Starting phenix.real_space_refine
on Thu Jul  2 11:09:59 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8hdp_34677/07_2026/8hdp_34677.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hdp_34677/07_2026/8hdp_34677.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hdp_34677/07_2026/8hdp_34677.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hdp_34677/07_2026/8hdp_34677.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8hdp_34677/07_2026/8hdp_34677.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8hdp_34677/07_2026/8hdp_34677.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hdp_34677/07_2026/8hdp_34677.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hdp_34677/07_2026/8hdp_34677.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    5280      2.51       5
     N    1430      2.21       5
     O    1519      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8282
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1985
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1985
          Classifications: {'peptide': 238}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 231}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 2594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2594
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    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: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 970
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "R"
      Number of atoms: 2166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2166
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 11, 'TRANS': 268}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "R"
      Number of atoms: 131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 131
          Unusual residues: {'ADN%rna3p': 1, 'CLR': 4}
          Classifications: {'undetermined': 5}
          Modifications used: {'rna3p': 1}
          Link IDs: {None: 4}
  Time building chain proxies: 1.98, per 1000 atoms: 0.24
  Number of scatterers: 8282
  At special positions: 0
  Unit cell: (95.68, 76.96, 130, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    1519      8.00
     N    1430      7.00
     C    5280      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, 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=2.03
    Simple disulfide: pdb=" SG  CYS R  78 " - pdb=" SG  CYS R 171 " 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: 0.72
  Conformation dependent library (CDL) restraints added in 426.9 milliseconds
  

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1960

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 10 sheets defined
      42.8% alpha, 20.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 39
      removed outlier: 4.267A  pdb=" N   GLU A  15 " --> pdb=" O   ASP A  11 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 56
    Processing helix  chain 'A' and resid 95 through 101
    Processing helix  chain 'A' and resid 114 through 130
      removed outlier: 3.636A  pdb=" N   GLN A 119 " --> pdb=" O   TYR A 115 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   GLU A 120 " --> pdb=" O   ASN A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 156
      removed outlier: 3.511A  pdb=" N   GLY A 156 " --> pdb=" O   LYS A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.243A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 170
      removed outlier: 3.537A  pdb=" N   TYR A 170 " --> pdb=" O   PHE A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 203
    Processing helix  chain 'A' and resid 222 through 243
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.556A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.777A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.702A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.825A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 6 through 35
    Processing helix  chain 'R' and resid 40 through 59
    Processing helix  chain 'R' and resid 59 through 69
    Processing helix  chain 'R' and resid 74 through 109
      removed outlier: 3.583A  pdb=" N   LEU R  81 " --> pdb=" O   GLY R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 112 through 117
    Processing helix  chain 'R' and resid 118 through 138
    Processing helix  chain 'R' and resid 138 through 144
      removed outlier: 3.814A  pdb=" N   LEU R 142 " --> pdb=" O   LEU R 138 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 184
    Processing helix  chain 'R' and resid 186 through 191
    Processing helix  chain 'R' and resid 191 through 214
    Processing helix  chain 'R' and resid 225 through 260
      removed outlier: 3.572A  pdb=" N   PHE R 243 " --> pdb=" O   ILE R 239 " (cutoff:3.500A)
      Proline residue:  R 249  - end of helix
    Processing helix  chain 'R' and resid 267 through 291
      removed outlier: 4.472A  pdb=" N   ASN R 273 " --> pdb=" O   LYS R 269 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   SER R 283 " --> pdb=" O   SER R 279 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   VAL R 284 " --> pdb=" O   HIS R 280 " (cutoff:3.500A)
      Proline residue:  R 287  - end of helix
    Processing helix  chain 'R' and resid 294 through 309
    Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65
      removed outlier: 6.317A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A  82 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   PHE A  84 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 9.602A  pdb=" N   ALA A 105 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 8.445A  pdb=" N   ILE A 107 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.605A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.965A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.365A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 103
      removed outlier: 6.891A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 5.651A  pdb=" N   CYS B 149 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   SER B 160 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   PHE B 151 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   VAL B 158 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.613A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 7.163A  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: 3.809A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.857A  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: 3.625A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 5.784A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 4.803A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)

    436 hydrogen bonds defined for protein.
    1236 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: 1.26

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1448
        1.33 -     1.45: 2236
        1.45 -     1.57: 4701
        1.57 -     1.70: 0
        1.70 -     1.82: 73
  Bond restraints: 8458
  Sorted by residual:
  bond pdb=" C4  ADN R 401 "
       pdb=" C5  ADN R 401 "
    ideal  model  delta    sigma   weight residual
    1.385  1.467 -0.082 2.00e-02 2.50e+03 1.67e+01
  bond pdb=" C5  ADN R 401 "
       pdb=" C6  ADN R 401 "
    ideal  model  delta    sigma   weight residual
    1.408  1.482 -0.074 2.00e-02 2.50e+03 1.38e+01
  bond pdb=" C   MET R 238 "
       pdb=" O   MET R 238 "
    ideal  model  delta    sigma   weight residual
    1.236  1.202  0.033 1.17e-02 7.31e+03 8.14e+00
  bond pdb=" N   TRP R 247 "
       pdb=" CA  TRP R 247 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.29e-02 6.01e+03 6.84e+00
  bond pdb=" N   GLU R 174 "
       pdb=" CA  GLU R 174 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.27e-02 6.20e+03 6.58e+00
  ... (remaining 8453 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.13: 11482
        6.13 -    12.26: 12
       12.26 -    18.38: 1
       18.38 -    24.51: 1
       24.51 -    30.64: 2
  Bond angle restraints: 11498
  Sorted by residual:
  angle pdb=" C17 CLR R 404 "
        pdb=" C13 CLR R 404 "
        pdb=" C18 CLR R 404 "
      ideal   model   delta    sigma   weight residual
     110.18   79.54   30.64 3.00e+00 1.11e-01 1.04e+02
  angle pdb=" C12 CLR R 404 "
        pdb=" C13 CLR R 404 "
        pdb=" C18 CLR R 404 "
      ideal   model   delta    sigma   weight residual
     111.01   81.73   29.28 3.00e+00 1.11e-01 9.52e+01
  angle pdb=" C14 CLR R 404 "
        pdb=" C13 CLR R 404 "
        pdb=" C18 CLR R 404 "
      ideal   model   delta    sigma   weight residual
     112.24   90.75   21.49 3.00e+00 1.11e-01 5.13e+01
  angle pdb=" C12 CLR R 404 "
        pdb=" C13 CLR R 404 "
        pdb=" C17 CLR R 404 "
      ideal   model   delta    sigma   weight residual
     116.52  130.09  -13.57 3.00e+00 1.11e-01 2.05e+01
  angle pdb=" C   LEU R 248 "
        pdb=" N   PRO R 249 "
        pdb=" CA  PRO R 249 "
      ideal   model   delta    sigma   weight residual
     119.84  115.03    4.81 1.25e+00 6.40e-01 1.48e+01
  ... (remaining 11493 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.89: 4894
       23.89 -    47.78: 85
       47.78 -    71.67: 12
       71.67 -    95.56: 2
       95.56 -   119.45: 1
  Dihedral angle restraints: 4994
    sinusoidal: 1963
      harmonic: 3031
  Sorted by residual:
  dihedral pdb=" C10 CLR R 402 "
           pdb=" C1  CLR R 402 "
           pdb=" C2  CLR R 402 "
           pdb=" C3  CLR R 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.83   62.62 -119.45     1      3.00e+01 1.11e-03 1.59e+01
  dihedral pdb=" N   GLN R   6 "
           pdb=" C   GLN R   6 "
           pdb=" CA  GLN R   6 "
           pdb=" CB  GLN R   6 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.23   -9.43     0      2.50e+00 1.60e-01 1.42e+01
  dihedral pdb=" N   PHE R 173 "
           pdb=" C   PHE R 173 "
           pdb=" CA  PHE R 173 "
           pdb=" CB  PHE R 173 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  132.18   -9.38     0      2.50e+00 1.60e-01 1.41e+01
  ... (remaining 4991 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.383: 1317
       0.383 -    0.766: 1
       0.766 -    1.149: 0
       1.149 -    1.532: 0
       1.532 -    1.914: 2
  Chirality restraints: 1320
  Sorted by residual:
  chirality pdb=" C13 CLR R 404 "
            pdb=" C12 CLR R 404 "
            pdb=" C14 CLR R 404 "
            pdb=" C17 CLR R 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -1.02   -1.91 2.00e-01 2.50e+01 9.16e+01
  chirality pdb=" CG  LEU R   3 "
            pdb=" CB  LEU R   3 "
            pdb=" CD1 LEU R   3 "
            pdb=" CD2 LEU R   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.89   -1.70 2.00e-01 2.50e+01 7.20e+01
  chirality pdb=" CA  GLN R   6 "
            pdb=" N   GLN R   6 "
            pdb=" C   GLN R   6 "
            pdb=" CB  GLN R   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.43 2.00e-01 2.50e+01 4.52e+00
  ... (remaining 1317 not shown)

  Planarity restraints: 1446
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA R 237 "   -0.013 2.00e-02 2.50e+03   2.69e-02 7.25e+00
        pdb=" C   ALA R 237 "    0.047 2.00e-02 2.50e+03
        pdb=" O   ALA R 237 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   MET R 238 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 173 "    0.010 2.00e-02 2.50e+03   2.14e-02 4.57e+00
        pdb=" C   PHE R 173 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   PHE R 173 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLU R 174 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO R 178 "    0.011 2.00e-02 2.50e+03   2.10e-02 4.39e+00
        pdb=" C   PRO R 178 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   PRO R 178 "    0.014 2.00e-02 2.50e+03
        pdb=" N   MET R 179 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1443 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.58: 108
        2.58 -     3.16: 7464
        3.16 -     3.74: 13104
        3.74 -     4.32: 18541
        4.32 -     4.90: 30724
  Nonbonded interactions: 69941
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 170 "
            pdb=" OD2 ASP A 195 "
     model   vdw
     2.006 3.040
  nonbonded pdb=" OG  SER R 235 "
            pdb=" NH2 ARG R 293 "
     model   vdw
     2.022 3.120
  nonbonded pdb=" O   MET B 325 "
            pdb=" ND2 ASN B 340 "
     model   vdw
     2.080 3.120
  nonbonded pdb=" OD1 ASP A 111 "
            pdb=" OG  SER A 113 "
     model   vdw
     2.114 3.040
  nonbonded pdb=" OG1 THR R  40 "
            pdb=" OD1 ASN R  43 "
     model   vdw
     2.136 3.040
  ... (remaining 69936 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:             0.820
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.800
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
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      :  0.003   0.082   8461  Z= 0.194
  Angle     :  0.754  30.642  11504  Z= 0.337
  Chirality :  0.085   1.914   1320
  Planarity :  0.003   0.041   1446
  Dihedral  :  9.480 119.454   3025
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  6.04 %
    Favored  : 93.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.79 (0.25), residues: 1027
  helix:  0.17 (0.25), residues: 401
  sheet: -2.09 (0.31), residues: 207
  loop : -1.98 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 237 
 TYR   0.005   0.001   TYR R  10 
 PHE   0.014   0.001   PHE R 173 
 TRP   0.009   0.001   TRP R 247 
 HIS   0.005   0.001   HIS R 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.19 ( 8458)
  covalent geometry    : angle       0.75377 /  0.34 (11498)
  SS BOND              : bond        0.00149 /  0.07 (    3)
  SS BOND              : angle       0.35947 /  0.23 (    6)
  hydrogen bonds       : bond        0.12068 /  8.19 (  436)
  hydrogen bonds       : angle       6.25935 /  4.40 ( 1236)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 289
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.8121 (tt) cc_final: 0.7907 (pt)
REVERT: A  212 TYR cc_start: 0.8614 (m-80) cc_final: 0.7916 (m-80)
REVERT: B    9 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8591 (pp30)
REVERT: B   10 GLU cc_start: 0.8695 (tp30) cc_final: 0.8449 (tp30)
REVERT: B   63 TRP cc_start: 0.8484 (m100) cc_final: 0.8247 (m100)
REVERT: B  171 ILE cc_start: 0.6986 (mp) cc_final: 0.6612 (mm)
REVERT: B  280 LYS cc_start: 0.8845 (tttm) cc_final: 0.8560 (ttpp)
REVERT: B  289 TYR cc_start: 0.8423 (m-80) cc_final: 0.7747 (m-80)
REVERT: B  297 TRP cc_start: 0.7497 (m100) cc_final: 0.7256 (m100)
REVERT: N   60 TYR cc_start: 0.8323 (m-80) cc_final: 0.7396 (m-80)
REVERT: N   87 LYS cc_start: 0.8319 (mtpt) cc_final: 0.8048 (mtmm)
REVERT: R  227 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7691 (pt0)
  outliers start: 5
  outliers final: 1
  residues processed: 293
  average time/residue: 0.1057
  time to fit residues: 40.4947
Evaluate side-chains
  179 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 178
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  239 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  12 GLN
A  75 GLN
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 119 GLN
A 123 ASN
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 HIS
B  62 HIS
B  88 ASN
B  91 HIS
B 119 ASN
B 156 GLN
B 230 ASN
B 295 ASN
R 175 ASN
R 280 HIS
R 282 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.104339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.079041 restraints weight = 17005.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 3.17
r_work: 0.3154 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.3892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8461  Z= 0.199
  Angle     :  0.804  32.088  11504  Z= 0.366
  Chirality :  0.069   1.955   1320
  Planarity :  0.004   0.058   1446
  Dihedral  :  5.536  99.059   1175
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 11.17 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.26), residues: 1027
  helix:  1.08 (0.26), residues: 392
  sheet: -1.61 (0.31), residues: 224
  loop : -1.00 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  19 
 TYR   0.014   0.001   TYR B  59 
 PHE   0.020   0.002   PHE R 173 
 TRP   0.015   0.002   TRP B 169 
 HIS   0.006   0.001   HIS A 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00449 /  0.20 ( 8458)
  covalent geometry    : angle       0.80370 /  0.37 (11498)
  SS BOND              : bond        0.00219 /  0.09 (    3)
  SS BOND              : angle       1.60325 /  0.59 (    6)
  hydrogen bonds       : bond        0.03542 /  2.42 (  436)
  hydrogen bonds       : angle       5.07965 /  3.59 ( 1236)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 170
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 ARG cc_start: 0.8560 (ptp90) cc_final: 0.8179 (ptp90)
REVERT: A  230 ASP cc_start: 0.8372 (m-30) cc_final: 0.8164 (m-30)
REVERT: B    9 GLN cc_start: 0.9197 (tm-30) cc_final: 0.8845 (pp30)
REVERT: B   10 GLU cc_start: 0.8946 (tp30) cc_final: 0.8665 (tp30)
REVERT: B   15 LYS cc_start: 0.9259 (ptpt) cc_final: 0.8996 (ptpp)
REVERT: B  138 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7829 (mm-30)
REVERT: B  280 LYS cc_start: 0.9062 (tttm) cc_final: 0.8810 (ttpp)
REVERT: N   32 TYR cc_start: 0.8485 (m-80) cc_final: 0.7957 (m-80)
REVERT: N   36 TRP cc_start: 0.8644 (m100) cc_final: 0.8406 (m100)
REVERT: N   38 ARG cc_start: 0.8097 (ptt-90) cc_final: 0.7883 (ptt90)
REVERT: N   51 ILE cc_start: 0.8267 (tt) cc_final: 0.7987 (pt)
REVERT: N   60 TYR cc_start: 0.8449 (m-80) cc_final: 0.7025 (m-80)
REVERT: N   80 TYR cc_start: 0.7962 (m-80) cc_final: 0.7571 (m-80)
REVERT: N  105 ARG cc_start: 0.8181 (mtp180) cc_final: 0.7974 (mtp180)
REVERT: N  115 TYR cc_start: 0.8690 (t80) cc_final: 0.8337 (t80)
REVERT: R  170 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7195 (mptt)
REVERT: R  227 GLN cc_start: 0.8450 (mm-40) cc_final: 0.7970 (pt0)
REVERT: R  229 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7193 (tm-30)
  outliers start: 29
  outliers final: 21
  residues processed: 188
  average time/residue: 0.1129
  time to fit residues: 27.9431
Evaluate side-chains
  158 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain R residue   58 LEU
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  228 ARG
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  248 LEU
Chi-restraints excluded: chain R residue  256 VAL
Chi-restraints excluded: chain R residue  303 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 94 optimal weight:    6.9990
   chunk 42 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9990
   chunk 26 optimal weight:    7.9990
   chunk 88 optimal weight:    0.8980
   chunk 100 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 49 optimal weight:    0.3980
   overall best weight:    0.7784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  31 GLN
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.105544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.080977 restraints weight = 16763.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 3.11
r_work: 0.3212 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.4268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8461  Z= 0.120
  Angle     :  0.738  30.676  11504  Z= 0.326
  Chirality :  0.068   1.976   1320
  Planarity :  0.004   0.058   1446
  Dihedral  :  5.137 101.956   1173
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.23 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.26), residues: 1027
  helix:  1.46 (0.26), residues: 394
  sheet: -1.08 (0.32), residues: 205
  loop : -0.88 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 117 
 TYR   0.010   0.001   TYR B 289 
 PHE   0.022   0.001   PHE B 199 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 ( 8458)
  covalent geometry    : angle       0.73727 /  0.33 (11498)
  SS BOND              : bond        0.00244 /  0.12 (    3)
  SS BOND              : angle       1.14245 /  0.52 (    6)
  hydrogen bonds       : bond        0.03216 /  2.20 (  436)
  hydrogen bonds       : angle       4.76590 /  3.38 ( 1236)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 156
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.8026 (tt) cc_final: 0.7598 (pt)
REVERT: A  169 ARG cc_start: 0.8566 (ptp90) cc_final: 0.8170 (ptp90)
REVERT: A  230 ASP cc_start: 0.8357 (m-30) cc_final: 0.8124 (m-30)
REVERT: B    9 GLN cc_start: 0.9197 (tm-30) cc_final: 0.8803 (pp30)
REVERT: B   10 GLU cc_start: 0.8918 (tp30) cc_final: 0.8553 (tp30)
REVERT: B   15 LYS cc_start: 0.9227 (ptpt) cc_final: 0.8983 (ptpp)
REVERT: B  138 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7805 (mm-30)
REVERT: B  280 LYS cc_start: 0.9003 (tttm) cc_final: 0.8526 (ttpp)
REVERT: B  336 LEU cc_start: 0.8826 (tt) cc_final: 0.8538 (tt)
REVERT: G   22 GLU cc_start: 0.8943 (tp30) cc_final: 0.8633 (tp30)
REVERT: G   29 LYS cc_start: 0.8887 (tppt) cc_final: 0.8640 (tppt)
REVERT: G   46 LYS cc_start: 0.9382 (tppt) cc_final: 0.9136 (tppt)
REVERT: G   47 GLU cc_start: 0.8814 (mp0) cc_final: 0.8567 (mp0)
REVERT: N   38 ARG cc_start: 0.8290 (ptt-90) cc_final: 0.8032 (ptt90)
REVERT: N   53 GLN cc_start: 0.8815 (mp10) cc_final: 0.8085 (mp10)
REVERT: N   60 TYR cc_start: 0.8444 (m-80) cc_final: 0.7066 (m-80)
REVERT: N   80 TYR cc_start: 0.8024 (m-80) cc_final: 0.7598 (m-80)
REVERT: R  227 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8010 (pt0)
REVERT: R  229 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7190 (tm-30)
  outliers start: 21
  outliers final: 15
  residues processed: 169
  average time/residue: 0.1106
  time to fit residues: 24.4082
Evaluate side-chains
  149 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  228 ARG
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  256 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 92 optimal weight:    8.9990
   chunk 79 optimal weight:    1.9990
   chunk 35 optimal weight:    0.1980
   chunk 91 optimal weight:    2.9990
   chunk 56 optimal weight:    8.9990
   chunk 19 optimal weight:    3.9990
   chunk 70 optimal weight:    8.9990
   overall best weight:    1.1986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 146 GLN
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.104233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.079771 restraints weight = 16898.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 3.06
r_work: 0.3189 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.4626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8461  Z= 0.135
  Angle     :  0.733  31.180  11504  Z= 0.323
  Chirality :  0.067   1.946   1320
  Planarity :  0.004   0.059   1446
  Dihedral  :  5.237 104.150   1173
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 13.68 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.26), residues: 1027
  helix:  1.53 (0.26), residues: 394
  sheet: -0.89 (0.32), residues: 220
  loop : -0.71 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  13 
 TYR   0.018   0.001   TYR R 308 
 PHE   0.017   0.001   PHE B 199 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.13 ( 8458)
  covalent geometry    : angle       0.73325 /  0.32 (11498)
  SS BOND              : bond        0.00248 /  0.11 (    3)
  SS BOND              : angle       0.83604 /  0.38 (    6)
  hydrogen bonds       : bond        0.03273 /  2.24 (  436)
  hydrogen bonds       : angle       4.67508 /  3.32 ( 1236)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 146
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8217 (m)
REVERT: A   62 ILE cc_start: 0.8074 (tt) cc_final: 0.7599 (pt)
REVERT: A  169 ARG cc_start: 0.8623 (ptp90) cc_final: 0.8302 (ptp90)
REVERT: A  210 TYR cc_start: 0.8717 (m-80) cc_final: 0.8471 (m-80)
REVERT: A  230 ASP cc_start: 0.8384 (m-30) cc_final: 0.8180 (m-30)
REVERT: B    8 ARG cc_start: 0.9129 (mmt90) cc_final: 0.8910 (mmt90)
REVERT: B    9 GLN cc_start: 0.9218 (tm-30) cc_final: 0.8830 (pp30)
REVERT: B   10 GLU cc_start: 0.8945 (tp30) cc_final: 0.8644 (tp30)
REVERT: B   15 LYS cc_start: 0.9216 (ptpt) cc_final: 0.8996 (ptpp)
REVERT: B  297 TRP cc_start: 0.8511 (m100) cc_final: 0.8175 (m100)
REVERT: B  336 LEU cc_start: 0.8910 (tt) cc_final: 0.8537 (tt)
REVERT: G   29 LYS cc_start: 0.8870 (tppt) cc_final: 0.8585 (tppt)
REVERT: N   38 ARG cc_start: 0.8306 (ptt-90) cc_final: 0.8051 (ptt90)
REVERT: N   53 GLN cc_start: 0.8844 (mp10) cc_final: 0.8481 (mp10)
REVERT: N   60 TYR cc_start: 0.8579 (m-80) cc_final: 0.8198 (m-80)
REVERT: N   80 TYR cc_start: 0.7998 (m-80) cc_final: 0.7570 (m-80)
REVERT: R  170 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7338 (mptt)
REVERT: R  177 VAL cc_start: 0.8991 (t) cc_final: 0.8676 (m)
REVERT: R  227 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8001 (pt0)
REVERT: R  229 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7086 (tm-30)
  outliers start: 32
  outliers final: 21
  residues processed: 169
  average time/residue: 0.1056
  time to fit residues: 23.3278
Evaluate side-chains
  157 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  179 MET
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  248 LEU
Chi-restraints excluded: chain R residue  256 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 72 optimal weight:    9.9990
   chunk 37 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9990
   chunk 100 optimal weight:    9.9990
   chunk 87 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    2.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.098646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.073927 restraints weight = 17200.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.84
r_work: 0.3097 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.5348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063   8461  Z= 0.244
  Angle     :  0.790  31.289  11504  Z= 0.359
  Chirality :  0.068   1.907   1320
  Planarity :  0.004   0.060   1446
  Dihedral  :  5.645 106.480   1173
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 14.82 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.26), residues: 1027
  helix:  1.41 (0.26), residues: 391
  sheet: -1.02 (0.31), residues: 225
  loop : -0.59 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 134 
 TYR   0.018   0.001   TYR N 115 
 PHE   0.017   0.002   PHE A  74 
 TRP   0.013   0.002   TRP B 211 
 HIS   0.004   0.001   HIS A  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00550 /  0.24 ( 8458)
  covalent geometry    : angle       0.78954 /  0.36 (11498)
  SS BOND              : bond        0.00171 /  0.07 (    3)
  SS BOND              : angle       1.17579 /  0.48 (    6)
  hydrogen bonds       : bond        0.03739 /  2.53 (  436)
  hydrogen bonds       : angle       4.93809 /  3.50 ( 1236)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 142
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.8112 (tt) cc_final: 0.7670 (pt)
REVERT: B    8 ARG cc_start: 0.9152 (mmt90) cc_final: 0.8938 (mmt90)
REVERT: B    9 GLN cc_start: 0.9154 (tm-30) cc_final: 0.8786 (pp30)
REVERT: B   10 GLU cc_start: 0.8958 (tp30) cc_final: 0.8605 (tp30)
REVERT: B   35 ASN cc_start: 0.8827 (m110) cc_final: 0.8533 (m-40)
REVERT: B  172 GLU cc_start: 0.8413 (mp0) cc_final: 0.7954 (pm20)
REVERT: B  262 MET cc_start: 0.8256 (mmm) cc_final: 0.7930 (mmm)
REVERT: B  280 LYS cc_start: 0.9149 (tttm) cc_final: 0.8892 (tttm)
REVERT: G   22 GLU cc_start: 0.9079 (tp30) cc_final: 0.8789 (tp30)
REVERT: G   29 LYS cc_start: 0.8928 (tppt) cc_final: 0.8593 (tppt)
REVERT: N   38 ARG cc_start: 0.8587 (ptt-90) cc_final: 0.8236 (ptt90)
REVERT: N   46 GLU cc_start: 0.7616 (tt0) cc_final: 0.7182 (tt0)
REVERT: N   53 GLN cc_start: 0.8892 (mp10) cc_final: 0.8281 (mp10)
REVERT: N   60 TYR cc_start: 0.8669 (m-80) cc_final: 0.8234 (m-80)
REVERT: N   80 TYR cc_start: 0.8109 (m-80) cc_final: 0.7772 (m-80)
REVERT: N   87 LYS cc_start: 0.8492 (tppt) cc_final: 0.8209 (tppt)
REVERT: R  170 LYS cc_start: 0.8281 (mmtt) cc_final: 0.7403 (mptt)
  outliers start: 35
  outliers final: 25
  residues processed: 167
  average time/residue: 0.1076
  time to fit residues: 23.5905
Evaluate side-chains
  156 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  179 MET
Chi-restraints excluded: chain R residue  228 ARG
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  248 LEU
Chi-restraints excluded: chain R residue  256 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 92 optimal weight:    0.0570
   chunk 19 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   chunk 2 optimal weight:    0.8980
   chunk 85 optimal weight:    4.9990
   chunk 93 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   overall best weight:    0.7498

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.102567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.078092 restraints weight = 16760.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 2.84
r_work: 0.3141 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.5273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8461  Z= 0.118
  Angle     :  0.731  30.289  11504  Z= 0.323
  Chirality :  0.067   1.936   1320
  Planarity :  0.004   0.060   1446
  Dihedral  :  5.396 105.206   1173
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 15.74 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.26), residues: 1027
  helix:  1.69 (0.26), residues: 390
  sheet: -0.57 (0.33), residues: 207
  loop : -0.47 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  13 
 TYR   0.018   0.001   TYR N 115 
 PHE   0.017   0.001   PHE B 199 
 TRP   0.012   0.001   TRP B 297 
 HIS   0.003   0.000   HIS A 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.12 ( 8458)
  covalent geometry    : angle       0.73121 /  0.32 (11498)
  SS BOND              : bond        0.00253 /  0.12 (    3)
  SS BOND              : angle       0.68007 /  0.33 (    6)
  hydrogen bonds       : bond        0.03292 /  2.22 (  436)
  hydrogen bonds       : angle       4.69534 /  3.35 ( 1236)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 146
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.8007 (tt) cc_final: 0.7586 (pt)
REVERT: B    8 ARG cc_start: 0.9160 (mmt90) cc_final: 0.8944 (mmt90)
REVERT: B    9 GLN cc_start: 0.9180 (tm-30) cc_final: 0.8806 (pp30)
REVERT: B   10 GLU cc_start: 0.8954 (tp30) cc_final: 0.8575 (tp30)
REVERT: B   35 ASN cc_start: 0.8837 (m110) cc_final: 0.8505 (m-40)
REVERT: B  280 LYS cc_start: 0.9077 (tttm) cc_final: 0.8362 (ttmm)
REVERT: G   22 GLU cc_start: 0.9042 (tp30) cc_final: 0.8636 (mm-30)
REVERT: G   29 LYS cc_start: 0.8937 (tppt) cc_final: 0.8613 (tppt)
REVERT: N    5 GLN cc_start: 0.7764 (mp10) cc_final: 0.7541 (mp10)
REVERT: N   38 ARG cc_start: 0.8574 (ptt-90) cc_final: 0.8142 (ptt90)
REVERT: N   46 GLU cc_start: 0.7657 (tt0) cc_final: 0.7176 (tt0)
REVERT: N   53 GLN cc_start: 0.8840 (mp10) cc_final: 0.8259 (mp10)
REVERT: N   60 TYR cc_start: 0.8607 (m-80) cc_final: 0.8208 (m-80)
REVERT: N   80 TYR cc_start: 0.8169 (m-80) cc_final: 0.7865 (m-80)
REVERT: N   87 LYS cc_start: 0.8469 (tppt) cc_final: 0.8206 (tppt)
REVERT: R  170 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7363 (mptt)
REVERT: R  173 PHE cc_start: 0.8208 (t80) cc_final: 0.7957 (t80)
REVERT: R  227 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7794 (tt0)
  outliers start: 28
  outliers final: 21
  residues processed: 164
  average time/residue: 0.1036
  time to fit residues: 22.5316
Evaluate side-chains
  156 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  190 CYS
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  248 LEU
Chi-restraints excluded: chain R residue  256 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 48 optimal weight:    8.9990
   chunk 6 optimal weight:    7.9990
   chunk 82 optimal weight:    0.8980
   chunk 14 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 58 optimal weight:    8.9990
   chunk 46 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0770
   chunk 5 optimal weight:    7.9990
   overall best weight:    1.9944

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.099943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.075340 restraints weight = 17094.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.86
r_work: 0.3087 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.5529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8461  Z= 0.179
  Angle     :  0.744  30.561  11504  Z= 0.332
  Chirality :  0.067   1.899   1320
  Planarity :  0.004   0.060   1446
  Dihedral  :  5.516 106.004   1173
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 16.76 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.26), residues: 1027
  helix:  1.64 (0.26), residues: 391
  sheet: -0.69 (0.33), residues: 223
  loop : -0.38 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG N  72 
 TYR   0.022   0.001   TYR N 115 
 PHE   0.015   0.001   PHE A  74 
 TRP   0.010   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00409 /  0.18 ( 8458)
  covalent geometry    : angle       0.74411 /  0.33 (11498)
  SS BOND              : bond        0.00320 /  0.12 (    3)
  SS BOND              : angle       0.99522 /  0.48 (    6)
  hydrogen bonds       : bond        0.03491 /  2.35 (  436)
  hydrogen bonds       : angle       4.73418 /  3.38 ( 1236)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 137
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.8068 (tt) cc_final: 0.7649 (pt)
REVERT: B    8 ARG cc_start: 0.9198 (mmt90) cc_final: 0.8948 (mmt90)
REVERT: B    9 GLN cc_start: 0.9201 (tm-30) cc_final: 0.8848 (pp30)
REVERT: B   10 GLU cc_start: 0.8963 (tp30) cc_final: 0.8573 (tp30)
REVERT: B   35 ASN cc_start: 0.8884 (m110) cc_final: 0.8427 (m-40)
REVERT: B  127 LYS cc_start: 0.9061 (mmtp) cc_final: 0.8372 (mmtt)
REVERT: B  172 GLU cc_start: 0.8395 (mp0) cc_final: 0.7994 (pm20)
REVERT: G   22 GLU cc_start: 0.9058 (tp30) cc_final: 0.8795 (tp30)
REVERT: G   29 LYS cc_start: 0.8954 (tppt) cc_final: 0.8641 (tppt)
REVERT: N    5 GLN cc_start: 0.7812 (mp10) cc_final: 0.7525 (mp10)
REVERT: N   19 ARG cc_start: 0.8384 (ttt90) cc_final: 0.8077 (ttt90)
REVERT: N   38 ARG cc_start: 0.8651 (ptt-90) cc_final: 0.8223 (ptt90)
REVERT: N   46 GLU cc_start: 0.7778 (tt0) cc_final: 0.7343 (tt0)
REVERT: N   53 GLN cc_start: 0.8788 (mp10) cc_final: 0.8466 (mp10)
REVERT: N   60 TYR cc_start: 0.8672 (m-80) cc_final: 0.7653 (m-80)
REVERT: N   80 TYR cc_start: 0.8208 (m-80) cc_final: 0.7871 (m-80)
REVERT: N   87 LYS cc_start: 0.8512 (tppt) cc_final: 0.8157 (tppt)
REVERT: R   39 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7331 (mp10)
REVERT: R  170 LYS cc_start: 0.8329 (mmtt) cc_final: 0.7447 (mptt)
REVERT: R  173 PHE cc_start: 0.8198 (t80) cc_final: 0.7970 (t80)
  outliers start: 33
  outliers final: 25
  residues processed: 162
  average time/residue: 0.1095
  time to fit residues: 23.4162
Evaluate side-chains
  155 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 129
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   39 GLN
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  179 MET
Chi-restraints excluded: chain R residue  228 ARG
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  248 LEU
Chi-restraints excluded: chain R residue  256 VAL
Chi-restraints excluded: chain R residue  283 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 94 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 39 optimal weight:   10.0000
   chunk 65 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.102074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.077608 restraints weight = 16714.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.86
r_work: 0.3135 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.5524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8461  Z= 0.125
  Angle     :  0.743  30.155  11504  Z= 0.329
  Chirality :  0.066   1.917   1320
  Planarity :  0.004   0.059   1446
  Dihedral  :  5.441 106.160   1173
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 17.33 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.27), residues: 1027
  helix:  1.73 (0.26), residues: 392
  sheet: -0.47 (0.34), residues: 207
  loop : -0.38 (0.32), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG G  13 
 TYR   0.022   0.001   TYR N 115 
 PHE   0.015   0.001   PHE B 199 
 TRP   0.011   0.001   TRP B 297 
 HIS   0.003   0.001   HIS A 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 8458)
  covalent geometry    : angle       0.74322 /  0.33 (11498)
  SS BOND              : bond        0.00136 /  0.06 (    3)
  SS BOND              : angle       1.02806 /  0.56 (    6)
  hydrogen bonds       : bond        0.03304 /  2.21 (  436)
  hydrogen bonds       : angle       4.64291 /  3.32 ( 1236)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 151
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.7988 (tt) cc_final: 0.7543 (pt)
REVERT: B    8 ARG cc_start: 0.9249 (mmt90) cc_final: 0.8969 (mmt90)
REVERT: B    9 GLN cc_start: 0.9208 (tm-30) cc_final: 0.8855 (pp30)
REVERT: B   10 GLU cc_start: 0.8963 (tp30) cc_final: 0.8563 (tp30)
REVERT: B   35 ASN cc_start: 0.8867 (m110) cc_final: 0.8420 (m-40)
REVERT: B  172 GLU cc_start: 0.8325 (mp0) cc_final: 0.7980 (pm20)
REVERT: B  280 LYS cc_start: 0.9050 (ttpp) cc_final: 0.8458 (ttmm)
REVERT: B  289 TYR cc_start: 0.8923 (m-80) cc_final: 0.8501 (m-80)
REVERT: G   22 GLU cc_start: 0.9022 (tp30) cc_final: 0.8632 (mm-30)
REVERT: G   29 LYS cc_start: 0.8885 (tppt) cc_final: 0.8615 (tppt)
REVERT: G   47 GLU cc_start: 0.8880 (mp0) cc_final: 0.8641 (mp0)
REVERT: N    5 GLN cc_start: 0.7768 (mp10) cc_final: 0.7433 (mp10)
REVERT: N   19 ARG cc_start: 0.8446 (ttt90) cc_final: 0.8172 (ttt90)
REVERT: N   38 ARG cc_start: 0.8643 (ptt-90) cc_final: 0.8193 (ptt90)
REVERT: N   46 GLU cc_start: 0.7762 (tt0) cc_final: 0.7321 (tt0)
REVERT: N   51 ILE cc_start: 0.7636 (pt) cc_final: 0.7423 (pt)
REVERT: N   53 GLN cc_start: 0.8814 (mp10) cc_final: 0.8246 (mp10)
REVERT: N   60 TYR cc_start: 0.8658 (m-80) cc_final: 0.8252 (m-80)
REVERT: N   78 THR cc_start: 0.9146 (m) cc_final: 0.8519 (p)
REVERT: N   80 TYR cc_start: 0.8254 (m-80) cc_final: 0.7665 (m-80)
REVERT: N   87 LYS cc_start: 0.8533 (tppt) cc_final: 0.8184 (tppt)
REVERT: R   39 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8075 (mm-40)
REVERT: R  170 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7393 (mptt)
REVERT: R  173 PHE cc_start: 0.8165 (t80) cc_final: 0.7897 (t80)
  outliers start: 30
  outliers final: 27
  residues processed: 173
  average time/residue: 0.1080
  time to fit residues: 24.8081
Evaluate side-chains
  171 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   39 GLN
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  228 ARG
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  248 LEU
Chi-restraints excluded: chain R residue  256 VAL
Chi-restraints excluded: chain R residue  283 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 5 optimal weight:    9.9990
   chunk 92 optimal weight:   10.0000
   chunk 41 optimal weight:    8.9990
   chunk 63 optimal weight:    7.9990
   chunk 99 optimal weight:    0.9980
   chunk 23 optimal weight:    9.9990
   chunk 59 optimal weight:    0.0040
   chunk 79 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   overall best weight:    1.9998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.099940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.075139 restraints weight = 16870.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 2.84
r_work: 0.3083 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.5691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8461  Z= 0.180
  Angle     :  0.771  30.285  11504  Z= 0.347
  Chirality :  0.067   1.889   1320
  Planarity :  0.004   0.059   1446
  Dihedral  :  5.543 106.849   1173
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 18.02 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.27), residues: 1027
  helix:  1.61 (0.26), residues: 392
  sheet: -0.55 (0.34), residues: 218
  loop : -0.35 (0.32), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  13 
 TYR   0.021   0.001   TYR N 115 
 PHE   0.015   0.001   PHE A  74 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.003   0.001   HIS R 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00412 /  0.18 ( 8458)
  covalent geometry    : angle       0.77132 /  0.35 (11498)
  SS BOND              : bond        0.00214 /  0.10 (    3)
  SS BOND              : angle       1.05322 /  0.54 (    6)
  hydrogen bonds       : bond        0.03494 /  2.35 (  436)
  hydrogen bonds       : angle       4.75979 /  3.39 ( 1236)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 145
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.8022 (tt) cc_final: 0.7567 (pt)
REVERT: B    8 ARG cc_start: 0.9201 (mmt90) cc_final: 0.8912 (mmt90)
REVERT: B    9 GLN cc_start: 0.9217 (tm-30) cc_final: 0.8860 (pp30)
REVERT: B   10 GLU cc_start: 0.8978 (tp30) cc_final: 0.8578 (tp30)
REVERT: B   35 ASN cc_start: 0.8882 (m110) cc_final: 0.8467 (m-40)
REVERT: B  172 GLU cc_start: 0.8358 (mp0) cc_final: 0.8030 (pm20)
REVERT: B  262 MET cc_start: 0.8290 (mmm) cc_final: 0.7994 (mmm)
REVERT: B  280 LYS cc_start: 0.9081 (ttpp) cc_final: 0.8532 (ttmm)
REVERT: G   22 GLU cc_start: 0.9068 (tp30) cc_final: 0.8672 (mm-30)
REVERT: G   29 LYS cc_start: 0.8879 (tppt) cc_final: 0.8625 (tppt)
REVERT: G   47 GLU cc_start: 0.8872 (mp0) cc_final: 0.8615 (mp0)
REVERT: N    5 GLN cc_start: 0.7729 (mp10) cc_final: 0.7400 (mp10)
REVERT: N   19 ARG cc_start: 0.8540 (ttt90) cc_final: 0.8289 (ttt90)
REVERT: N   38 ARG cc_start: 0.8631 (ptt-90) cc_final: 0.8202 (ptt90)
REVERT: N   46 GLU cc_start: 0.7819 (tt0) cc_final: 0.7371 (tt0)
REVERT: N   53 GLN cc_start: 0.8756 (mp10) cc_final: 0.8198 (mp10)
REVERT: N   60 TYR cc_start: 0.8727 (m-80) cc_final: 0.8246 (m-80)
REVERT: N   78 THR cc_start: 0.9188 (m) cc_final: 0.8555 (p)
REVERT: N   80 TYR cc_start: 0.8245 (m-80) cc_final: 0.7636 (m-80)
REVERT: N   87 LYS cc_start: 0.8499 (tppt) cc_final: 0.8125 (tppt)
REVERT: R   39 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7315 (mp10)
REVERT: R  170 LYS cc_start: 0.8351 (mmtt) cc_final: 0.7455 (mptt)
REVERT: R  173 PHE cc_start: 0.8159 (t80) cc_final: 0.7863 (t80)
  outliers start: 30
  outliers final: 23
  residues processed: 169
  average time/residue: 0.1007
  time to fit residues: 22.9444
Evaluate side-chains
  162 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   39 GLN
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  248 LEU
Chi-restraints excluded: chain R residue  256 VAL
Chi-restraints excluded: chain R residue  283 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 73 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 91 optimal weight:    0.6980
   chunk 98 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9990
   chunk 41 optimal weight:    6.9990
   chunk 52 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.102000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.077437 restraints weight = 16717.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.87
r_work: 0.3132 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.5727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8461  Z= 0.127
  Angle     :  0.757  30.006  11504  Z= 0.341
  Chirality :  0.066   1.902   1320
  Planarity :  0.004   0.059   1446
  Dihedral  :  5.436 106.862   1173
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.59 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.27), residues: 1027
  helix:  1.64 (0.26), residues: 392
  sheet: -0.47 (0.33), residues: 227
  loop : -0.39 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G  13 
 TYR   0.023   0.001   TYR N 115 
 PHE   0.014   0.001   PHE B 199 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 8458)
  covalent geometry    : angle       0.75689 /  0.34 (11498)
  SS BOND              : bond        0.00132 /  0.05 (    3)
  SS BOND              : angle       0.88772 /  0.48 (    6)
  hydrogen bonds       : bond        0.03423 /  2.29 (  436)
  hydrogen bonds       : angle       4.69047 /  3.34 ( 1236)

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

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

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2054 Ramachandran restraints generated.
    1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 147
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.8017 (tt) cc_final: 0.7605 (pt)
REVERT: B    9 GLN cc_start: 0.9244 (tm-30) cc_final: 0.8879 (pp30)
REVERT: B   10 GLU cc_start: 0.8984 (tp30) cc_final: 0.8587 (tp30)
REVERT: B   35 ASN cc_start: 0.8709 (m110) cc_final: 0.8378 (m-40)
REVERT: B  172 GLU cc_start: 0.8314 (mp0) cc_final: 0.7976 (pm20)
REVERT: B  280 LYS cc_start: 0.9070 (ttpp) cc_final: 0.8557 (ttmm)
REVERT: B  289 TYR cc_start: 0.8934 (m-80) cc_final: 0.8457 (m-80)
REVERT: B  297 TRP cc_start: 0.8507 (m100) cc_final: 0.8097 (m100)
REVERT: G   22 GLU cc_start: 0.9080 (tp30) cc_final: 0.8679 (tp30)
REVERT: G   29 LYS cc_start: 0.8820 (tppt) cc_final: 0.8563 (tppt)
REVERT: G   47 GLU cc_start: 0.8866 (mp0) cc_final: 0.8627 (mp0)
REVERT: N    3 GLN cc_start: 0.8376 (mt0) cc_final: 0.8168 (mt0)
REVERT: N    6 GLU cc_start: 0.6904 (pt0) cc_final: 0.6626 (pt0)
REVERT: N   19 ARG cc_start: 0.8591 (ttt90) cc_final: 0.8364 (ttt90)
REVERT: N   46 GLU cc_start: 0.7812 (tt0) cc_final: 0.7455 (tt0)
REVERT: N   51 ILE cc_start: 0.7625 (pt) cc_final: 0.7354 (pt)
REVERT: N   53 GLN cc_start: 0.8812 (mp10) cc_final: 0.8276 (mp10)
REVERT: N   60 TYR cc_start: 0.8712 (m-80) cc_final: 0.8281 (m-80)
REVERT: N   78 THR cc_start: 0.9128 (m) cc_final: 0.8484 (p)
REVERT: N   80 TYR cc_start: 0.8250 (m-80) cc_final: 0.7681 (m-80)
REVERT: N  122 THR cc_start: 0.8379 (m) cc_final: 0.8056 (p)
REVERT: R   39 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8074 (mm-40)
REVERT: R  170 LYS cc_start: 0.8203 (mmtt) cc_final: 0.7403 (mptt)
REVERT: R  173 PHE cc_start: 0.8128 (t80) cc_final: 0.7857 (t80)
  outliers start: 28
  outliers final: 26
  residues processed: 168
  average time/residue: 0.1007
  time to fit residues: 22.8244
Evaluate side-chains
  173 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 146
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   39 GLN
Chi-restraints excluded: chain R residue   46 LEU
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  236 LEU
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  248 LEU
Chi-restraints excluded: chain R residue  256 VAL
Chi-restraints excluded: chain R residue  283 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 94 optimal weight:    0.3980
   chunk 29 optimal weight:    0.0370
   chunk 12 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 90 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.8060

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.102424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.077986 restraints weight = 16798.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 2.88
r_work: 0.3146 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.5744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8461  Z= 0.123
  Angle     :  0.757  30.014  11504  Z= 0.339
  Chirality :  0.066   1.899   1320
  Planarity :  0.004   0.059   1446
  Dihedral  :  5.369 106.843   1173
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.59 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.27), residues: 1027
  helix:  1.67 (0.26), residues: 393
  sheet: -0.37 (0.34), residues: 225
  loop : -0.42 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G  13 
 TYR   0.023   0.001   TYR N 115 
 PHE   0.014   0.001   PHE B 199 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 ( 8458)
  covalent geometry    : angle       0.75648 /  0.34 (11498)
  SS BOND              : bond        0.00120 /  0.05 (    3)
  SS BOND              : angle       0.92052 /  0.50 (    6)
  hydrogen bonds       : bond        0.03348 /  2.25 (  436)
  hydrogen bonds       : angle       4.63460 /  3.30 ( 1236)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2125.13 seconds
wall clock time: 37 minutes 14.35 seconds (2234.35 seconds total)