Starting phenix.real_space_refine
on Thu Mar 13 01:03:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hdp_34677/03_2025/8hdp_34677.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hdp_34677/03_2025/8hdp_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_34677/03_2025/8hdp_34677.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hdp_34677/03_2025/8hdp_34677.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hdp_34677/03_2025/8hdp_34677.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hdp_34677/03_2025/8hdp_34677.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.04, per 1000 atoms: 0.61
  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: 2.42
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.95
  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: 2.60

  Time building geometry restraints manager: 2.80 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=" C1' ADN R 401 "
        pdb=" C2' ADN R 401 "
        pdb=" C3' ADN R 401 "
      ideal   model   delta    sigma   weight residual
     101.30  105.27   -3.97 1.00e+00 1.00e+00 1.58e+01
  ... (remaining 11493 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.51: 5158
       34.51 -    69.01: 71
       69.01 -   103.52: 5
      103.52 -   138.02: 1
      138.02 -   172.53: 5
  Dihedral angle restraints: 5240
    sinusoidal: 2209
      harmonic: 3031
  Sorted by residual:
  dihedral pdb=" C16 CLR R 404 "
           pdb=" C13 CLR R 404 "
           pdb=" C17 CLR R 404 "
           pdb=" C18 CLR R 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -78.02   94.51 -172.53     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" C18 CLR R 404 "
           pdb=" C13 CLR R 404 "
           pdb=" C17 CLR R 404 "
           pdb=" C20 CLR R 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     312.73  144.58  168.15     1      3.00e+01 1.11e-03 2.11e+01
  dihedral pdb=" C15 CLR R 404 "
           pdb=" C13 CLR R 404 "
           pdb=" C14 CLR R 404 "
           pdb=" C18 CLR R 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.18  -96.05  165.23     1      3.00e+01 1.11e-03 2.10e+01
  ... (remaining 5237 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:             0.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.020
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
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   8458  Z= 0.211
  Angle     :  0.755  30.642  11498  Z= 0.343
  Chirality :  0.085   1.914   1320
  Planarity :  0.003   0.041   1446
  Dihedral  : 12.508 172.528   3271
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 7.86
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (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
 TRP   0.009   0.001   TRP R 247 
 HIS   0.005   0.001   HIS R 251 
 PHE   0.014   0.001   PHE R 173 
 TYR   0.005   0.001   TYR R  10 
 ARG   0.002   0.000   ARG A 237 

*********************** 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  : 0.957 
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: 0.7915 (m-80)
REVERT: B    9 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8586 (pp30)
REVERT: B   10 GLU cc_start: 0.8695 (tp30) cc_final: 0.8409 (tp30)
REVERT: B   63 TRP cc_start: 0.8484 (m100) cc_final: 0.8248 (m100)
REVERT: B  171 ILE cc_start: 0.6986 (mp) cc_final: 0.6614 (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: 0.7748 (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: 0.2517
  time to fit residues: 95.4209
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  : 1.022 
-------------------------------------------------------------------------------
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 85 optimal weight:    1.9990
   chunk 76 optimal weight:    8.9990
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    8.9990
   chunk 79 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 58 optimal weight:    5.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A  12 GLN
A  75 GLN
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 119 GLN
A 123 ASN
B  62 HIS
B  91 HIS
B 119 ASN
B 156 GLN
B 230 ASN
B 295 ASN
R 175 ASN
R 280 HIS
** R 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.109142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.084652 restraints weight = 16784.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 3.17
r_work: 0.3269 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8458  Z= 0.223
  Angle     :  0.766  30.957  11498  Z= 0.342
  Chirality :  0.067   1.897   1320
  Planarity :  0.004   0.057   1446
  Dihedral  : 11.972 166.520   1421
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 12.31 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.26), residues: 1027
  helix:  1.15 (0.26), residues: 392
  sheet: -1.46 (0.31), residues: 214
  loop : -1.15 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.006   0.001   HIS A 209 
 PHE   0.019   0.001   PHE R 173 
 TYR   0.010   0.001   TYR N  95 
 ARG   0.005   0.001   ARG B  19 

*********************** 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
  203 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 178
  time to evaluate  : 0.914 
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  230 ASP cc_start: 0.8349 (m-30) cc_final: 0.8100 (m-30)
REVERT: B    9 GLN cc_start: 0.9179 (tm-30) cc_final: 0.8826 (pp30)
REVERT: B   10 GLU cc_start: 0.8909 (tp30) cc_final: 0.8642 (tp30)
REVERT: B   15 LYS cc_start: 0.9246 (ptpt) cc_final: 0.8977 (ptpp)
REVERT: B  155 ASN cc_start: 0.7814 (t0) cc_final: 0.7504 (t0)
REVERT: B  226 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7754 (mt-10)
REVERT: B  280 LYS cc_start: 0.9075 (tttm) cc_final: 0.8624 (ttpp)
REVERT: N   32 TYR cc_start: 0.8256 (m-80) cc_final: 0.7771 (m-80)
REVERT: N   36 TRP cc_start: 0.8730 (m100) cc_final: 0.8496 (m100)
REVERT: N   60 TYR cc_start: 0.8472 (m-80) cc_final: 0.8052 (m-80)
REVERT: N   65 LYS cc_start: 0.8636 (tptm) cc_final: 0.8221 (tppp)
REVERT: N   87 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7750 (mtmm)
REVERT: N   90 ASP cc_start: 0.6616 (m-30) cc_final: 0.6203 (m-30)
REVERT: N  114 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8769 (t)
REVERT: R  227 GLN cc_start: 0.8421 (mm-40) cc_final: 0.7946 (pt0)
REVERT: R  229 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7182 (tm-30)
  outliers start: 25
  outliers final: 17
  residues processed: 194
  average time/residue: 0.2550
  time to fit residues: 64.1093
Evaluate side-chains
  158 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
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  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 N residue  114 THR
Chi-restraints excluded: chain R residue   58 LEU
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  228 ARG
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 96 optimal weight:    0.5980
   chunk 65 optimal weight:    6.9990
   chunk 88 optimal weight:    0.3980
   chunk 46 optimal weight:    2.9990
   chunk 62 optimal weight:   20.0000
   chunk 61 optimal weight:   10.0000
   chunk 97 optimal weight:    0.0770
   chunk 92 optimal weight:    5.9990
   chunk 99 optimal weight:    0.8980
   chunk 94 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 282 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 = 0.3836 r_free = 0.3836 target = 0.109199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.084636 restraints weight = 16923.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 3.21
r_work: 0.3283 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.3736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8458  Z= 0.163
  Angle     :  0.731  30.592  11498  Z= 0.318
  Chirality :  0.065   1.853   1320
  Planarity :  0.004   0.057   1446
  Dihedral  : 11.546 170.440   1419
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 13.91 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.26), residues: 1027
  helix:  1.50 (0.26), residues: 394
  sheet: -1.07 (0.32), residues: 221
  loop : -0.99 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 209 
 PHE   0.016   0.001   PHE B 199 
 TYR   0.012   0.001   TYR N 115 
 ARG   0.005   0.000   ARG A 169 

*********************** 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
  178 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 153
  time to evaluate  : 0.918 
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   56 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8803 (pt)
REVERT: A   60 MET cc_start: 0.6132 (tpp) cc_final: 0.5717 (tpp)
REVERT: A   62 ILE cc_start: 0.8042 (tt) cc_final: 0.7743 (pt)
REVERT: A  230 ASP cc_start: 0.8392 (m-30) cc_final: 0.8127 (m-30)
REVERT: B    9 GLN cc_start: 0.9150 (tm-30) cc_final: 0.8769 (pp30)
REVERT: B   10 GLU cc_start: 0.8910 (tp30) cc_final: 0.8591 (tp30)
REVERT: B   23 LYS cc_start: 0.9225 (pttt) cc_final: 0.8983 (pttp)
REVERT: B   35 ASN cc_start: 0.8703 (m110) cc_final: 0.8431 (m-40)
REVERT: B  155 ASN cc_start: 0.7635 (t0) cc_final: 0.7399 (t0)
REVERT: B  280 LYS cc_start: 0.9017 (tttm) cc_final: 0.8797 (tttm)
REVERT: B  336 LEU cc_start: 0.8706 (tt) cc_final: 0.8466 (tt)
REVERT: B  339 TRP cc_start: 0.8897 (m100) cc_final: 0.8558 (m100)
REVERT: G   47 GLU cc_start: 0.8824 (mp0) cc_final: 0.8618 (mp0)
REVERT: N   51 ILE cc_start: 0.7715 (pt) cc_final: 0.7420 (pt)
REVERT: N   53 GLN cc_start: 0.8799 (mp10) cc_final: 0.8492 (mp10)
REVERT: N   60 TYR cc_start: 0.8612 (m-80) cc_final: 0.8373 (m-80)
REVERT: N  105 ARG cc_start: 0.8195 (mtp180) cc_final: 0.7939 (mtp180)
REVERT: R   96 LEU cc_start: 0.8364 (mt) cc_final: 0.8128 (mt)
REVERT: R  227 GLN cc_start: 0.8471 (mm-40) cc_final: 0.7995 (pt0)
REVERT: R  229 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7233 (tm-30)
  outliers start: 25
  outliers final: 18
  residues processed: 169
  average time/residue: 0.2641
  time to fit residues: 57.7881
Evaluate side-chains
  153 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
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 B residue   29 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  160 SER
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   70 ILE
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  128 VAL
Chi-restraints excluded: chain R residue  228 ARG
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  256 VAL
Chi-restraints excluded: chain R residue  303 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 52 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 37 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 58 optimal weight:    9.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 HIS
B 340 ASN
** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.100179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.075403 restraints weight = 16774.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.94
r_work: 0.3103 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.4740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   8458  Z= 0.353
  Angle     :  0.796  31.572  11498  Z= 0.357
  Chirality :  0.066   1.824   1320
  Planarity :  0.004   0.058   1446
  Dihedral  : 11.608 167.759   1419
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 14.48 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.26), residues: 1027
  helix:  1.36 (0.26), residues: 396
  sheet: -1.03 (0.32), residues: 222
  loop : -0.70 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A  41 
 PHE   0.015   0.002   PHE A  74 
 TYR   0.014   0.001   TYR B 145 
 ARG   0.006   0.001   ARG B 129 

*********************** 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
  173 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 142
  time to evaluate  : 1.025 
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: 0.8083 (tt) cc_final: 0.7614 (pt)
REVERT: A  169 ARG cc_start: 0.8569 (ptp90) cc_final: 0.8368 (ptp90)
REVERT: B    9 GLN cc_start: 0.9192 (tm-30) cc_final: 0.8818 (pp30)
REVERT: B   10 GLU cc_start: 0.9016 (tp30) cc_final: 0.8618 (tp30)
REVERT: B  280 LYS cc_start: 0.9126 (tttm) cc_final: 0.8876 (ttpp)
REVERT: G   22 GLU cc_start: 0.9033 (tp30) cc_final: 0.8675 (tp30)
REVERT: N   53 GLN cc_start: 0.8930 (mp10) cc_final: 0.8259 (mp10)
REVERT: N   60 TYR cc_start: 0.8600 (m-80) cc_final: 0.8189 (m-80)
REVERT: N   87 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8250 (tppt)
REVERT: N  115 TYR cc_start: 0.8636 (t80) cc_final: 0.8322 (t80)
REVERT: R  170 LYS cc_start: 0.8308 (mmtt) cc_final: 0.7398 (mptt)
REVERT: R  177 VAL cc_start: 0.9113 (t) cc_final: 0.8819 (m)
  outliers start: 31
  outliers final: 22
  residues processed: 167
  average time/residue: 0.2978
  time to fit residues: 65.0576
Evaluate side-chains
  151 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue  110 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   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 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  128 VAL
Chi-restraints excluded: chain R residue  228 ARG
Chi-restraints excluded: chain R residue  245 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 70 optimal weight:    8.9990
   chunk 78 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 42 optimal weight:    0.1980
   chunk 31 optimal weight:    0.9990
   chunk 96 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 6 optimal weight:    5.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
B 340 ASN
N   3 GLN
N  31 ASN
** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.102963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.078397 restraints weight = 16451.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.95
r_work: 0.3171 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.4904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8458  Z= 0.189
  Angle     :  0.746  30.678  11498  Z= 0.327
  Chirality :  0.065   1.820   1320
  Planarity :  0.004   0.060   1446
  Dihedral  : 11.426 171.806   1419
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 16.08 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.26), residues: 1027
  helix:  1.58 (0.26), residues: 391
  sheet: -0.74 (0.32), residues: 222
  loop : -0.56 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.000   HIS A 209 
 PHE   0.017   0.001   PHE N 103 
 TYR   0.021   0.001   TYR R 308 
 ARG   0.007   0.000   ARG G  13 

*********************** 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
  165 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 1.275 
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   60 MET cc_start: 0.5549 (tpt) cc_final: 0.5001 (mmm)
REVERT: A   62 ILE cc_start: 0.8125 (tt) cc_final: 0.7613 (pt)
REVERT: A  169 ARG cc_start: 0.8570 (ptp90) cc_final: 0.8228 (ptp90)
REVERT: A  230 ASP cc_start: 0.8348 (m-30) cc_final: 0.8097 (m-30)
REVERT: B    9 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8813 (pp30)
REVERT: B   10 GLU cc_start: 0.8991 (tp30) cc_final: 0.8606 (tp30)
REVERT: B   35 ASN cc_start: 0.8765 (m110) cc_final: 0.8509 (m110)
REVERT: B  127 LYS cc_start: 0.9067 (mmtm) cc_final: 0.8212 (mmtt)
REVERT: B  280 LYS cc_start: 0.9088 (tttm) cc_final: 0.8313 (ttmm)
REVERT: B  297 TRP cc_start: 0.8539 (m100) cc_final: 0.8121 (m100)
REVERT: G   13 ARG cc_start: 0.9285 (mtp85) cc_final: 0.9026 (mmm-85)
REVERT: G   15 LEU cc_start: 0.9413 (tp) cc_final: 0.9125 (pp)
REVERT: G   17 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8730 (mp0)
REVERT: G   22 GLU cc_start: 0.9026 (tp30) cc_final: 0.8769 (tp30)
REVERT: N   53 GLN cc_start: 0.8872 (mp10) cc_final: 0.8212 (mp10)
REVERT: N   60 TYR cc_start: 0.8617 (m-80) cc_final: 0.7468 (m-80)
REVERT: N  115 TYR cc_start: 0.8450 (t80) cc_final: 0.8233 (t80)
REVERT: R   39 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7986 (mm-40)
REVERT: R  170 LYS cc_start: 0.8304 (mmtt) cc_final: 0.7376 (mptt)
REVERT: R  173 PHE cc_start: 0.8285 (t80) cc_final: 0.8010 (t80)
  outliers start: 26
  outliers final: 20
  residues processed: 158
  average time/residue: 0.2955
  time to fit residues: 61.3285
Evaluate side-chains
  154 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
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  296 VAL
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   84 ASN
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  128 VAL
Chi-restraints excluded: chain R residue  190 CYS
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 56 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 67 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 29 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   chunk 36 optimal weight:    8.9990
   chunk 25 optimal weight:    6.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    2.6986

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 146 GLN
B  88 ASN
B 340 ASN
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.099374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.074506 restraints weight = 16866.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.83
r_work: 0.3111 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.5322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   8458  Z= 0.333
  Angle     :  0.782  31.197  11498  Z= 0.351
  Chirality :  0.066   1.816   1320
  Planarity :  0.004   0.060   1446
  Dihedral  : 11.507 169.650   1419
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 14.94 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.26), residues: 1027
  helix:  1.50 (0.26), residues: 391
  sheet: -0.76 (0.32), residues: 225
  loop : -0.49 (0.32), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 211 
 HIS   0.003   0.001   HIS A  41 
 PHE   0.016   0.001   PHE A  74 
 TYR   0.012   0.001   TYR N  95 
 ARG   0.007   0.001   ARG N  72 

*********************** 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
  165 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 133
  time to evaluate  : 0.982 
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: A   62 ILE cc_start: 0.8179 (tt) cc_final: 0.7691 (pt)
REVERT: A  169 ARG cc_start: 0.8614 (ptp90) cc_final: 0.8348 (ptp90)
REVERT: B    9 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8823 (pp30)
REVERT: B   10 GLU cc_start: 0.9033 (tp30) cc_final: 0.8636 (tp30)
REVERT: B  280 LYS cc_start: 0.9144 (tttm) cc_final: 0.8905 (ttpp)
REVERT: G   22 GLU cc_start: 0.9059 (tp30) cc_final: 0.8811 (tp30)
REVERT: N    5 GLN cc_start: 0.7864 (mp10) cc_final: 0.7563 (mp10)
REVERT: N   38 ARG cc_start: 0.8454 (ptt-90) cc_final: 0.8240 (ptt90)
REVERT: N   53 GLN cc_start: 0.8849 (mp10) cc_final: 0.8296 (mp10)
REVERT: N   60 TYR cc_start: 0.8620 (m-80) cc_final: 0.7525 (m-80)
REVERT: R  170 LYS cc_start: 0.8473 (mmtt) cc_final: 0.7492 (mptt)
  outliers start: 32
  outliers final: 27
  residues processed: 154
  average time/residue: 0.3029
  time to fit residues: 60.3514
Evaluate side-chains
  153 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
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  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  191 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   17 GLU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue    3 GLN
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  128 VAL
Chi-restraints excluded: chain R residue  179 MET
Chi-restraints excluded: chain R residue  190 CYS
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 2 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 81 optimal weight:    2.9990
   chunk 100 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 69 optimal weight:   10.0000
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
B 340 ASN
N   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.100366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.075641 restraints weight = 16842.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.84
r_work: 0.3096 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.5462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8458  Z= 0.249
  Angle     :  0.765  30.834  11498  Z= 0.338
  Chirality :  0.065   1.808   1320
  Planarity :  0.004   0.061   1446
  Dihedral  : 11.448 171.989   1419
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 16.31 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.26), residues: 1027
  helix:  1.55 (0.26), residues: 391
  sheet: -0.60 (0.33), residues: 224
  loop : -0.43 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 209 
 PHE   0.015   0.001   PHE A  74 
 TYR   0.034   0.001   TYR N 115 
 ARG   0.005   0.000   ARG N  72 

*********************** 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
  169 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 138
  time to evaluate  : 1.036 
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   60 MET cc_start: 0.5347 (tpt) cc_final: 0.4840 (mmm)
REVERT: A   62 ILE cc_start: 0.8140 (tt) cc_final: 0.7647 (pt)
REVERT: A  169 ARG cc_start: 0.8613 (ptp90) cc_final: 0.8394 (ptp90)
REVERT: B    9 GLN cc_start: 0.9202 (tm-30) cc_final: 0.8820 (pp30)
REVERT: B   10 GLU cc_start: 0.9020 (tp30) cc_final: 0.8620 (tp30)
REVERT: G   22 GLU cc_start: 0.8990 (tp30) cc_final: 0.8752 (tp30)
REVERT: G   32 LYS cc_start: 0.8895 (tppt) cc_final: 0.8625 (tppt)
REVERT: N   38 ARG cc_start: 0.8563 (ptt-90) cc_final: 0.8209 (ptt90)
REVERT: N   46 GLU cc_start: 0.7628 (tt0) cc_final: 0.7258 (tt0)
REVERT: N   51 ILE cc_start: 0.7946 (pt) cc_final: 0.7728 (pt)
REVERT: N   53 GLN cc_start: 0.8842 (mp10) cc_final: 0.8470 (mp10)
REVERT: N   60 TYR cc_start: 0.8666 (m-80) cc_final: 0.7599 (m-80)
REVERT: R   39 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7252 (mp10)
REVERT: R  170 LYS cc_start: 0.8438 (mmtt) cc_final: 0.7496 (mptt)
REVERT: R  173 PHE cc_start: 0.8222 (t80) cc_final: 0.7939 (t80)
  outliers start: 31
  outliers final: 27
  residues processed: 157
  average time/residue: 0.2982
  time to fit residues: 61.4950
Evaluate side-chains
  158 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
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  191 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   17 GLU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   39 GLN
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  128 VAL
Chi-restraints excluded: chain R residue  179 MET
Chi-restraints excluded: chain R residue  190 CYS
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 14 optimal weight:    8.9990
   chunk 8 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
N   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.102170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.077337 restraints weight = 16932.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.89
r_work: 0.3167 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.5439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8458  Z= 0.188
  Angle     :  0.751  30.640  11498  Z= 0.332
  Chirality :  0.064   1.815   1320
  Planarity :  0.004   0.060   1446
  Dihedral  : 11.379 172.296   1419
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 17.67 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.27), residues: 1027
  helix:  1.65 (0.26), residues: 390
  sheet: -0.37 (0.34), residues: 209
  loop : -0.35 (0.32), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.003   0.000   HIS A 209 
 PHE   0.015   0.001   PHE B 199 
 TYR   0.019   0.001   TYR N 115 
 ARG   0.008   0.000   ARG G  13 

*********************** 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
  172 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 144
  time to evaluate  : 0.971 
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: symmetry clash
REVERT: A   60 MET cc_start: 0.5503 (tpt) cc_final: 0.5049 (mmm)
REVERT: A   62 ILE cc_start: 0.8088 (tt) cc_final: 0.7595 (pt)
REVERT: A  169 ARG cc_start: 0.8637 (ptp90) cc_final: 0.8434 (ptp90)
REVERT: A  230 ASP cc_start: 0.8419 (m-30) cc_final: 0.8203 (m-30)
REVERT: B    9 GLN cc_start: 0.9215 (tm-30) cc_final: 0.8856 (pp30)
REVERT: B   10 GLU cc_start: 0.9010 (tp30) cc_final: 0.8619 (tp30)
REVERT: B  280 LYS cc_start: 0.9074 (ttpp) cc_final: 0.8507 (ttmm)
REVERT: G   22 GLU cc_start: 0.8996 (tp30) cc_final: 0.8742 (tp30)
REVERT: G   47 GLU cc_start: 0.8925 (mp0) cc_final: 0.8678 (mp0)
REVERT: N    5 GLN cc_start: 0.7704 (mp10) cc_final: 0.7431 (mp10)
REVERT: N   19 ARG cc_start: 0.8433 (ttt90) cc_final: 0.8124 (ttt90)
REVERT: N   38 ARG cc_start: 0.8554 (ptt-90) cc_final: 0.8192 (ptt90)
REVERT: N   46 GLU cc_start: 0.7640 (tt0) cc_final: 0.7289 (tt0)
REVERT: N   53 GLN cc_start: 0.8822 (mp10) cc_final: 0.8315 (mp10)
REVERT: N   60 TYR cc_start: 0.8656 (m-80) cc_final: 0.7587 (m-80)
REVERT: R   39 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7170 (mp10)
REVERT: R  170 LYS cc_start: 0.8400 (mmtt) cc_final: 0.7475 (mptt)
REVERT: R  173 PHE cc_start: 0.8197 (t80) cc_final: 0.7894 (t80)
  outliers start: 28
  outliers final: 24
  residues processed: 161
  average time/residue: 0.2609
  time to fit residues: 54.8812
Evaluate side-chains
  160 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 135
  time to evaluate  : 1.452 
-------------------------------------------------------------------------------
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  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   17 GLU
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   39 GLN
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  128 VAL
Chi-restraints excluded: chain R residue  190 CYS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    9.9990
   chunk 59 optimal weight:    1.9990
   chunk 55 optimal weight:    8.9990
   chunk 61 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 72 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 73 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 58 optimal weight:   10.0000
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
N   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.100979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.076214 restraints weight = 16994.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.88
r_work: 0.3108 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.5578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8458  Z= 0.232
  Angle     :  0.760  30.745  11498  Z= 0.337
  Chirality :  0.065   1.808   1320
  Planarity :  0.004   0.060   1446
  Dihedral  : 11.386 172.396   1419
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 17.67 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.27), residues: 1027
  helix:  1.67 (0.26), residues: 390
  sheet: -0.42 (0.34), residues: 209
  loop : -0.35 (0.32), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 332 
 HIS   0.003   0.001   HIS A 209 
 PHE   0.015   0.001   PHE A  74 
 TYR   0.021   0.001   TYR N 115 
 ARG   0.004   0.000   ARG B 129 

*********************** 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
  165 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 0.994 
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: A   60 MET cc_start: 0.5487 (tpt) cc_final: 0.5074 (mmm)
REVERT: A   62 ILE cc_start: 0.8018 (tt) cc_final: 0.7525 (pt)
REVERT: A  230 ASP cc_start: 0.8444 (m-30) cc_final: 0.8243 (m-30)
REVERT: B    9 GLN cc_start: 0.9223 (tm-30) cc_final: 0.8871 (pp30)
REVERT: B   10 GLU cc_start: 0.9012 (tp30) cc_final: 0.8622 (tp30)
REVERT: B  280 LYS cc_start: 0.9079 (ttpp) cc_final: 0.8531 (ttmm)
REVERT: B  289 TYR cc_start: 0.9003 (m-80) cc_final: 0.8547 (m-80)
REVERT: G   22 GLU cc_start: 0.8985 (tp30) cc_final: 0.8731 (tp30)
REVERT: G   29 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8625 (mmmt)
REVERT: G   32 LYS cc_start: 0.8895 (tppt) cc_final: 0.8680 (tppt)
REVERT: G   47 GLU cc_start: 0.8914 (mp0) cc_final: 0.8653 (mp0)
REVERT: N    5 GLN cc_start: 0.7731 (mp10) cc_final: 0.7392 (mp10)
REVERT: N   19 ARG cc_start: 0.8492 (ttt90) cc_final: 0.8201 (ttt90)
REVERT: N   38 ARG cc_start: 0.8603 (ptt-90) cc_final: 0.8184 (ptt90)
REVERT: N   46 GLU cc_start: 0.7730 (tt0) cc_final: 0.7334 (tt0)
REVERT: N   51 ILE cc_start: 0.7792 (pt) cc_final: 0.7480 (pt)
REVERT: N   53 GLN cc_start: 0.8781 (mp10) cc_final: 0.8184 (mp10)
REVERT: N   60 TYR cc_start: 0.8683 (m-80) cc_final: 0.7628 (m-80)
REVERT: N   78 THR cc_start: 0.9057 (m) cc_final: 0.8411 (p)
REVERT: R   39 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7221 (mp10)
REVERT: R  170 LYS cc_start: 0.8410 (mmtt) cc_final: 0.7484 (mptt)
REVERT: R  173 PHE cc_start: 0.8216 (t80) cc_final: 0.7941 (t80)
  outliers start: 28
  outliers final: 26
  residues processed: 156
  average time/residue: 0.2571
  time to fit residues: 52.2033
Evaluate side-chains
  156 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
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   17 GLU
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   39 GLN
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  128 VAL
Chi-restraints excluded: chain R residue  190 CYS
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 69 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
N   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.101788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.077085 restraints weight = 16798.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.86
r_work: 0.3120 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.5590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8458  Z= 0.211
  Angle     :  0.770  30.650  11498  Z= 0.343
  Chirality :  0.065   1.810   1320
  Planarity :  0.004   0.060   1446
  Dihedral  : 11.368 172.697   1419
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.70 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.27), residues: 1027
  helix:  1.63 (0.26), residues: 396
  sheet: -0.43 (0.33), residues: 209
  loop : -0.38 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 209 
 PHE   0.014   0.001   PHE A  74 
 TYR   0.020   0.001   TYR N 115 
 ARG   0.012   0.001   ARG G  13 

********************** 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
  165 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 1.043 
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: symmetry clash
REVERT: A   60 MET cc_start: 0.5472 (tpt) cc_final: 0.5058 (mmm)
REVERT: A   62 ILE cc_start: 0.8033 (tt) cc_final: 0.7546 (pt)
REVERT: B    9 GLN cc_start: 0.9233 (tm-30) cc_final: 0.8864 (pp30)
REVERT: B   10 GLU cc_start: 0.9025 (tp30) cc_final: 0.8638 (tp30)
REVERT: B  280 LYS cc_start: 0.9087 (ttpp) cc_final: 0.8557 (ttmm)
REVERT: B  289 TYR cc_start: 0.8992 (m-80) cc_final: 0.8591 (m-80)
REVERT: G   22 GLU cc_start: 0.9034 (tp30) cc_final: 0.8782 (tp30)
REVERT: G   32 LYS cc_start: 0.8892 (tppt) cc_final: 0.8670 (tppt)
REVERT: G   47 GLU cc_start: 0.8909 (mp0) cc_final: 0.8653 (mp0)
REVERT: N    5 GLN cc_start: 0.7640 (mp10) cc_final: 0.7304 (mp10)
REVERT: N   19 ARG cc_start: 0.8509 (ttt90) cc_final: 0.8223 (ttt90)
REVERT: N   38 ARG cc_start: 0.8577 (ptt-90) cc_final: 0.8169 (ptt90)
REVERT: N   46 GLU cc_start: 0.7744 (tt0) cc_final: 0.7369 (tt0)
REVERT: N   51 ILE cc_start: 0.7689 (pt) cc_final: 0.7387 (pt)
REVERT: N   53 GLN cc_start: 0.8750 (mp10) cc_final: 0.8211 (mp10)
REVERT: N   60 TYR cc_start: 0.8685 (m-80) cc_final: 0.8195 (m-80)
REVERT: N   78 THR cc_start: 0.8981 (m) cc_final: 0.8407 (p)
REVERT: R   39 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7169 (mp10)
REVERT: R  170 LYS cc_start: 0.8428 (mmtt) cc_final: 0.7427 (mptt)
REVERT: R  173 PHE cc_start: 0.8146 (t80) cc_final: 0.7862 (t80)
  outliers start: 27
  outliers final: 26
  residues processed: 155
  average time/residue: 0.2631
  time to fit residues: 53.2912
Evaluate side-chains
  158 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 131
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
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  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   17 GLU
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain R residue    5 THR
Chi-restraints excluded: chain R residue   39 GLN
Chi-restraints excluded: chain R residue   84 PHE
Chi-restraints excluded: chain R residue  101 VAL
Chi-restraints excluded: chain R residue  128 VAL
Chi-restraints excluded: chain R residue  190 CYS
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 16 optimal weight:    0.0070
   chunk 86 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 38 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 19 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.8000

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
N   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.102733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.077997 restraints weight = 16962.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.89
r_work: 0.3139 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.5660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8458  Z= 0.187
  Angle     :  0.763  30.580  11498  Z= 0.339
  Chirality :  0.065   1.812   1320
  Planarity :  0.004   0.060   1446
  Dihedral  : 11.327 172.877   1419
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 19.38 %
    Favored  : 77.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.27), residues: 1027
  helix:  1.61 (0.26), residues: 398
  sheet: -0.56 (0.33), residues: 223
  loop : -0.40 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP N  36 
 HIS   0.003   0.000   HIS A 209 
 PHE   0.013   0.001   PHE A  74 
 TYR   0.018   0.001   TYR N 115 
 ARG   0.009   0.000   ARG G  13 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4812.07 seconds
wall clock time: 85 minutes 26.11 seconds (5126.11 seconds total)