Starting phenix.real_space_refine
on Fri Nov 15 06:21:54 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmp_34902/11_2024/8hmp_34902.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmp_34902/11_2024/8hmp_34902.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmp_34902/11_2024/8hmp_34902.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmp_34902/11_2024/8hmp_34902.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmp_34902/11_2024/8hmp_34902.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmp_34902/11_2024/8hmp_34902.cif"
  }
  resolution = 2.77
  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=   0.000
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: 5
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    5294      2.51       5
     N    1433      2.21       5
     O    1532      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 63 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 8319
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 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: 2308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2308
          Classifications: {'peptide': 285}
          Link IDs: {'PTRANS': 12, 'TRANS': 272}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1980
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1980
          Classifications: {'peptide': 239}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 232}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 34
          Unusual residues: {'EN6': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.95, per 1000 atoms: 0.84
  Number of scatterers: 8319
  At special positions: 0
  Unit cell: (94.8486, 94.2939, 125.355, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      57     16.00
     F       3      9.00
     O    1532      8.00
     N    1433      7.00
     C    5294      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  27 " - pdb=" SG  CYS R  40 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 114 " - pdb=" SG  CYS R 193 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 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: 2.03
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1966

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 10 sheets defined
      40.4% alpha, 20.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'B' and resid 3 through 26
      removed outlier: 3.642A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 22
    Processing helix  chain 'G' and resid 31 through 44
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.568A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 41 through 68
      removed outlier: 4.063A  pdb=" N   VAL R  46 " --> pdb=" O   PHE R  42 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ILE R  47 " --> pdb=" O   GLU R  43 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   HIS R  66 " --> pdb=" O   ILE R  62 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ALA R  68 " --> pdb=" O   VAL R  64 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 75 through 104
      removed outlier: 3.901A  pdb=" N   PHE R  79 " --> pdb=" O   THR R  75 " (cutoff:3.500A)
      Proline residue:  R  97  - end of helix
      removed outlier: 4.254A  pdb=" N   LEU R 102 " --> pdb=" O   THR R  98 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   HIS R 103 " --> pdb=" O   LEU R  99 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 109 through 145
      removed outlier: 3.739A  pdb=" N   THR R 113 " --> pdb=" O   HIS R 109 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 148 through 153
    Processing helix  chain 'R' and resid 154 through 174
      removed outlier: 3.720A  pdb=" N   PHE R 173 " --> pdb=" O   SER R 169 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 179
      removed outlier: 3.797A  pdb=" N   PHE R 178 " --> pdb=" O   LEU R 174 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 185 through 189
      removed outlier: 4.006A  pdb=" N   ILE R 189 " --> pdb=" O   HIS R 186 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 190 through 196
      removed outlier: 3.636A  pdb=" N   ALA R 194 " --> pdb=" O   PHE R 190 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 206 through 244
      Proline residue:  R 214  - end of helix
    Processing helix  chain 'R' and resid 263 through 289
      removed outlier: 4.284A  pdb=" N   LEU R 267 " --> pdb=" O   TYR R 263 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   PHE R 268 " --> pdb=" O   ALA R 264 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   ARG R 269 " --> pdb=" O   MET R 265 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR R 271 " --> pdb=" O   LEU R 267 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   SER R 272 " --> pdb=" O   PHE R 268 " (cutoff:3.500A)
      Proline residue:  R 280  - end of helix
    Processing helix  chain 'R' and resid 295 through 309
    Processing helix  chain 'R' and resid 311 through 321
      removed outlier: 3.613A  pdb=" N   TYR R 317 " --> pdb=" O   ASN R 313 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   SER R 320 " --> pdb=" O   ILE R 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 10 through 39
    Processing helix  chain 'A' and resid 52 through 63
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.506A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.507A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.330A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.606A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.875A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.686A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.995A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.770A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.992A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.372A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.044A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.173A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.633A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.506A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'N' and resid 10 through 11
      removed outlier: 6.795A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 6.192A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.158A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.799A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)

    409 hydrogen bonds defined for protein.
    1182 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: 2.61

  Time building geometry restraints manager: 2.30 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2510
        1.34 -     1.46: 2252
        1.46 -     1.59: 3671
        1.59 -     1.71: 0
        1.71 -     1.84: 76
  Bond restraints: 8509
  Sorted by residual:
  bond pdb=" C1  EN6 R 401 "
       pdb=" N1  EN6 R 401 "
    ideal  model  delta    sigma   weight residual
    1.410  1.510 -0.100 2.00e-02 2.50e+03 2.50e+01
  bond pdb=" C22 EN6 R 401 "
       pdb=" N3  EN6 R 401 "
    ideal  model  delta    sigma   weight residual
    1.344  1.442 -0.098 2.00e-02 2.50e+03 2.39e+01
  bond pdb=" C17 EN6 R 401 "
       pdb=" C18 EN6 R 401 "
    ideal  model  delta    sigma   weight residual
    1.381  1.435 -0.054 2.00e-02 2.50e+03 7.20e+00
  bond pdb=" C17 EN6 R 401 "
       pdb=" N1  EN6 R 401 "
    ideal  model  delta    sigma   weight residual
    1.356  1.406 -0.050 2.00e-02 2.50e+03 6.27e+00
  bond pdb=" C18 EN6 R 401 "
       pdb=" C22 EN6 R 401 "
    ideal  model  delta    sigma   weight residual
    1.479  1.525 -0.046 2.00e-02 2.50e+03 5.38e+00
  ... (remaining 8504 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.14: 11373
        3.14 -     6.29: 150
        6.29 -     9.43: 14
        9.43 -    12.57: 5
       12.57 -    15.72: 1
  Bond angle restraints: 11543
  Sorted by residual:
  angle pdb=" CB  MET R 276 "
        pdb=" CG  MET R 276 "
        pdb=" SD  MET R 276 "
      ideal   model   delta    sigma   weight residual
     112.70  128.42  -15.72 3.00e+00 1.11e-01 2.74e+01
  angle pdb=" C   VAL R  64 "
        pdb=" N   PHE R  65 "
        pdb=" CA  PHE R  65 "
      ideal   model   delta    sigma   weight residual
     120.58  112.87    7.71 1.71e+00 3.42e-01 2.03e+01
  angle pdb=" N   GLN R 115 "
        pdb=" CA  GLN R 115 "
        pdb=" CB  GLN R 115 "
      ideal   model   delta    sigma   weight residual
     110.12  116.30   -6.18 1.47e+00 4.63e-01 1.76e+01
  angle pdb=" CA  GLN R 115 "
        pdb=" CB  GLN R 115 "
        pdb=" CG  GLN R 115 "
      ideal   model   delta    sigma   weight residual
     114.10  121.79   -7.69 2.00e+00 2.50e-01 1.48e+01
  angle pdb=" C   HIS R  72 "
        pdb=" N   HIS R  73 "
        pdb=" CA  HIS R  73 "
      ideal   model   delta    sigma   weight residual
     121.54  128.81   -7.27 1.91e+00 2.74e-01 1.45e+01
  ... (remaining 11538 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.41: 4833
       27.41 -    54.82: 164
       54.82 -    82.23: 26
       82.23 -   109.64: 1
      109.64 -   137.04: 1
  Dihedral angle restraints: 5025
    sinusoidal: 1979
      harmonic: 3046
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -12.36  -73.64     1      1.00e+01 1.00e-02 6.90e+01
  dihedral pdb=" CA  CYS N  99 "
           pdb=" C   CYS N  99 "
           pdb=" N   PRO N 100 "
           pdb=" CA  PRO N 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.64  -35.36     0      5.00e+00 4.00e-02 5.00e+01
  dihedral pdb=" CB  CYS R 114 "
           pdb=" SG  CYS R 114 "
           pdb=" SG  CYS R 193 "
           pdb=" CB  CYS R 193 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -142.01   56.01     1      1.00e+01 1.00e-02 4.23e+01
  ... (remaining 5022 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 884
       0.051 -    0.102: 295
       0.102 -    0.153: 87
       0.153 -    0.204: 16
       0.204 -    0.255: 5
  Chirality restraints: 1287
  Sorted by residual:
  chirality pdb=" CB  ILE B 157 "
            pdb=" CA  ILE B 157 "
            pdb=" CG1 ILE B 157 "
            pdb=" CG2 ILE B 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CA  MET R 276 "
            pdb=" N   MET R 276 "
            pdb=" C   MET R 276 "
            pdb=" CB  MET R 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CA  LEU R 279 "
            pdb=" N   LEU R 279 "
            pdb=" C   LEU R 279 "
            pdb=" CB  LEU R 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.45e+00
  ... (remaining 1284 not shown)

  Planarity restraints: 1465
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "    0.034 2.00e-02 2.50e+03   2.59e-02 1.34e+01
        pdb=" CG  TYR B  59 "   -0.062 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE R 244 "    0.058 5.00e-02 4.00e+02   8.78e-02 1.23e+01
        pdb=" N   PRO R 245 "   -0.152 5.00e-02 4.00e+02
        pdb=" CA  PRO R 245 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO R 245 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 278 "   -0.018 2.00e-02 2.50e+03   1.96e-02 9.60e+00
        pdb=" CG  TRP R 278 "    0.049 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 278 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 278 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 278 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 278 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 278 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 278 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 278 "   -0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 278 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1462 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1275
        2.76 -     3.30: 7980
        3.30 -     3.83: 14436
        3.83 -     4.37: 17191
        4.37 -     4.90: 29413
  Nonbonded interactions: 70295
  Sorted by model distance:
  nonbonded pdb=" O   THR R 199 "
            pdb=" OG  SER R 290 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OE2 GLU B 260 "
            pdb=" OG1 THR B 263 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.318 3.040
  ... (remaining 70290 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.560
  Find NCS groups from input model:        0.070
  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:12.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.100   8509  Z= 0.331
  Angle     :  0.919  15.717  11543  Z= 0.489
  Chirality :  0.057   0.255   1287
  Planarity :  0.006   0.088   1465
  Dihedral  : 14.082 137.044   3047
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.24), residues: 1031
  helix:  0.01 (0.25), residues: 390
  sheet:  0.04 (0.31), residues: 232
  loop : -1.16 (0.28), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.003   TRP R 278 
 HIS   0.011   0.001   HIS A 357 
 PHE   0.024   0.002   PHE N 108 
 TYR   0.062   0.003   TYR B  59 
 ARG   0.008   0.001   ARG R 291 

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

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
REVERT: B  219 ARG cc_start: 0.7591 (mmm-85) cc_final: 0.7257 (mmm-85)
REVERT: N   73 ASP cc_start: 0.7515 (m-30) cc_final: 0.7017 (m-30)
REVERT: N   80 TYR cc_start: 0.8167 (m-80) cc_final: 0.7628 (m-80)
REVERT: R  190 PHE cc_start: 0.7995 (m-80) cc_final: 0.7732 (m-80)
REVERT: R  198 LEU cc_start: 0.8008 (mt) cc_final: 0.7681 (mm)
REVERT: R  200 SER cc_start: 0.7924 (p) cc_final: 0.7630 (p)
REVERT: R  220 CYS cc_start: 0.7605 (m) cc_final: 0.7173 (m)
REVERT: R  265 MET cc_start: 0.5522 (tmm) cc_final: 0.4651 (mtt)
REVERT: A  307 LYS cc_start: 0.8154 (mppt) cc_final: 0.7895 (mmtm)
REVERT: A  311 TYR cc_start: 0.8130 (m-80) cc_final: 0.7914 (m-80)
REVERT: A  343 ASP cc_start: 0.7294 (m-30) cc_final: 0.6963 (m-30)
REVERT: A  369 THR cc_start: 0.7789 (p) cc_final: 0.7573 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 1.2341
  time to fit residues: 317.8692
Evaluate side-chains
  192 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
B 266 HIS
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  77 ASN
R  81 GLN
A  14 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8509  Z= 0.312
  Angle     :  0.683  15.574  11543  Z= 0.358
  Chirality :  0.047   0.162   1287
  Planarity :  0.005   0.065   1465
  Dihedral  :  7.660 153.639   1156
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 11.38 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    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:  0.01 (0.25), residues: 1031
  helix:  1.01 (0.26), residues: 388
  sheet:  0.10 (0.32), residues: 233
  loop : -0.95 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 339 
 HIS   0.010   0.002   HIS A 357 
 PHE   0.021   0.002   PHE A 212 
 TYR   0.032   0.002   TYR B  59 
 ARG   0.005   0.001   ARG A 265 

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

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 205
  time to evaluate  : 0.950 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.7320 (m-10)
REVERT: B  219 ARG cc_start: 0.7567 (mmm-85) cc_final: 0.7155 (mmm-85)
REVERT: N   73 ASP cc_start: 0.7493 (m-30) cc_final: 0.7272 (m-30)
REVERT: R  137 VAL cc_start: 0.8512 (p) cc_final: 0.7718 (m)
REVERT: R  212 TYR cc_start: 0.6925 (m-80) cc_final: 0.6629 (m-10)
REVERT: R  265 MET cc_start: 0.5644 (tmm) cc_final: 0.4561 (mtt)
REVERT: A   25 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8029 (ttmp)
REVERT: A   35 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7875 (mp10)
REVERT: A   61 ARG cc_start: 0.7238 (mtt180) cc_final: 0.6979 (mtt180)
REVERT: A  343 ASP cc_start: 0.7595 (m-30) cc_final: 0.7292 (m-30)
  outliers start: 23
  outliers final: 11
  residues processed: 211
  average time/residue: 1.2567
  time to fit residues: 281.4885
Evaluate side-chains
  196 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 182
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   65 PHE
Chi-restraints excluded: chain R residue  132 LEU
Chi-restraints excluded: chain R residue  164 LEU
Chi-restraints excluded: chain R residue  279 LEU
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   25 LYS
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue  254 ASN
Chi-restraints excluded: chain A residue  367 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 81 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 73 optimal weight:    0.6980
   chunk 90 optimal weight:    0.5980
   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  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
N  77 ASN
R 151 GLN
A  14 ASN
A 362 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8509  Z= 0.204
  Angle     :  0.610  14.839  11543  Z= 0.315
  Chirality :  0.045   0.157   1287
  Planarity :  0.004   0.052   1465
  Dihedral  :  7.449 156.853   1156
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 14.36 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    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:  0.27 (0.25), residues: 1031
  helix:  1.44 (0.26), residues: 388
  sheet:  0.08 (0.31), residues: 231
  loop : -0.94 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 339 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.018   0.002   PHE A 212 
 TYR   0.022   0.002   TYR B  59 
 ARG   0.006   0.000   ARG A 265 

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

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 194
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.7018 (m-10)
REVERT: B  219 ARG cc_start: 0.7564 (mmm-85) cc_final: 0.7067 (mmm-85)
REVERT: N   73 ASP cc_start: 0.7457 (m-30) cc_final: 0.7231 (m-30)
REVERT: R  137 VAL cc_start: 0.8485 (p) cc_final: 0.7677 (m)
REVERT: R  143 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.8004 (tp)
REVERT: R  190 PHE cc_start: 0.8054 (m-80) cc_final: 0.7828 (m-80)
REVERT: R  265 MET cc_start: 0.5600 (tmm) cc_final: 0.4467 (mtt)
REVERT: A   25 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7991 (ttmp)
REVERT: A   35 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7844 (mp10)
  outliers start: 27
  outliers final: 15
  residues processed: 209
  average time/residue: 1.1482
  time to fit residues: 255.9830
Evaluate side-chains
  201 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 182
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   65 PHE
Chi-restraints excluded: chain R residue  115 GLN
Chi-restraints excluded: chain R residue  132 LEU
Chi-restraints excluded: chain R residue  143 ILE
Chi-restraints excluded: chain R residue  200 SER
Chi-restraints excluded: chain R residue  279 LEU
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   25 LYS
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  346 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0070
   chunk 43 optimal weight:    4.9990
   chunk 61 optimal weight:    0.5980
   chunk 92 optimal weight:    0.6980
   chunk 97 optimal weight:    0.1980
   chunk 48 optimal weight:    0.0980
   chunk 87 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 81 optimal weight:    0.5980
   overall best weight:    0.2998

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
N  77 ASN
R 151 GLN
A  14 ASN
A 362 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8509  Z= 0.155
  Angle     :  0.554  11.952  11543  Z= 0.289
  Chirality :  0.043   0.155   1287
  Planarity :  0.004   0.051   1465
  Dihedral  :  7.195 156.165   1156
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 15.80 %
    Favored  : 81.10 %
  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:  0.40 (0.25), residues: 1031
  helix:  1.62 (0.26), residues: 388
  sheet:  0.08 (0.30), residues: 233
  loop : -0.91 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.018   0.001   PHE A 212 
 TYR   0.023   0.001   TYR R 284 
 ARG   0.005   0.000   ARG A 265 

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

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 194
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.7358 (OUTLIER) cc_final: 0.6727 (m-10)
REVERT: B  219 ARG cc_start: 0.7354 (mmm-85) cc_final: 0.7137 (mmm-85)
REVERT: B  262 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7432 (mmt)
REVERT: N   80 TYR cc_start: 0.8187 (m-80) cc_final: 0.7960 (m-80)
REVERT: R  143 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7945 (tp)
REVERT: R  198 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7544 (mm)
REVERT: R  265 MET cc_start: 0.5635 (tmm) cc_final: 0.4399 (mtt)
REVERT: R  284 TYR cc_start: 0.8161 (t80) cc_final: 0.7882 (t80)
REVERT: A   17 LYS cc_start: 0.8343 (pttm) cc_final: 0.8073 (pttm)
REVERT: A   25 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7946 (ttmp)
REVERT: A   35 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7781 (mp10)
  outliers start: 28
  outliers final: 13
  residues processed: 211
  average time/residue: 1.1160
  time to fit residues: 251.4861
Evaluate side-chains
  204 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain R residue   65 PHE
Chi-restraints excluded: chain R residue   81 GLN
Chi-restraints excluded: chain R residue  115 GLN
Chi-restraints excluded: chain R residue  143 ILE
Chi-restraints excluded: chain R residue  198 LEU
Chi-restraints excluded: chain R residue  200 SER
Chi-restraints excluded: chain R residue  279 LEU
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue   25 LYS
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  241 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 72 optimal weight:    0.0000
   chunk 40 optimal weight:    0.5980
   chunk 83 optimal weight:    5.9990
   chunk 67 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.8186

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
N  77 ASN
R 151 GLN
A  14 ASN
A 362 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   8509  Z= 0.241
  Angle     :  0.606  14.826  11543  Z= 0.316
  Chirality :  0.045   0.183   1287
  Planarity :  0.004   0.052   1465
  Dihedral  :  7.320 156.717   1156
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 16.69 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.12 %
    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:  0.34 (0.26), residues: 1031
  helix:  1.52 (0.26), residues: 389
  sheet:  0.07 (0.31), residues: 231
  loop : -0.90 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 339 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.020   0.002   PHE A 212 
 TYR   0.025   0.002   TYR B  59 
 ARG   0.005   0.000   ARG A 265 

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

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 194
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.7637 (OUTLIER) cc_final: 0.7182 (m-10)
REVERT: B  197 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.5916 (mtm110)
REVERT: B  219 ARG cc_start: 0.7463 (mmm-85) cc_final: 0.7136 (mmm-85)
REVERT: R  143 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7968 (tp)
REVERT: R  212 TYR cc_start: 0.6899 (m-80) cc_final: 0.6597 (m-80)
REVERT: R  265 MET cc_start: 0.5579 (tmm) cc_final: 0.4427 (mtt)
REVERT: R  284 TYR cc_start: 0.8209 (t80) cc_final: 0.7927 (t80)
REVERT: A   25 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7978 (ttmp)
REVERT: A   35 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7851 (mp10)
REVERT: A  296 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8337 (mt)
  outliers start: 34
  outliers final: 17
  residues processed: 214
  average time/residue: 1.1768
  time to fit residues: 268.3802
Evaluate side-chains
  206 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 183
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   65 PHE
Chi-restraints excluded: chain R residue  132 LEU
Chi-restraints excluded: chain R residue  143 ILE
Chi-restraints excluded: chain R residue  200 SER
Chi-restraints excluded: chain R residue  279 LEU
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   25 LYS
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  254 ASN
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  369 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0170
   chunk 24 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 45 optimal weight:    0.1980
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   chunk 94 optimal weight:    0.6980
   overall best weight:    0.4818

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R 151 GLN
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8509  Z= 0.186
  Angle     :  0.587  13.406  11543  Z= 0.305
  Chirality :  0.043   0.182   1287
  Planarity :  0.004   0.052   1465
  Dihedral  :  7.197 156.219   1156
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 18.01 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.26), residues: 1031
  helix:  1.52 (0.26), residues: 391
  sheet:  0.02 (0.31), residues: 239
  loop : -0.80 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.018   0.001   PHE A 212 
 TYR   0.020   0.001   TYR B  59 
 ARG   0.005   0.000   ARG A 265 

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

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 191
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.7007 (m-10)
REVERT: B  219 ARG cc_start: 0.7378 (mmm-85) cc_final: 0.7096 (mmm-85)
REVERT: R  143 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7977 (tp)
REVERT: R  265 MET cc_start: 0.5579 (tmm) cc_final: 0.4401 (mtt)
REVERT: R  284 TYR cc_start: 0.8171 (t80) cc_final: 0.7893 (t80)
REVERT: A   25 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7978 (ttmp)
REVERT: A   35 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7793 (mp10)
REVERT: A  296 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8359 (mt)
  outliers start: 31
  outliers final: 18
  residues processed: 210
  average time/residue: 1.1788
  time to fit residues: 263.8137
Evaluate side-chains
  209 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 186
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   65 PHE
Chi-restraints excluded: chain R residue  132 LEU
Chi-restraints excluded: chain R residue  143 ILE
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  200 SER
Chi-restraints excluded: chain R residue  279 LEU
Chi-restraints excluded: chain R residue  286 LEU
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue   25 LYS
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  369 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0870
   chunk 54 optimal weight:    8.9990
   chunk 97 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.7762

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
N  77 ASN
R 151 GLN
A  14 ASN
A 362 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8509  Z= 0.234
  Angle     :  0.614  14.586  11543  Z= 0.321
  Chirality :  0.045   0.197   1287
  Planarity :  0.004   0.053   1465
  Dihedral  :  7.277 156.299   1156
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 18.67 %
    Favored  : 77.68 %
  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:  0.35 (0.26), residues: 1031
  helix:  1.50 (0.27), residues: 391
  sheet:  0.01 (0.31), residues: 234
  loop : -0.84 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 339 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.019   0.002   PHE A 212 
 TYR   0.025   0.002   TYR B  59 
 ARG   0.006   0.000   ARG A 265 

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

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 188
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.7178 (m-10)
REVERT: B  219 ARG cc_start: 0.7407 (mmm-85) cc_final: 0.7098 (mmm-85)
REVERT: R  143 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7958 (tp)
REVERT: R  212 TYR cc_start: 0.6915 (m-80) cc_final: 0.6651 (m-80)
REVERT: R  265 MET cc_start: 0.5553 (tmm) cc_final: 0.4419 (mtt)
REVERT: R  284 TYR cc_start: 0.8173 (t80) cc_final: 0.7898 (t80)
REVERT: A   25 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7959 (ttmp)
REVERT: A   35 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7830 (mp10)
REVERT: A  296 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8357 (mt)
  outliers start: 33
  outliers final: 18
  residues processed: 206
  average time/residue: 1.2151
  time to fit residues: 266.7820
Evaluate side-chains
  208 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 185
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   65 PHE
Chi-restraints excluded: chain R residue   81 GLN
Chi-restraints excluded: chain R residue  132 LEU
Chi-restraints excluded: chain R residue  143 ILE
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  200 SER
Chi-restraints excluded: chain R residue  279 LEU
Chi-restraints excluded: chain R residue  286 LEU
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   25 LYS
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  369 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 19 optimal weight:    0.2980
   chunk 18 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0270
   chunk 48 optimal weight:    0.3980
   chunk 9 optimal weight:    0.9980
   chunk 76 optimal weight:    0.5980
   chunk 88 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.3838

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
N  31 ASN
N  77 ASN
N 120 GLN
R 151 GLN
A  14 ASN
A 362 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8509  Z= 0.175
  Angle     :  0.597  13.123  11543  Z= 0.309
  Chirality :  0.043   0.198   1287
  Planarity :  0.004   0.053   1465
  Dihedral  :  7.156 155.870   1156
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 19.45 %
    Favored  : 77.13 %
  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:  0.43 (0.26), residues: 1031
  helix:  1.55 (0.27), residues: 391
  sheet:  0.06 (0.31), residues: 238
  loop : -0.79 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.018   0.001   PHE A 212 
 TYR   0.021   0.001   TYR R 284 
 ARG   0.006   0.000   ARG A 265 

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

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 189
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.6855 (m-10)
REVERT: B  219 ARG cc_start: 0.7391 (mmm-85) cc_final: 0.7101 (mmm-85)
REVERT: R  115 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8059 (mp10)
REVERT: R  143 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7849 (tp)
REVERT: R  265 MET cc_start: 0.5518 (tmm) cc_final: 0.4359 (mtt)
REVERT: R  284 TYR cc_start: 0.8142 (t80) cc_final: 0.7863 (t80)
REVERT: A   25 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7951 (ttmp)
REVERT: A   35 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7766 (mp10)
  outliers start: 31
  outliers final: 18
  residues processed: 209
  average time/residue: 1.1235
  time to fit residues: 250.7239
Evaluate side-chains
  209 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 186
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain R residue   65 PHE
Chi-restraints excluded: chain R residue   81 GLN
Chi-restraints excluded: chain R residue  115 GLN
Chi-restraints excluded: chain R residue  132 LEU
Chi-restraints excluded: chain R residue  143 ILE
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  200 SER
Chi-restraints excluded: chain R residue  279 LEU
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue   25 LYS
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  369 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 95 optimal weight:    0.0270
   chunk 58 optimal weight:    0.3980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
N  31 ASN
N  77 ASN
N 120 GLN
R 151 GLN
A 362 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8509  Z= 0.204
  Angle     :  0.618  13.772  11543  Z= 0.320
  Chirality :  0.044   0.198   1287
  Planarity :  0.004   0.053   1465
  Dihedral  :  7.194 156.433   1156
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 19.89 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.26), residues: 1031
  helix:  1.52 (0.26), residues: 391
  sheet:  0.00 (0.31), residues: 239
  loop : -0.73 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 339 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.022   0.002   PHE R 300 
 TYR   0.023   0.002   TYR B  59 
 ARG   0.007   0.000   ARG A 265 

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

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 187
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.6991 (m-10)
REVERT: B   75 GLN cc_start: 0.8414 (mt0) cc_final: 0.8208 (mt0)
REVERT: B  219 ARG cc_start: 0.7433 (mmm-85) cc_final: 0.7094 (mmm-85)
REVERT: R  143 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7867 (tp)
REVERT: R  212 TYR cc_start: 0.6866 (m-80) cc_final: 0.6649 (m-80)
REVERT: R  265 MET cc_start: 0.5558 (tmm) cc_final: 0.4415 (mtt)
REVERT: R  284 TYR cc_start: 0.8141 (t80) cc_final: 0.7848 (t80)
REVERT: R  286 LEU cc_start: 0.8730 (mm) cc_final: 0.8509 (mm)
REVERT: A   25 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7974 (ttmp)
REVERT: A   35 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7765 (mp10)
REVERT: A  307 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.8015 (mmtm)
  outliers start: 29
  outliers final: 16
  residues processed: 207
  average time/residue: 1.1229
  time to fit residues: 247.7909
Evaluate side-chains
  205 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 184
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   65 PHE
Chi-restraints excluded: chain R residue   81 GLN
Chi-restraints excluded: chain R residue  132 LEU
Chi-restraints excluded: chain R residue  143 ILE
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  200 SER
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue   25 LYS
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  369 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 66 optimal weight:    0.2980
   chunk 100 optimal weight:    0.5980
   chunk 92 optimal weight:    0.5980
   chunk 80 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 61 optimal weight:    0.3980
   chunk 49 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0670
   chunk 85 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:
N 120 GLN
R 151 GLN
A 362 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8509  Z= 0.174
  Angle     :  0.608  12.962  11543  Z= 0.314
  Chirality :  0.043   0.198   1287
  Planarity :  0.004   0.053   1465
  Dihedral  :  7.127 156.569   1156
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 20.66 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.26), residues: 1031
  helix:  1.55 (0.27), residues: 391
  sheet:  0.18 (0.31), residues: 234
  loop : -0.76 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.029   0.001   PHE R 300 
 TYR   0.022   0.001   TYR R 284 
 ARG   0.007   0.000   ARG A 265 

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

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

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

  2062 Ramachandran restraints generated.
    1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 192
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.6793 (m-10)
REVERT: B   75 GLN cc_start: 0.8393 (mt0) cc_final: 0.8084 (mt0)
REVERT: B  219 ARG cc_start: 0.7392 (mmm-85) cc_final: 0.7082 (mmm-85)
REVERT: N   77 ASN cc_start: 0.8149 (m-40) cc_final: 0.7910 (m110)
REVERT: R  115 GLN cc_start: 0.8406 (mp10) cc_final: 0.7746 (mp10)
REVERT: R  209 CYS cc_start: 0.5560 (m) cc_final: 0.5226 (p)
REVERT: R  265 MET cc_start: 0.5563 (tmm) cc_final: 0.4420 (mtt)
REVERT: R  284 TYR cc_start: 0.8107 (t80) cc_final: 0.7861 (t80)
REVERT: R  286 LEU cc_start: 0.8669 (mm) cc_final: 0.8401 (mm)
REVERT: A   25 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7952 (ttmp)
REVERT: A   35 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7781 (mp10)
  outliers start: 25
  outliers final: 16
  residues processed: 209
  average time/residue: 1.1079
  time to fit residues: 247.5536
Evaluate side-chains
  209 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 190
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain N residue   96 CYS
Chi-restraints excluded: chain N residue  110 VAL
Chi-restraints excluded: chain R residue   65 PHE
Chi-restraints excluded: chain R residue   81 GLN
Chi-restraints excluded: chain R residue  132 LEU
Chi-restraints excluded: chain R residue  158 LEU
Chi-restraints excluded: chain R residue  200 SER
Chi-restraints excluded: chain A residue    9 THR
Chi-restraints excluded: chain A residue   25 LYS
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  369 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 73 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 80 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 82 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 57 optimal weight:    0.4980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
N  31 ASN
N 120 GLN
R 151 GLN
A 362 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.193090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.152604 restraints weight = 9402.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3802 rms_B_bonded: 2.14
r_work: 0.3675 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3533 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8509  Z= 0.217
  Angle     :  0.648  14.096  11543  Z= 0.332
  Chirality :  0.045   0.204   1287
  Planarity :  0.005   0.076   1465
  Dihedral  :  7.225 157.109   1156
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 21.22 %
    Favored  : 76.13 %
  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:  0.41 (0.26), residues: 1031
  helix:  1.48 (0.27), residues: 391
  sheet:  0.01 (0.31), residues: 239
  loop : -0.71 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 339 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.030   0.002   PHE R 300 
 TYR   0.023   0.002   TYR B  59 
 ARG   0.007   0.000   ARG A 265 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4759.87 seconds
wall clock time: 86 minutes 41.64 seconds (5201.64 seconds total)