop : -1.33 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 156 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.015   0.002   PHE A 212 
 TYR   0.013   0.001   TYR A 339 
 ARG   0.007   0.000   ARG A 280 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 148
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
REVERT: R  303 THR cc_start: 0.5150 (OUTLIER) cc_final: 0.4907 (p)
REVERT: R  377 ARG cc_start: 0.7284 (mtp85) cc_final: 0.6699 (tmt170)
REVERT: A  222 PHE cc_start: 0.7926 (m-80) cc_final: 0.7668 (m-80)
REVERT: A  278 ASN cc_start: 0.9172 (m-40) cc_final: 0.8613 (m110)
REVERT: A  284 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8297 (p)
REVERT: B   42 ARG cc_start: 0.7663 (tpt90) cc_final: 0.7067 (ttt90)
REVERT: B   59 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7518 (m-80)
REVERT: B  258 ASP cc_start: 0.7906 (t70) cc_final: 0.7070 (t0)
REVERT: B  260 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8064 (tt0)
REVERT: N  120 GLN cc_start: 0.7543 (mm110) cc_final: 0.7205 (mt0)
  outliers start: 51
  outliers final: 33
  residues processed: 177
  average time/residue: 1.0277
  time to fit residues: 196.3911
Evaluate side-chains
  175 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 138
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  112 SER
Chi-restraints excluded: chain R residue  118 VAL
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  209 GLU
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain R residue  303 THR
Chi-restraints excluded: chain R residue  339 VAL
Chi-restraints excluded: chain R residue  353 SER
Chi-restraints excluded: chain R residue  360 SER
Chi-restraints excluded: chain R residue  361 VAL
Chi-restraints excluded: chain R residue  379 HIS
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain B residue   27 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   90 ASP
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 99 optimal weight:    9.9990
   chunk 82 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** R 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.3842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9019  Z= 0.209
  Angle     :  0.499   7.056  12196  Z= 0.265
  Chirality :  0.041   0.177   1354
  Planarity :  0.004   0.035   1517
  Dihedral  :  6.837  58.277   1597
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 18.45 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    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:  0.22 (0.26), residues: 1050
  helix:  1.98 (0.25), residues: 416
  sheet: -0.67 (0.32), residues: 216
  loop : -1.31 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.014   0.001   TYR N  60 
 ARG   0.008   0.000   ARG A 280 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 46
    poor density    : 145
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
REVERT: R  145 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6914 (ttp80)
REVERT: R  182 GLN cc_start: 0.7997 (tp-100) cc_final: 0.7580 (tp-100)
REVERT: R  303 THR cc_start: 0.5129 (OUTLIER) cc_final: 0.4908 (p)
REVERT: R  377 ARG cc_start: 0.7276 (mtp85) cc_final: 0.6669 (tmt170)
REVERT: A   35 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7095 (mt0)
REVERT: A  222 PHE cc_start: 0.7872 (m-80) cc_final: 0.7653 (m-80)
REVERT: A  284 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8317 (p)
REVERT: B   42 ARG cc_start: 0.7680 (tpt90) cc_final: 0.7066 (ttt90)
REVERT: B   59 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.7493 (m-80)
REVERT: B  234 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8806 (m-80)
REVERT: B  258 ASP cc_start: 0.7939 (t70) cc_final: 0.7063 (t0)
REVERT: B  260 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8082 (tt0)
REVERT: N  120 GLN cc_start: 0.7584 (mm110) cc_final: 0.7197 (mt0)
  outliers start: 46
  outliers final: 31
  residues processed: 168
  average time/residue: 1.0295
  time to fit residues: 186.1410
Evaluate side-chains
  175 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 138
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  112 SER
Chi-restraints excluded: chain R residue  118 VAL
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  145 ARG
Chi-restraints excluded: chain R residue  209 GLU
Chi-restraints excluded: chain R residue  244 VAL
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain R residue  303 THR
Chi-restraints excluded: chain R residue  339 VAL
Chi-restraints excluded: chain R residue  361 VAL
Chi-restraints excluded: chain R residue  379 HIS
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain B residue   27 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   90 ASP
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 96 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 56 optimal weight:    0.1980
   chunk 72 optimal weight:    0.6980
   chunk 83 optimal weight:   10.0000
   chunk 55 optimal weight:    8.9990
   chunk 99 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0770
   chunk 60 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
** R 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 382 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.3857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9019  Z= 0.134
  Angle     :  0.462   6.657  12196  Z= 0.245
  Chirality :  0.040   0.182   1354
  Planarity :  0.003   0.035   1517
  Dihedral  :  6.293  57.009   1597
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.28 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.26), residues: 1050
  helix:  2.22 (0.25), residues: 416
  sheet: -0.62 (0.32), residues: 218
  loop : -1.24 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.013   0.001   PHE R 260 
 TYR   0.009   0.001   TYR R 272 
 ARG   0.007   0.000   ARG A 280 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 148
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
REVERT: R  145 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6827 (ttp80)
REVERT: R  303 THR cc_start: 0.5132 (OUTLIER) cc_final: 0.4895 (p)
REVERT: R  377 ARG cc_start: 0.7260 (mtp85) cc_final: 0.6619 (tmt170)
REVERT: A  265 ARG cc_start: 0.7215 (mmm160) cc_final: 0.6888 (mtp85)
REVERT: A  284 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8338 (p)
REVERT: A  389 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6774 (ttm110)
REVERT: B   42 ARG cc_start: 0.7663 (tpt90) cc_final: 0.7071 (ttt90)
REVERT: B   59 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.7514 (m-80)
REVERT: B  234 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8992 (m-80)
REVERT: B  258 ASP cc_start: 0.7856 (t70) cc_final: 0.7027 (t0)
REVERT: N  120 GLN cc_start: 0.7496 (mm110) cc_final: 0.7109 (mt0)
  outliers start: 37
  outliers final: 18
  residues processed: 167
  average time/residue: 1.0853
  time to fit residues: 195.7957
Evaluate side-chains
  162 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  118 VAL
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  145 ARG
Chi-restraints excluded: chain R residue  209 GLU
Chi-restraints excluded: chain R residue  303 THR
Chi-restraints excluded: chain R residue  345 ILE
Chi-restraints excluded: chain R residue  361 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  389 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0010
   chunk 63 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 49 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 78 optimal weight:    5.9990
   chunk 90 optimal weight:    0.8980
   chunk 95 optimal weight:    2.9990
   overall best weight:    0.7790

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

Flipped N/Q/H residues before XYZ refinement:
** R 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  35 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.3937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9019  Z= 0.154
  Angle     :  0.476   5.538  12196  Z= 0.252
  Chirality :  0.040   0.184   1354
  Planarity :  0.003   0.034   1517
  Dihedral  :  6.202  55.981   1597
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.82 %
    Favored  : 75.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.26), residues: 1050
  helix:  2.28 (0.25), residues: 417
  sheet: -0.52 (0.32), residues: 218
  loop : -1.21 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  99 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.013   0.001   PHE R 260 
 TYR   0.010   0.001   TYR R 363 
 ARG   0.008   0.000   ARG A 280 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 143
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
REVERT: R  145 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6867 (ttp80)
REVERT: R  303 THR cc_start: 0.5160 (OUTLIER) cc_final: 0.4939 (p)
REVERT: R  377 ARG cc_start: 0.7261 (mtp85) cc_final: 0.6620 (tmt170)
REVERT: A   29 GLN cc_start: 0.7885 (tp40) cc_final: 0.6914 (tt0)
REVERT: A  265 ARG cc_start: 0.7236 (mmm160) cc_final: 0.6916 (mtp85)
REVERT: A  284 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8333 (p)
REVERT: B   42 ARG cc_start: 0.7676 (tpt90) cc_final: 0.7088 (ttt90)
REVERT: B   59 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.7525 (m-80)
REVERT: B  234 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8997 (m-80)
REVERT: B  258 ASP cc_start: 0.7920 (t70) cc_final: 0.7064 (t0)
REVERT: N  120 GLN cc_start: 0.7452 (mm110) cc_final: 0.7070 (mt0)
  outliers start: 37
  outliers final: 25
  residues processed: 161
  average time/residue: 1.0600
  time to fit residues: 183.8558
Evaluate side-chains
  168 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 138
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  118 VAL
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  145 ARG
Chi-restraints excluded: chain R residue  209 GLU
Chi-restraints excluded: chain R residue  303 THR
Chi-restraints excluded: chain R residue  361 VAL
Chi-restraints excluded: chain R residue  379 HIS
Chi-restraints excluded: chain U residue    9 LEU
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   76 LYS
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:   10.0000
   chunk 92 optimal weight:    0.8980
   chunk 95 optimal weight:    3.9990
   chunk 55 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 28 optimal weight:    5.9990
   chunk 83 optimal weight:   10.0000
   chunk 87 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** R 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 382 GLN
A  23 ASN
B  88 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.4130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9019  Z= 0.251
  Angle     :  0.535   7.039  12196  Z= 0.282
  Chirality :  0.042   0.194   1354
  Planarity :  0.004   0.032   1517
  Dihedral  :  6.686  56.263   1597
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 20.39 %
    Favored  : 74.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    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:  0.39 (0.26), residues: 1050
  helix:  2.13 (0.25), residues: 417
  sheet: -0.60 (0.32), residues: 220
  loop : -1.21 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.013   0.002   PHE A 212 
 TYR   0.011   0.001   TYR A 339 
 ARG   0.008   0.000   ARG A 280 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 143
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
REVERT: R  182 GLN cc_start: 0.8066 (tp-100) cc_final: 0.7717 (tp-100)
REVERT: R  303 THR cc_start: 0.5379 (OUTLIER) cc_final: 0.5128 (p)
REVERT: R  377 ARG cc_start: 0.7295 (mtp85) cc_final: 0.6598 (tpt90)
REVERT: A   29 GLN cc_start: 0.7961 (tp40) cc_final: 0.6959 (tt0)
REVERT: A  265 ARG cc_start: 0.7216 (mmm160) cc_final: 0.6917 (mtp85)
REVERT: A  284 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8406 (p)
REVERT: B   42 ARG cc_start: 0.7689 (tpt90) cc_final: 0.7084 (ttt90)
REVERT: B   59 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7489 (m-80)
REVERT: B  234 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8996 (m-80)
REVERT: B  258 ASP cc_start: 0.7983 (t70) cc_final: 0.7445 (t0)
REVERT: N   60 TYR cc_start: 0.8775 (m-80) cc_final: 0.8547 (m-80)
REVERT: N  120 GLN cc_start: 0.7612 (mm110) cc_final: 0.7220 (mt0)
  outliers start: 43
  outliers final: 25
  residues processed: 164
  average time/residue: 1.0695
  time to fit residues: 188.7900
Evaluate side-chains
  167 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 138
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  118 VAL
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  209 GLU
Chi-restraints excluded: chain R residue  303 THR
Chi-restraints excluded: chain R residue  339 VAL
Chi-restraints excluded: chain R residue  343 VAL
Chi-restraints excluded: chain R residue  361 VAL
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   30 SER
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 102 optimal weight:    4.9990
   chunk 94 optimal weight:    4.9990
   chunk 81 optimal weight:    0.0980
   chunk 8 optimal weight:    6.9990
   chunk 63 optimal weight:    0.8980
   chunk 50 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** R 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  23 ASN
B  88 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.4117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9019  Z= 0.158
  Angle     :  0.495   6.799  12196  Z= 0.261
  Chirality :  0.041   0.227   1354
  Planarity :  0.003   0.035   1517
  Dihedral  :  6.318  55.685   1597
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.22 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.26), residues: 1050
  helix:  2.27 (0.25), residues: 417
  sheet: -0.49 (0.32), residues: 228
  loop : -1.18 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP B  99 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.020   0.001   PHE A 222 
 TYR   0.009   0.001   TYR R 272 
 ARG   0.008   0.000   ARG A 280 

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 139
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
REVERT: R  303 THR cc_start: 0.5468 (OUTLIER) cc_final: 0.5231 (p)
REVERT: R  377 ARG cc_start: 0.7278 (mtp85) cc_final: 0.6663 (tmt170)
REVERT: A   29 GLN cc_start: 0.7930 (tp40) cc_final: 0.6932 (tt0)
REVERT: A  265 ARG cc_start: 0.7190 (mmm160) cc_final: 0.6878 (mtp85)
REVERT: A  284 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8411 (p)
REVERT: B   42 ARG cc_start: 0.7702 (tpt90) cc_final: 0.7089 (ttt90)
REVERT: B   59 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7491 (m-80)
REVERT: B  258 ASP cc_start: 0.7925 (t70) cc_final: 0.7385 (t0)
REVERT: N  120 GLN cc_start: 0.7534 (mm110) cc_final: 0.7163 (mt0)
  outliers start: 27
  outliers final: 22
  residues processed: 152
  average time/residue: 1.0848
  time to fit residues: 177.2624
Evaluate side-chains
  159 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  118 VAL
Chi-restraints excluded: chain R residue  120 VAL
Chi-restraints excluded: chain R residue  209 GLU
Chi-restraints excluded: chain R residue  303 THR
Chi-restraints excluded: chain R residue  339 VAL
Chi-restraints excluded: chain R residue  343 VAL
Chi-restraints excluded: chain R residue  361 VAL
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   54 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  126 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   chunk 22 optimal weight:    0.4980
   chunk 81 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** R 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.175942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.133138 restraints weight = 11039.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3822 rms_B_bonded: 3.02
r_work: 0.3647 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.4108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9019  Z= 0.158
  Angle     :  0.495   7.921  12196  Z= 0.262
  Chirality :  0.041   0.269   1354
  Planarity :  0.003   0.034   1517
  Dihedral  :  6.145  54.729   1597
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.33 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.26), residues: 1050
  helix:  2.43 (0.26), residues: 415
  sheet: -0.44 (0.32), residues: 230
  loop : -1.15 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B  99 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.017   0.001   PHE A 212 
 TYR   0.010   0.001   TYR R 346 
 ARG   0.009   0.000   ARG A 280 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3646.20 seconds
wall clock time: 65 minutes 23.67 seconds (3923.67 seconds total)