Starting phenix.real_space_refine
on Thu Nov 14 19:50:06 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8inr_35601/11_2024/8inr_35601.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8inr_35601/11_2024/8inr_35601.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8inr_35601/11_2024/8inr_35601.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8inr_35601/11_2024/8inr_35601.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8inr_35601/11_2024/8inr_35601.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8inr_35601/11_2024/8inr_35601.cif"
  }
  resolution = 2.73
  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=  -0.001 sd=   0.064
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
     Ca      1      9.91       5
     S      62      5.16       5
     C    4582      2.51       5
     N    1255      2.21       5
     O    1319      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 7219
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2137
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 5, 'TRANS': 265}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 114
          Classifications: {'peptide': 13}
          Link IDs: {'PTRANS': 1, 'TRANS': 11}
    Chain: "A"
      Number of atoms: 1950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1950
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 228}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2607
          Classifications: {'peptide': 340}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "G"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 410
          Classifications: {'peptide': 53}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
    Chain: "R"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.60, per 1000 atoms: 0.64
  Number of scatterers: 7219
  At special positions: 0
  Unit cell: (82.467, 96.39, 126.378, 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)
     Ca      1     19.99
     S      62     16.00
     O    1319      8.00
     N    1255      7.00
     C    4582      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 264 " - pdb=" SG  CYS R 270 " distance=2.03

  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: 1.76
  Conformation dependent library (CDL) restraints added in 997.6 milliseconds
  

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1732

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      46.6% alpha, 17.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'R' and resid 39 through 63
      removed outlier: 3.712A  pdb=" N   PHE R  43 " --> pdb=" O   ALA R  39 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   LEU R  46 " --> pdb=" O   VAL R  42 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLY R  47 " --> pdb=" O   PHE R  43 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 69 through 100
    Processing helix  chain 'R' and resid 107 through 146
    Processing helix  chain 'R' and resid 147 through 153
      removed outlier: 3.805A  pdb=" N   TYR R 150 " --> pdb=" O   ALA R 147 " (cutoff:3.500A)
      removed outlier: 5.669A  pdb=" N   HIS R 151 " --> pdb=" O   LEU R 148 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 155 through 180
    Processing helix  chain 'R' and resid 183 through 221
      removed outlier: 4.065A  pdb=" N   ILE R 187 " --> pdb=" O   SER R 183 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   LEU R 201 " --> pdb=" O   MET R 197 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   HIS R 207 " --> pdb=" O   SER R 203 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   MET R 208 " --> pdb=" O   LEU R 204 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   THR R 214 " --> pdb=" O   LEU R 210 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 232 through 264
      removed outlier: 4.067A  pdb=" N   GLY R 236 " --> pdb=" O   THR R 232 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   VAL R 246 " --> pdb=" O   MET R 242 " (cutoff:3.500A)
      Proline residue:  R 253  - end of helix
    Processing helix  chain 'R' and resid 267 through 275
    Processing helix  chain 'R' and resid 276 through 296
      removed outlier: 3.748A  pdb=" N   LEU R 283 " --> pdb=" O   MET R 279 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   SER R 288 " --> pdb=" O   ILE R 284 " (cutoff:3.500A)
      Proline residue:  R 292  - end of helix
    Processing helix  chain 'R' and resid 299 through 311
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 3.712A  pdb=" N   LYS A  17 " --> pdb=" O   SER A  13 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
      removed outlier: 3.710A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.615A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.631A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 314 through 318
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.958A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 5 through 25
    Processing helix  chain 'B' and resid 31 through 35
      removed outlier: 3.526A  pdb=" N   THR B  34 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ASN B  35 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 31 through 35'
    Processing helix  chain 'G' and resid 11 through 24
      removed outlier: 3.827A  pdb=" N   GLU G  22 " --> pdb=" O   GLN G  18 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 34
    Processing helix  chain 'G' and resid 40 through 44
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.859A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 6.156A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 9.417A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.769A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.575A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 52
      removed outlier: 5.800A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.765A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.599A  pdb=" N   CYS B 121 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.757A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.261A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU B 210 " --> pdb=" O   GLN B 220 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 4.267A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.355A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)

    382 hydrogen bonds defined for protein.
    1092 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: 2.30

  Time building geometry restraints manager: 2.04 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2246
        1.33 -     1.45: 1253
        1.45 -     1.57: 3771
        1.57 -     1.69: 0
        1.69 -     1.81: 93
  Bond restraints: 7363
  Sorted by residual:
  bond pdb=" CA  GLU R  92 "
       pdb=" C   GLU R  92 "
    ideal  model  delta    sigma   weight residual
    1.524  1.475  0.049 1.26e-02 6.30e+03 1.48e+01
  bond pdb=" C   GLU R  92 "
       pdb=" N   THR R  93 "
    ideal  model  delta    sigma   weight residual
    1.335  1.297  0.038 1.31e-02 5.83e+03 8.49e+00
  bond pdb=" CB  LYS A  53 "
       pdb=" CG  LYS A  53 "
    ideal  model  delta    sigma   weight residual
    1.520  1.448  0.072 3.00e-02 1.11e+03 5.82e+00
  bond pdb=" CG1 ILE R 144 "
       pdb=" CD1 ILE R 144 "
    ideal  model  delta    sigma   weight residual
    1.513  1.429  0.084 3.90e-02 6.57e+02 4.60e+00
  bond pdb=" CA  GLU L   5 "
       pdb=" CB  GLU L   5 "
    ideal  model  delta    sigma   weight residual
    1.533  1.499  0.034 1.65e-02 3.67e+03 4.30e+00
  ... (remaining 7358 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 9668
        2.27 -     4.53: 253
        4.53 -     6.80: 30
        6.80 -     9.07: 7
        9.07 -    11.33: 2
  Bond angle restraints: 9960
  Sorted by residual:
  angle pdb=" N   GLU R  92 "
        pdb=" CA  GLU R  92 "
        pdb=" C   GLU R  92 "
      ideal   model   delta    sigma   weight residual
     111.14  104.28    6.86 1.08e+00 8.57e-01 4.03e+01
  angle pdb=" C   GLU L   5 "
        pdb=" CA  GLU L   5 "
        pdb=" CB  GLU L   5 "
      ideal   model   delta    sigma   weight residual
     110.62   99.29   11.33 1.86e+00 2.89e-01 3.71e+01
  angle pdb=" N   ALA B 305 "
        pdb=" CA  ALA B 305 "
        pdb=" C   ALA B 305 "
      ideal   model   delta    sigma   weight residual
     114.75  109.39    5.36 1.26e+00 6.30e-01 1.81e+01
  angle pdb=" C   PHE B 234 "
        pdb=" N   PHE B 235 "
        pdb=" CA  PHE B 235 "
      ideal   model   delta    sigma   weight residual
     121.80  131.63   -9.83 2.44e+00 1.68e-01 1.62e+01
  angle pdb=" N   HIS L   6 "
        pdb=" CA  HIS L   6 "
        pdb=" C   HIS L   6 "
      ideal   model   delta    sigma   weight residual
     110.64  116.24   -5.60 1.48e+00 4.57e-01 1.43e+01
  ... (remaining 9955 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.26: 3957
       17.26 -    34.53: 360
       34.53 -    51.79: 64
       51.79 -    69.06: 11
       69.06 -    86.32: 6
  Dihedral angle restraints: 4398
    sinusoidal: 1731
      harmonic: 2667
  Sorted by residual:
  dihedral pdb=" C   GLU L   5 "
           pdb=" N   GLU L   5 "
           pdb=" CA  GLU L   5 "
           pdb=" CB  GLU L   5 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.14  -12.46     0      2.50e+00 1.60e-01 2.48e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.65   24.35     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CA  GLU A 392 "
           pdb=" C   GLU A 392 "
           pdb=" N   LEU A 393 "
           pdb=" CA  LEU A 393 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.20   22.80     0      5.00e+00 4.00e-02 2.08e+01
  ... (remaining 4395 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 602
       0.040 -    0.081: 350
       0.081 -    0.121: 137
       0.121 -    0.162: 31
       0.162 -    0.202: 12
  Chirality restraints: 1132
  Sorted by residual:
  chirality pdb=" CG  LEU B 255 "
            pdb=" CB  LEU B 255 "
            pdb=" CD1 LEU B 255 "
            pdb=" CD2 LEU B 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  LEU R 134 "
            pdb=" N   LEU R 134 "
            pdb=" C   LEU R 134 "
            pdb=" CB  LEU R 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.80e-01
  chirality pdb=" CA  PHE B 234 "
            pdb=" N   PHE B 234 "
            pdb=" C   PHE B 234 "
            pdb=" CB  PHE B 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.31e-01
  ... (remaining 1129 not shown)

  Planarity restraints: 1260
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 222 "   -0.035 5.00e-02 4.00e+02   5.35e-02 4.57e+00
        pdb=" N   PRO R 223 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO R 223 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO R 223 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU L   5 "    0.010 2.00e-02 2.50e+03   2.07e-02 4.29e+00
        pdb=" C   GLU L   5 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   GLU L   5 "    0.014 2.00e-02 2.50e+03
        pdb=" N   HIS L   6 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "    0.032 5.00e-02 4.00e+02   4.87e-02 3.79e+00
        pdb=" N   PRO B 194 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1257 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 338
        2.70 -     3.25: 7264
        3.25 -     3.80: 12006
        3.80 -     4.35: 14793
        4.35 -     4.90: 25596
  Nonbonded interactions: 59997
  Sorted by model distance:
  nonbonded pdb=" O   PHE L   7 "
            pdb="CA    CA R 501 "
     model   vdw
     2.153 2.510
  nonbonded pdb=" OH  TYR A 318 "
            pdb=" OD2 ASP A 343 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" ND2 ASN B 237 "
            pdb=" OD1 ASP G  36 "
     model   vdw
     2.177 3.120
  nonbonded pdb=" O   TYR R  97 "
            pdb=" ND2 ASN R 101 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" O   ASP B 228 "
            pdb=" OG  SER B 245 "
     model   vdw
     2.277 3.040
  ... (remaining 59992 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:             0.810
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.470
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6374
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      :  0.012   0.084   7363  Z= 0.750
  Angle     :  0.883  11.334   9960  Z= 0.502
  Chirality :  0.058   0.202   1132
  Planarity :  0.005   0.053   1260
  Dihedral  : 13.812  86.324   2663
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.27), residues: 898
  helix:  0.26 (0.25), residues: 396
  sheet: -1.48 (0.36), residues: 181
  loop : -1.61 (0.33), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP B  63 
 HIS   0.015   0.003   HIS B  91 
 PHE   0.031   0.003   PHE B 151 
 TYR   0.031   0.002   TYR B 105 
 ARG   0.013   0.001   ARG B 197 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
REVERT: R  152 HIS cc_start: 0.7071 (m170) cc_final: 0.6828 (m-70)
REVERT: R  153 ILE cc_start: 0.7774 (mt) cc_final: 0.7429 (mt)
REVERT: R  279 MET cc_start: 0.6807 (mmm) cc_final: 0.6517 (mmm)
REVERT: R  302 MET cc_start: 0.7347 (ttm) cc_final: 0.7086 (ttt)
REVERT: A  216 LYS cc_start: 0.7497 (mtmm) cc_final: 0.7206 (mtpp)
REVERT: A  271 ASN cc_start: 0.7191 (m110) cc_final: 0.6973 (m-40)
REVERT: A  335 THR cc_start: 0.7705 (t) cc_final: 0.7458 (m)
REVERT: A  347 ARG cc_start: 0.6586 (ttm-80) cc_final: 0.6091 (ttm-80)
REVERT: A  373 ARG cc_start: 0.7637 (tpp-160) cc_final: 0.7075 (tpp-160)
REVERT: A  378 ASP cc_start: 0.7121 (m-30) cc_final: 0.6907 (m-30)
REVERT: A  390 GLN cc_start: 0.7416 (pt0) cc_final: 0.7206 (pt0)
REVERT: B   43 ILE cc_start: 0.7343 (mp) cc_final: 0.7122 (mm)
REVERT: B  188 MET cc_start: 0.7984 (mmm) cc_final: 0.7298 (mmm)
REVERT: B  239 ASN cc_start: 0.7596 (m-40) cc_final: 0.7371 (m-40)
REVERT: B  298 ASP cc_start: 0.7463 (m-30) cc_final: 0.7230 (m-30)
REVERT: B  314 ARG cc_start: 0.7121 (ttp-170) cc_final: 0.6813 (ttp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 1.3129
  time to fit residues: 200.5602
Evaluate side-chains
  92 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 1.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 70 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 81 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
L   6 HIS
A  31 GLN
A 213 GLN
A 236 GLN
A 279 ASN
A 292 ASN
B 119 ASN
B 155 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6475
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7363  Z= 0.228
  Angle     :  0.587   7.329   9960  Z= 0.320
  Chirality :  0.044   0.142   1132
  Planarity :  0.004   0.042   1260
  Dihedral  :  5.311  64.200    994
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 10.41 %
    Favored  : 87.06 %
  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: -0.24 (0.28), residues: 898
  helix:  1.36 (0.26), residues: 386
  sheet: -1.10 (0.38), residues: 175
  loop : -1.39 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP R 167 
 HIS   0.008   0.002   HIS A 220 
 PHE   0.020   0.002   PHE A 222 
 TYR   0.016   0.001   TYR R  72 
 ARG   0.003   0.000   ARG B 150 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
REVERT: R  279 MET cc_start: 0.6672 (mmm) cc_final: 0.6344 (mmm)
REVERT: R  285 MET cc_start: 0.6785 (mtp) cc_final: 0.6585 (mtp)
REVERT: A  347 ARG cc_start: 0.6831 (ttm-80) cc_final: 0.6240 (ttm-80)
REVERT: A  373 ARG cc_start: 0.7903 (tpp-160) cc_final: 0.7543 (tpp-160)
REVERT: B   43 ILE cc_start: 0.7330 (mp) cc_final: 0.7123 (mm)
REVERT: B   59 TYR cc_start: 0.7136 (OUTLIER) cc_final: 0.6312 (m-80)
REVERT: B  217 MET cc_start: 0.7362 (pmm) cc_final: 0.7154 (pmm)
REVERT: B  221 THR cc_start: 0.7509 (m) cc_final: 0.7249 (m)
REVERT: B  239 ASN cc_start: 0.7300 (m-40) cc_final: 0.7089 (m-40)
REVERT: B  275 SER cc_start: 0.7939 (p) cc_final: 0.7696 (m)
  outliers start: 20
  outliers final: 6
  residues processed: 116
  average time/residue: 1.2266
  time to fit residues: 150.9557
Evaluate side-chains
  96 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  179 LEU
Chi-restraints excluded: chain L residue   11 LYS
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  309 GLU
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   72 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 45 optimal weight:    0.4980
   chunk 25 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0870
   chunk 72 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
L   6 HIS
A 236 GLN
A 279 ASN
B 230 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6487
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7363  Z= 0.195
  Angle     :  0.524   6.096   9960  Z= 0.287
  Chirality :  0.042   0.140   1132
  Planarity :  0.004   0.042   1260
  Dihedral  :  4.926  65.627    994
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 13.32 %
    Favored  : 83.38 %
  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:  0.13 (0.29), residues: 898
  helix:  1.79 (0.27), residues: 389
  sheet: -1.16 (0.37), residues: 182
  loop : -1.22 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 234 
 HIS   0.006   0.001   HIS A 362 
 PHE   0.017   0.002   PHE A 222 
 TYR   0.010   0.001   TYR B 289 
 ARG   0.002   0.000   ARG A 374 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   65 LYS cc_start: 0.7827 (mptt) cc_final: 0.7493 (mptt)
REVERT: R  234 MET cc_start: 0.5574 (mmm) cc_final: 0.4999 (tpt)
REVERT: R  274 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.7128 (mtp)
REVERT: R  279 MET cc_start: 0.6772 (mmm) cc_final: 0.6435 (mmm)
REVERT: R  285 MET cc_start: 0.6890 (mtp) cc_final: 0.6677 (mtp)
REVERT: R  297 PHE cc_start: 0.6682 (m-80) cc_final: 0.5759 (t80)
REVERT: A  216 LYS cc_start: 0.7787 (mtmm) cc_final: 0.7428 (mttm)
REVERT: A  373 ARG cc_start: 0.7798 (tpp-160) cc_final: 0.7393 (tpp-160)
REVERT: B   59 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6351 (m-80)
REVERT: B  217 MET cc_start: 0.7339 (pmm) cc_final: 0.7125 (pmm)
REVERT: B  239 ASN cc_start: 0.7228 (m-40) cc_final: 0.6939 (m-40)
REVERT: B  275 SER cc_start: 0.8034 (p) cc_final: 0.7700 (m)
REVERT: G   38 MET cc_start: 0.5684 (OUTLIER) cc_final: 0.5148 (tmm)
  outliers start: 26
  outliers final: 7
  residues processed: 114
  average time/residue: 1.1078
  time to fit residues: 134.1320
Evaluate side-chains
  103 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  274 MET
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   38 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 42 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0170
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
L   6 HIS
A 213 GLN
A 267 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6498
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7363  Z= 0.196
  Angle     :  0.514   6.066   9960  Z= 0.281
  Chirality :  0.042   0.181   1132
  Planarity :  0.004   0.042   1260
  Dihedral  :  4.851  68.267    994
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 14.72 %
    Favored  : 81.60 %
  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:  0.33 (0.29), residues: 898
  helix:  1.91 (0.27), residues: 389
  sheet: -0.98 (0.37), residues: 180
  loop : -1.11 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.009   0.001   HIS A 220 
 PHE   0.014   0.002   PHE B 151 
 TYR   0.010   0.001   TYR R  72 
 ARG   0.005   0.000   ARG A 342 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 99
  time to evaluate  : 0.832 
Fit side-chains
REVERT: R   43 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.5353 (t80)
REVERT: R   65 LYS cc_start: 0.7768 (mptt) cc_final: 0.7452 (mptt)
REVERT: R  234 MET cc_start: 0.5574 (OUTLIER) cc_final: 0.4987 (tpt)
REVERT: R  279 MET cc_start: 0.6577 (mmm) cc_final: 0.6307 (mmm)
REVERT: R  285 MET cc_start: 0.6900 (mtp) cc_final: 0.6639 (mtp)
REVERT: R  297 PHE cc_start: 0.6836 (m-80) cc_final: 0.5917 (t80)
REVERT: A  221 MET cc_start: 0.8534 (ttm) cc_final: 0.8315 (ttp)
REVERT: A  363 PHE cc_start: 0.8646 (m-80) cc_final: 0.8442 (m-80)
REVERT: A  373 ARG cc_start: 0.7733 (tpp-160) cc_final: 0.7293 (tpp-160)
REVERT: B   59 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.6356 (m-80)
REVERT: B  195 ASP cc_start: 0.7310 (p0) cc_final: 0.6943 (p0)
REVERT: B  239 ASN cc_start: 0.7383 (m-40) cc_final: 0.7041 (m-40)
REVERT: B  275 SER cc_start: 0.8107 (p) cc_final: 0.7752 (m)
  outliers start: 29
  outliers final: 10
  residues processed: 113
  average time/residue: 1.0975
  time to fit residues: 132.0473
Evaluate side-chains
  106 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   43 PHE
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  234 MET
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  309 GLU
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  334 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 64 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
R 152 HIS
R 215 HIS
L   6 HIS
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6529
moved from start:          0.3491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7363  Z= 0.223
  Angle     :  0.536  10.650   9960  Z= 0.289
  Chirality :  0.043   0.306   1132
  Planarity :  0.004   0.044   1260
  Dihedral  :  4.848  67.787    994
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 16.24 %
    Favored  : 80.08 %
  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 (0.29), residues: 898
  helix:  1.88 (0.27), residues: 390
  sheet: -0.98 (0.37), residues: 183
  loop : -1.03 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.011   0.001   HIS A 220 
 PHE   0.016   0.002   PHE B 151 
 TYR   0.012   0.001   TYR B 289 
 ARG   0.004   0.000   ARG A 342 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 99
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
REVERT: R   43 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.5330 (t80)
REVERT: R   65 LYS cc_start: 0.7798 (mptt) cc_final: 0.7493 (mptt)
REVERT: R  217 LYS cc_start: 0.6700 (OUTLIER) cc_final: 0.6412 (mtmp)
REVERT: R  234 MET cc_start: 0.5618 (mmm) cc_final: 0.5036 (tpt)
REVERT: R  279 MET cc_start: 0.6669 (mmm) cc_final: 0.6431 (mmm)
REVERT: R  285 MET cc_start: 0.6905 (mtp) cc_final: 0.6661 (mtp)
REVERT: R  297 PHE cc_start: 0.6867 (m-80) cc_final: 0.5979 (t80)
REVERT: A  221 MET cc_start: 0.8585 (ttm) cc_final: 0.8371 (ttp)
REVERT: A  229 ASP cc_start: 0.6216 (OUTLIER) cc_final: 0.5883 (p0)
REVERT: A  373 ARG cc_start: 0.7848 (tpp-160) cc_final: 0.7424 (tpp-160)
REVERT: B   59 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.6397 (m-80)
REVERT: B  124 TYR cc_start: 0.8395 (m-80) cc_final: 0.8055 (m-80)
REVERT: B  195 ASP cc_start: 0.7328 (p0) cc_final: 0.6978 (p0)
REVERT: B  219 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6711 (mmm-85)
REVERT: B  275 SER cc_start: 0.8152 (p) cc_final: 0.7783 (m)
REVERT: B  323 ASP cc_start: 0.7055 (p0) cc_final: 0.6635 (p0)
REVERT: G   38 MET cc_start: 0.5763 (tmm) cc_final: 0.5060 (tmm)
  outliers start: 29
  outliers final: 14
  residues processed: 117
  average time/residue: 1.0328
  time to fit residues: 128.8167
Evaluate side-chains
  112 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   43 PHE
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  217 LYS
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  309 GLU
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  325 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 51 optimal weight:   20.0000
   chunk 21 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0040
   chunk 72 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0370
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 83 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.4470

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

Flipped N/Q/H residues before XYZ refinement:
R 152 HIS
L   6 HIS
A 220 HIS
A 390 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6491
moved from start:          0.3672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7363  Z= 0.159
  Angle     :  0.490   8.403   9960  Z= 0.266
  Chirality :  0.042   0.273   1132
  Planarity :  0.003   0.044   1260
  Dihedral  :  4.718  69.711    994
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 16.62 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.29), residues: 898
  helix:  2.07 (0.27), residues: 392
  sheet: -1.00 (0.37), residues: 181
  loop : -0.96 (0.34), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.020   0.001   PHE R 169 
 TYR   0.011   0.001   TYR R  72 
 ARG   0.003   0.000   ARG A 342 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 101
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
REVERT: R   43 PHE cc_start: 0.6660 (OUTLIER) cc_final: 0.5208 (t80)
REVERT: R   65 LYS cc_start: 0.7645 (mptt) cc_final: 0.7358 (mptt)
REVERT: R  217 LYS cc_start: 0.6597 (OUTLIER) cc_final: 0.6297 (mtmp)
REVERT: R  234 MET cc_start: 0.5547 (OUTLIER) cc_final: 0.4992 (tpt)
REVERT: R  279 MET cc_start: 0.6586 (mmm) cc_final: 0.6356 (mmm)
REVERT: R  285 MET cc_start: 0.6881 (mtp) cc_final: 0.6643 (mtp)
REVERT: R  297 PHE cc_start: 0.6881 (m-80) cc_final: 0.5939 (t80)
REVERT: A   29 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6531 (tp-100)
REVERT: A  356 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6935 (mmp80)
REVERT: A  373 ARG cc_start: 0.7785 (tpp-160) cc_final: 0.7359 (tpp-160)
REVERT: A  392 GLU cc_start: 0.7402 (mp0) cc_final: 0.6652 (mt-10)
REVERT: B  124 TYR cc_start: 0.8248 (m-80) cc_final: 0.7940 (m-80)
REVERT: B  195 ASP cc_start: 0.7323 (p0) cc_final: 0.6960 (p0)
REVERT: B  219 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6704 (mmm-85)
REVERT: B  275 SER cc_start: 0.8198 (p) cc_final: 0.7780 (m)
REVERT: G   38 MET cc_start: 0.5710 (tmm) cc_final: 0.4976 (tmm)
  outliers start: 30
  outliers final: 14
  residues processed: 117
  average time/residue: 0.9087
  time to fit residues: 112.9827
Evaluate side-chains
  116 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   43 PHE
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  179 LEU
Chi-restraints excluded: chain R residue  217 LYS
Chi-restraints excluded: chain R residue  234 MET
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  309 GLU
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  334 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0670
   chunk 48 optimal weight:    0.0870
   chunk 86 optimal weight:    8.9990
   chunk 54 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 40 optimal weight:    0.5980
   chunk 53 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   overall best weight:    0.4696

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

Flipped N/Q/H residues before XYZ refinement:
R 152 HIS
L   6 HIS
A 390 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6487
moved from start:          0.3813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7363  Z= 0.163
  Angle     :  0.493   7.028   9960  Z= 0.268
  Chirality :  0.041   0.245   1132
  Planarity :  0.003   0.046   1260
  Dihedral  :  4.663  70.086    994
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 17.64 %
    Favored  : 78.68 %
  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:  0.66 (0.29), residues: 898
  helix:  2.20 (0.27), residues: 392
  sheet: -0.91 (0.37), residues: 179
  loop : -0.92 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.012   0.001   HIS A 220 
 PHE   0.014   0.001   PHE A 222 
 TYR   0.013   0.001   TYR R  72 
 ARG   0.003   0.000   ARG A 342 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   43 PHE cc_start: 0.6634 (OUTLIER) cc_final: 0.5125 (t80)
REVERT: R   65 LYS cc_start: 0.7580 (mptt) cc_final: 0.7326 (mptt)
REVERT: R  217 LYS cc_start: 0.6548 (OUTLIER) cc_final: 0.6246 (mtmp)
REVERT: R  234 MET cc_start: 0.5556 (mmm) cc_final: 0.5004 (tpt)
REVERT: R  279 MET cc_start: 0.6581 (mmm) cc_final: 0.6361 (mmm)
REVERT: R  285 MET cc_start: 0.6874 (mtp) cc_final: 0.6631 (mtp)
REVERT: R  297 PHE cc_start: 0.6826 (m-80) cc_final: 0.5974 (t80)
REVERT: A  216 LYS cc_start: 0.7626 (mtmm) cc_final: 0.7287 (mttm)
REVERT: A  356 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6905 (mmp80)
REVERT: A  373 ARG cc_start: 0.7729 (tpp-160) cc_final: 0.7238 (tpp-160)
REVERT: B  124 TYR cc_start: 0.8246 (m-80) cc_final: 0.7933 (m-80)
REVERT: B  195 ASP cc_start: 0.7354 (p0) cc_final: 0.6966 (p0)
REVERT: B  219 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6679 (mmm-85)
REVERT: B  275 SER cc_start: 0.8208 (p) cc_final: 0.7795 (m)
  outliers start: 29
  outliers final: 17
  residues processed: 117
  average time/residue: 1.0367
  time to fit residues: 128.6316
Evaluate side-chains
  116 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   43 PHE
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  179 LEU
Chi-restraints excluded: chain R residue  217 LYS
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  233 LYS
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  309 GLU
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  334 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 68 optimal weight:    5.9990
   chunk 78 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
R 152 HIS
L   6 HIS
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6532
moved from start:          0.3867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7363  Z= 0.223
  Angle     :  0.535   6.668   9960  Z= 0.291
  Chirality :  0.043   0.234   1132
  Planarity :  0.004   0.046   1260
  Dihedral  :  4.783  68.234    994
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 17.64 %
    Favored  : 78.17 %
  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:  0.62 (0.29), residues: 898
  helix:  2.11 (0.26), residues: 391
  sheet: -0.96 (0.37), residues: 174
  loop : -0.84 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.010   0.001   HIS A 220 
 PHE   0.022   0.002   PHE R 169 
 TYR   0.012   0.001   TYR R  72 
 ARG   0.003   0.000   ARG A 342 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 99
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
REVERT: R   43 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.5179 (t80)
REVERT: R   65 LYS cc_start: 0.7608 (mptt) cc_final: 0.7342 (mptt)
REVERT: R  217 LYS cc_start: 0.6691 (OUTLIER) cc_final: 0.6402 (mtmp)
REVERT: R  234 MET cc_start: 0.5613 (mmm) cc_final: 0.5019 (tpt)
REVERT: R  279 MET cc_start: 0.6618 (mmm) cc_final: 0.6375 (mmm)
REVERT: R  297 PHE cc_start: 0.6841 (m-80) cc_final: 0.5984 (t80)
REVERT: A   29 GLN cc_start: 0.7123 (mm-40) cc_final: 0.6239 (tp-100)
REVERT: A  356 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6994 (mmp80)
REVERT: A  373 ARG cc_start: 0.7720 (tpp-160) cc_final: 0.7231 (tpp-160)
REVERT: A  392 GLU cc_start: 0.7417 (mp0) cc_final: 0.6632 (mt-10)
REVERT: B   59 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6376 (m-80)
REVERT: B  124 TYR cc_start: 0.8407 (m-80) cc_final: 0.8111 (m-80)
REVERT: B  219 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6671 (mmm-85)
REVERT: B  323 ASP cc_start: 0.7092 (p0) cc_final: 0.6454 (p0)
  outliers start: 33
  outliers final: 18
  residues processed: 116
  average time/residue: 1.1532
  time to fit residues: 142.4404
Evaluate side-chains
  123 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   43 PHE
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  217 LYS
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  309 GLU
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  334 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 73 optimal weight:    4.9990
   chunk 76 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
R 152 HIS
L   6 HIS
** A  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 GLN
B  16 ASN
G  18 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6545
moved from start:          0.3984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7363  Z= 0.237
  Angle     :  0.560  11.950   9960  Z= 0.299
  Chirality :  0.044   0.334   1132
  Planarity :  0.004   0.045   1260
  Dihedral  :  4.830  68.613    994
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.65 %
    Favored  : 78.30 %
  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 (0.28), residues: 898
  helix:  2.06 (0.26), residues: 388
  sheet: -1.02 (0.37), residues: 176
  loop : -0.85 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 234 
 HIS   0.010   0.001   HIS A 220 
 PHE   0.016   0.002   PHE B 151 
 TYR   0.014   0.002   TYR R  72 
 ARG   0.003   0.000   ARG A 342 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
REVERT: R   43 PHE cc_start: 0.6854 (OUTLIER) cc_final: 0.5253 (t80)
REVERT: R   65 LYS cc_start: 0.7625 (mptt) cc_final: 0.7354 (mptt)
REVERT: R  217 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6409 (mtmp)
REVERT: R  234 MET cc_start: 0.5632 (mmm) cc_final: 0.5031 (tpt)
REVERT: R  279 MET cc_start: 0.6651 (mmm) cc_final: 0.6403 (mmm)
REVERT: R  297 PHE cc_start: 0.6857 (m-80) cc_final: 0.5991 (t80)
REVERT: A   29 GLN cc_start: 0.7225 (mm-40) cc_final: 0.6514 (tp-100)
REVERT: A  232 ARG cc_start: 0.7802 (ptt180) cc_final: 0.7593 (ttp-170)
REVERT: A  323 ASP cc_start: 0.6851 (p0) cc_final: 0.6575 (p0)
REVERT: A  356 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6984 (mmp80)
REVERT: A  373 ARG cc_start: 0.7806 (tpp-160) cc_final: 0.7337 (tpp-160)
REVERT: A  392 GLU cc_start: 0.7422 (mp0) cc_final: 0.6675 (mt-10)
REVERT: B  124 TYR cc_start: 0.8390 (m-80) cc_final: 0.7993 (m-80)
REVERT: B  219 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6684 (mmm-85)
REVERT: B  323 ASP cc_start: 0.7087 (p0) cc_final: 0.6489 (p0)
  outliers start: 24
  outliers final: 18
  residues processed: 108
  average time/residue: 1.1429
  time to fit residues: 131.2141
Evaluate side-chains
  114 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   43 PHE
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  217 LYS
Chi-restraints excluded: chain A residue   26 ILE
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  309 GLU
Chi-restraints excluded: chain A residue  356 ARG
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  325 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 40 optimal weight:    0.1980
   chunk 59 optimal weight:    3.9990
   chunk 89 optimal weight:    0.4980
   chunk 82 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0970
   chunk 56 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
R 152 HIS
L   6 HIS
** A  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6549
moved from start:          0.4044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7363  Z= 0.241
  Angle     :  0.558  10.852   9960  Z= 0.301
  Chirality :  0.044   0.294   1132
  Planarity :  0.004   0.045   1260
  Dihedral  :  4.864  68.701    994
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 18.91 %
    Favored  : 77.92 %
  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:  0.55 (0.28), residues: 898
  helix:  2.03 (0.26), residues: 388
  sheet: -0.91 (0.38), residues: 170
  loop : -0.89 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 234 
 HIS   0.016   0.001   HIS A 220 
 PHE   0.022   0.002   PHE R 169 
 TYR   0.017   0.002   TYR R  72 
 ARG   0.003   0.000   ARG A 342 

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

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

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1796 Ramachandran restraints generated.
    898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
REVERT: R   43 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.5233 (t80)
REVERT: R   65 LYS cc_start: 0.7627 (mptt) cc_final: 0.7354 (mptt)
REVERT: R  217 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.6403 (mtmp)
REVERT: R  234 MET cc_start: 0.5649 (OUTLIER) cc_final: 0.5040 (tpt)
REVERT: R  279 MET cc_start: 0.6667 (mmm) cc_final: 0.6419 (mmm)
REVERT: R  297 PHE cc_start: 0.6861 (m-80) cc_final: 0.5982 (t80)
REVERT: L   11 LYS cc_start: 0.5839 (mppt) cc_final: 0.5471 (mmmt)
REVERT: A  232 ARG cc_start: 0.7822 (ptt180) cc_final: 0.7603 (ttp-170)
REVERT: A  373 ARG cc_start: 0.7720 (tpp-160) cc_final: 0.7238 (tpp-160)
REVERT: A  392 GLU cc_start: 0.7520 (mp0) cc_final: 0.6745 (mt-10)
REVERT: B  124 TYR cc_start: 0.8421 (m-80) cc_final: 0.8029 (m-80)
REVERT: B  219 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6688 (mmm-85)
  outliers start: 25
  outliers final: 17
  residues processed: 111
  average time/residue: 1.1971
  time to fit residues: 140.5981
Evaluate side-chains
  116 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   43 PHE
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue   99 LEU
Chi-restraints excluded: chain R residue  217 LYS
Chi-restraints excluded: chain R residue  234 MET
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  309 GLU
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  325 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 13 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
R 152 HIS
L   6 HIS
** A  50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.206042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.166625 restraints weight = 7380.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3958 rms_B_bonded: 2.34
r_work: 0.3703 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3584 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.4134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7363  Z= 0.231
  Angle     :  0.553  11.015   9960  Z= 0.299
  Chirality :  0.044   0.308   1132
  Planarity :  0.004   0.045   1260
  Dihedral  :  4.840  69.076    994
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.04 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.28), residues: 898
  helix:  2.04 (0.26), residues: 388
  sheet: -1.08 (0.37), residues: 178
  loop : -0.89 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 234 
 HIS   0.018   0.002   HIS A 220 
 PHE   0.016   0.002   PHE B 151 
 TYR   0.018   0.001   TYR R  72 
 ARG   0.003   0.000   ARG A 342 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2971.20 seconds
wall clock time: 59 minutes 8.91 seconds (3548.91 seconds total)