Starting phenix.real_space_refine
on Thu Jul  2 08:50:32 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7f4d_31448/07_2026/7f4d_31448.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f4d_31448/07_2026/7f4d_31448.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f4d_31448/07_2026/7f4d_31448.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f4d_31448/07_2026/7f4d_31448.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f4d_31448/07_2026/7f4d_31448.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f4d_31448/07_2026/7f4d_31448.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7f4d_31448/07_2026/7f4d_31448.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7f4d_31448/07_2026/7f4d_31448.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      56      5.16       5
     C    5102      2.51       5
     N    1411      2.21       5
     O    1477      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8047
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "G"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 433
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "A"
      Number of atoms: 1942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1942
          Classifications: {'peptide': 234}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "B"
      Number of atoms: 2575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2575
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "R"
      Number of atoms: 2028
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 2028
          Classifications: {'peptide': 263}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 256}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "M"
      Number of atoms: 101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 101
          Classifications: {'peptide': 12}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 10}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "R"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.44, per 1000 atoms: 0.18
  Number of scatterers: 8047
  At special positions: 0
  Unit cell: (120.175, 99.275, 84.645, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      56     16.00
     O    1477      8.00
     N    1411      7.00
     C    5102      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 267 " - pdb=" SG  CYS R 273 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 402.9 milliseconds
  

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1942

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 10 sheets defined
      45.0% alpha, 20.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.596A  pdb=" N   ALA G  12 " --> pdb=" O   SER G   8 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 59 through 63
      removed outlier: 3.721A  pdb=" N   ARG G  62 " --> pdb=" O   ASN G  59 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   GLU G  63 " --> pdb=" O   PRO G  60 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 59 through 63'
    Processing helix  chain 'A' and resid 13 through 39
    Processing helix  chain 'A' and resid 48 through 51
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 62 through 64
      No H-bonds generated for 'chain 'A' and resid 62 through 64'
    Processing helix  chain 'A' and resid 233 through 239
    Processing helix  chain 'A' and resid 252 through 279
      removed outlier: 3.980A  pdb=" N   GLN A 267 " --> pdb=" O   TYR A 253 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   GLU A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 285
      removed outlier: 4.177A  pdb=" N   THR A 284 " --> pdb=" O   TRP A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.677A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'R' and resid 43 through 66
      removed outlier: 4.143A  pdb=" N   SER R  47 " --> pdb=" O   GLY R  43 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 70
    Processing helix  chain 'R' and resid 71 through 103
    Processing helix  chain 'R' and resid 109 through 148
    Processing helix  chain 'R' and resid 151 through 156
    Processing helix  chain 'R' and resid 157 through 182
    Processing helix  chain 'R' and resid 185 through 226
      removed outlier: 3.785A  pdb=" N   LEU R 189 " --> pdb=" O   HIS R 185 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 238 through 267
      removed outlier: 3.517A  pdb=" N   PHE R 250 " --> pdb=" O   LEU R 246 " (cutoff:3.500A)
      Proline residue:  R 256  - end of helix
    Processing helix  chain 'R' and resid 270 through 278
    Processing helix  chain 'R' and resid 279 through 299
      Proline residue:  R 295  - end of helix
    Processing helix  chain 'R' and resid 302 through 307
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.220A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.340A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.607A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.612A  pdb=" N   GLN N   5 " --> pdb=" O   ALA N  23 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'N' and resid 10 through 12
      removed outlier: 5.995A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.542A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.505A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.617A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.863A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.600A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.567A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.188A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 234
      removed outlier: 6.371A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.348A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    463 hydrogen bonds defined for protein.
    1299 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: 0.83

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2239
        1.33 -     1.46: 2028
        1.46 -     1.59: 3859
        1.59 -     1.72: 0
        1.72 -     1.85: 77
  Bond restraints: 8203
  Sorted by residual:
  bond pdb=" C   GLY R 136 "
       pdb=" O   GLY R 136 "
    ideal  model  delta    sigma   weight residual
    1.234  1.206  0.028 1.20e-02 6.94e+03 5.39e+00
  bond pdb=" C   TRP N  47 "
       pdb=" N   VAL N  48 "
    ideal  model  delta    sigma   weight residual
    1.333  1.364 -0.030 1.46e-02 4.69e+03 4.31e+00
  bond pdb=" CG  HIS R 217 "
       pdb=" CD2 HIS R 217 "
    ideal  model  delta    sigma   weight residual
    1.354  1.332  0.022 1.10e-02 8.26e+03 3.92e+00
  bond pdb=" C   GLU M   5 "
       pdb=" N   HIS M   6 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 1.35e-02 5.49e+03 3.71e+00
  bond pdb=" CZ  ARG A 232 "
       pdb=" NH2 ARG A 232 "
    ideal  model  delta    sigma   weight residual
    1.330  1.305  0.025 1.30e-02 5.92e+03 3.58e+00
  ... (remaining 8198 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 10340
        1.91 -     3.82: 691
        3.82 -     5.73: 73
        5.73 -     7.64: 8
        7.64 -     9.56: 1
  Bond angle restraints: 11113
  Sorted by residual:
  angle pdb=" C   ASP B 291 "
        pdb=" N   PHE B 292 "
        pdb=" CA  PHE B 292 "
      ideal   model   delta    sigma   weight residual
     121.70  131.26   -9.56 1.80e+00 3.09e-01 2.82e+01
  angle pdb=" N   ASP B 291 "
        pdb=" CA  ASP B 291 "
        pdb=" C   ASP B 291 "
      ideal   model   delta    sigma   weight residual
     112.23  117.02   -4.79 1.26e+00 6.30e-01 1.44e+01
  angle pdb=" N   PHE M   7 "
        pdb=" CA  PHE M   7 "
        pdb=" C   PHE M   7 "
      ideal   model   delta    sigma   weight residual
     108.14  102.64    5.50 1.52e+00 4.33e-01 1.31e+01
  angle pdb=" C   LEU R  93 "
        pdb=" N   GLU R  94 "
        pdb=" CA  GLU R  94 "
      ideal   model   delta    sigma   weight residual
     121.58  114.78    6.80 1.95e+00 2.63e-01 1.22e+01
  angle pdb=" C   TYR R 148 "
        pdb=" N   ALA R 149 "
        pdb=" CA  ALA R 149 "
      ideal   model   delta    sigma   weight residual
     120.38  124.87   -4.49 1.37e+00 5.33e-01 1.07e+01
  ... (remaining 11108 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 4552
       17.62 -    35.24: 280
       35.24 -    52.85: 43
       52.85 -    70.47: 18
       70.47 -    88.09: 2
  Dihedral angle restraints: 4895
    sinusoidal: 1898
      harmonic: 2997
  Sorted by residual:
  dihedral pdb=" CA  ASP B  66 "
           pdb=" C   ASP B  66 "
           pdb=" N   SER B  67 "
           pdb=" CA  SER B  67 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.34  -29.66     0      5.00e+00 4.00e-02 3.52e+01
  dihedral pdb=" CA  CYS B 204 "
           pdb=" C   CYS B 204 "
           pdb=" N   ASP B 205 "
           pdb=" CA  ASP B 205 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.23   28.77     0      5.00e+00 4.00e-02 3.31e+01
  dihedral pdb=" CA  TYR B 105 "
           pdb=" C   TYR B 105 "
           pdb=" N   ALA B 106 "
           pdb=" CA  ALA B 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.53   28.47     0      5.00e+00 4.00e-02 3.24e+01
  ... (remaining 4892 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 734
       0.048 -    0.095: 400
       0.095 -    0.143: 119
       0.143 -    0.191: 16
       0.191 -    0.238: 6
  Chirality restraints: 1275
  Sorted by residual:
  chirality pdb=" CA  VAL B 315 "
            pdb=" N   VAL B 315 "
            pdb=" C   VAL B 315 "
            pdb=" CB  VAL B 315 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CG  LEU B 308 "
            pdb=" CB  LEU B 308 "
            pdb=" CD1 LEU B 308 "
            pdb=" CD2 LEU B 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  GLU R  94 "
            pdb=" N   GLU R  94 "
            pdb=" C   GLU R  94 "
            pdb=" CB  GLU R  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1272 not shown)

  Planarity restraints: 1413
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR R  74 "   -0.001 2.00e-02 2.50e+03   2.95e-02 1.74e+01
        pdb=" CG  TYR R  74 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR R  74 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD2 TYR R  74 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR R  74 "    0.024 2.00e-02 2.50e+03
        pdb=" CE2 TYR R  74 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  TYR R  74 "    0.048 2.00e-02 2.50e+03
        pdb=" OH  TYR R  74 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 314 "   -0.252 9.50e-02 1.11e+02   1.16e-01 1.74e+01
        pdb=" NE  ARG B 314 "    0.033 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 314 "   -0.050 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 314 "    0.020 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 314 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 281 "   -0.030 2.00e-02 2.50e+03   2.19e-02 1.20e+01
        pdb=" CG  TRP A 281 "    0.058 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 281 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 281 "   -0.015 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 281 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 281 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 281 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 281 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 281 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 281 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1410 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 70
        2.59 -     3.17: 7184
        3.17 -     3.74: 13253
        3.74 -     4.32: 19002
        4.32 -     4.90: 31194
  Nonbonded interactions: 70703
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP R 117 "
            pdb="CA    CA R 501 "
     model   vdw
     2.011 2.510
  nonbonded pdb=" O   GLU M   5 "
            pdb="CA    CA R 501 "
     model   vdw
     2.068 2.510
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   SER R 127 "
            pdb=" OG  SER R 131 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   THR B  86 "
            pdb=" OG1 THR B  87 "
     model   vdw
     2.289 3.040
  ... (remaining 70698 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:             0.520
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.350
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
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      :  0.009   0.068   8205  Z= 0.503
  Angle     :  1.066   9.555  11117  Z= 0.630
  Chirality :  0.060   0.238   1275
  Planarity :  0.010   0.121   1413
  Dihedral  : 12.497  88.088   2947
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.24), residues: 1014
  helix: -0.12 (0.22), residues: 402
  sheet: -0.18 (0.37), residues: 211
  loop : -1.16 (0.29), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.053   0.005   ARG B 314 
 TYR   0.048   0.007   TYR R  74 
 PHE   0.030   0.005   PHE A 246 
 TRP   0.058   0.009   TRP A 281 
 HIS   0.016   0.004   HIS R 153 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00936 /  0.50 ( 8203)
  covalent geometry    : angle       1.06561 /  0.63 (11113)
  SS BOND              : bond        0.00388 /  0.19 (    2)
  SS BOND              : angle       1.23694 /  0.71 (    4)
  hydrogen bonds       : bond        0.14781 / 10.00 (  463)
  hydrogen bonds       : angle       7.19128 /  5.09 ( 1299)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   16 VAL cc_start: 0.8961 (t) cc_final: 0.8760 (p)
REVERT: G   20 LYS cc_start: 0.9226 (mtmt) cc_final: 0.8257 (mtmm)
REVERT: G   21 MET cc_start: 0.8619 (mpp) cc_final: 0.8245 (mpm)
REVERT: G   22 GLU cc_start: 0.8542 (tt0) cc_final: 0.8139 (tm-30)
REVERT: G   29 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8742 (mmmt)
REVERT: G   32 LYS cc_start: 0.9141 (tttt) cc_final: 0.8804 (ttmm)
REVERT: A   29 GLN cc_start: 0.8388 (tp40) cc_final: 0.7833 (mm-40)
REVERT: A  221 MET cc_start: 0.8799 (ttm) cc_final: 0.8418 (ttm)
REVERT: A  271 ASN cc_start: 0.8766 (m-40) cc_final: 0.8526 (m110)
REVERT: A  378 ASP cc_start: 0.8018 (m-30) cc_final: 0.7533 (m-30)
REVERT: N   18 LEU cc_start: 0.8998 (tp) cc_final: 0.8782 (tp)
REVERT: N   38 ARG cc_start: 0.8576 (ptt180) cc_final: 0.8190 (ptt-90)
REVERT: N   46 GLU cc_start: 0.7696 (tt0) cc_final: 0.7233 (tt0)
REVERT: N   76 LYS cc_start: 0.9087 (mtpp) cc_final: 0.8624 (mtpm)
REVERT: N   80 TYR cc_start: 0.8438 (m-80) cc_final: 0.8036 (m-80)
REVERT: N   90 ASP cc_start: 0.8585 (m-30) cc_final: 0.7887 (m-30)
REVERT: N  107 CYS cc_start: 0.8354 (m) cc_final: 0.5531 (m)
REVERT: N  123 GLN cc_start: 0.8480 (tp40) cc_final: 0.8108 (mm-40)
REVERT: B    9 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8740 (tm-30)
REVERT: B  169 TRP cc_start: 0.8921 (m100) cc_final: 0.8409 (m100)
REVERT: B  186 ASP cc_start: 0.7074 (t0) cc_final: 0.6774 (t0)
REVERT: B  209 LYS cc_start: 0.8501 (mttm) cc_final: 0.8283 (mttm)
REVERT: B  262 MET cc_start: 0.7954 (tpp) cc_final: 0.7549 (tpp)
REVERT: B  277 SER cc_start: 0.9016 (t) cc_final: 0.8740 (t)
REVERT: B  337 LYS cc_start: 0.7765 (mttt) cc_final: 0.7484 (mmmm)
REVERT: R   56 ASN cc_start: 0.9245 (m-40) cc_final: 0.8937 (m110)
REVERT: R   91 ASN cc_start: 0.8500 (t0) cc_final: 0.8114 (t0)
REVERT: R  303 GLN cc_start: 0.8351 (mm110) cc_final: 0.7490 (mm-40)
REVERT: M    7 PHE cc_start: 0.8802 (t80) cc_final: 0.8542 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 248
  average time/residue: 0.5947
  time to fit residues: 155.1857
Evaluate side-chains
  168 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  18 GLN
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  35 ASN
B  36 ASN
** B  75 GLN ** 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 = 0.3450 r_free = 0.3450 target = 0.086672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.065880 restraints weight = 17910.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 3.19
r_work: 0.2883 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.2677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8205  Z= 0.163
  Angle     :  0.683   8.328  11117  Z= 0.359
  Chirality :  0.043   0.148   1275
  Planarity :  0.004   0.041   1413
  Dihedral  :  5.382  25.088   1120
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 11.29 %
    Favored  : 86.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.26), residues: 1014
  helix:  1.69 (0.24), residues: 403
  sheet: -0.40 (0.35), residues: 210
  loop : -0.47 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  61 
 TYR   0.018   0.002   TYR N  95 
 PHE   0.017   0.002   PHE G  61 
 TRP   0.025   0.002   TRP B 339 
 HIS   0.003   0.001   HIS B 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.16 ( 8203)
  covalent geometry    : angle       0.68339 /  0.36 (11113)
  SS BOND              : bond        0.00276 /  0.13 (    2)
  SS BOND              : angle       0.85396 /  0.39 (    4)
  hydrogen bonds       : bond        0.04565 /  3.11 (  463)
  hydrogen bonds       : angle       5.23694 /  3.64 ( 1299)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 181
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   20 LYS cc_start: 0.8841 (mtmt) cc_final: 0.8349 (mtmm)
REVERT: G   22 GLU cc_start: 0.8483 (tt0) cc_final: 0.7988 (tm-30)
REVERT: G   48 ASP cc_start: 0.8753 (t0) cc_final: 0.8513 (t0)
REVERT: G   58 GLU cc_start: 0.8769 (mp0) cc_final: 0.8547 (pm20)
REVERT: A   16 ASP cc_start: 0.9033 (t0) cc_final: 0.8748 (t0)
REVERT: A  209 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8179 (tp30)
REVERT: A  268 GLU cc_start: 0.9061 (tt0) cc_final: 0.8808 (tt0)
REVERT: A  271 ASN cc_start: 0.9103 (m-40) cc_final: 0.8815 (m-40)
REVERT: A  327 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8739 (pm20)
REVERT: A  378 ASP cc_start: 0.8487 (m-30) cc_final: 0.7991 (m-30)
REVERT: N   33 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8218 (tmtp)
REVERT: N   46 GLU cc_start: 0.8348 (tt0) cc_final: 0.7659 (tt0)
REVERT: N   73 ASP cc_start: 0.8256 (t0) cc_final: 0.7896 (t0)
REVERT: N   76 LYS cc_start: 0.9309 (mtpp) cc_final: 0.9091 (mtpp)
REVERT: N   82 GLN cc_start: 0.9008 (tp40) cc_final: 0.8737 (tp40)
REVERT: N   83 MET cc_start: 0.9112 (mtm) cc_final: 0.8844 (mtp)
REVERT: N   87 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8249 (mttp)
REVERT: N   90 ASP cc_start: 0.8821 (m-30) cc_final: 0.8502 (m-30)
REVERT: N  107 CYS cc_start: 0.8316 (m) cc_final: 0.7907 (m)
REVERT: N  120 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8824 (mm-40)
REVERT: B  172 GLU cc_start: 0.8473 (pp20) cc_final: 0.8158 (pp20)
REVERT: B  186 ASP cc_start: 0.7322 (t0) cc_final: 0.6680 (t0)
REVERT: B  188 MET cc_start: 0.8630 (mmm) cc_final: 0.8150 (mmm)
REVERT: B  189 SER cc_start: 0.9272 (t) cc_final: 0.9053 (p)
REVERT: B  217 MET cc_start: 0.8821 (ptm) cc_final: 0.8503 (ppp)
REVERT: B  262 MET cc_start: 0.8806 (tpp) cc_final: 0.8207 (ttm)
REVERT: B  267 ASP cc_start: 0.9068 (p0) cc_final: 0.8777 (p0)
REVERT: B  275 SER cc_start: 0.8901 (OUTLIER) cc_final: 0.8526 (m)
REVERT: B  277 SER cc_start: 0.9283 (t) cc_final: 0.8992 (t)
REVERT: R   56 ASN cc_start: 0.9024 (m-40) cc_final: 0.8822 (m110)
REVERT: R  126 SER cc_start: 0.8701 (t) cc_final: 0.8467 (m)
REVERT: R  226 LYS cc_start: 0.7994 (mttt) cc_final: 0.7720 (mmmt)
REVERT: R  238 LYS cc_start: 0.8222 (ttmt) cc_final: 0.8007 (ttmt)
REVERT: R  290 ASN cc_start: 0.8132 (t0) cc_final: 0.7898 (t0)
REVERT: R  303 GLN cc_start: 0.8149 (mm110) cc_final: 0.7650 (mm-40)
REVERT: M   11 LYS cc_start: 0.9199 (mppt) cc_final: 0.8901 (mmmm)
  outliers start: 19
  outliers final: 3
  residues processed: 190
  average time/residue: 0.5036
  time to fit residues: 101.7530
Evaluate side-chains
  160 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 152
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  327 GLU
Chi-restraints excluded: chain N residue   33 LYS
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  284 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 83 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 67 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 82 optimal weight:    0.7980
   overall best weight:    2.1588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  18 GLN
N   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.084624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.063509 restraints weight = 17785.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 3.11
r_work: 0.2827 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.3260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8205  Z= 0.209
  Angle     :  0.648   8.495  11117  Z= 0.335
  Chirality :  0.042   0.162   1275
  Planarity :  0.004   0.037   1413
  Dihedral  :  4.933  26.905   1120
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.40 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.26), residues: 1014
  helix:  2.08 (0.24), residues: 406
  sheet: -0.70 (0.34), residues: 206
  loop : -0.49 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G  13 
 TYR   0.017   0.002   TYR N  95 
 PHE   0.018   0.002   PHE G  61 
 TRP   0.021   0.002   TRP B 169 
 HIS   0.006   0.001   HIS B 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00471 /  0.21 ( 8203)
  covalent geometry    : angle       0.64751 /  0.33 (11113)
  SS BOND              : bond        0.00780 /  0.41 (    2)
  SS BOND              : angle       0.65766 /  0.33 (    4)
  hydrogen bonds       : bond        0.04267 /  2.88 (  463)
  hydrogen bonds       : angle       4.94172 /  3.41 ( 1299)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 167
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   17 GLU cc_start: 0.9105 (pt0) cc_final: 0.8856 (tm-30)
REVERT: G   21 MET cc_start: 0.8960 (mmp) cc_final: 0.8442 (mmp)
REVERT: G   22 GLU cc_start: 0.8427 (tt0) cc_final: 0.7895 (tm-30)
REVERT: G   26 ASP cc_start: 0.9067 (t0) cc_final: 0.8841 (t0)
REVERT: G   58 GLU cc_start: 0.8667 (mp0) cc_final: 0.8132 (pm20)
REVERT: A  209 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8098 (tp30)
REVERT: A  268 GLU cc_start: 0.9096 (tt0) cc_final: 0.8850 (tt0)
REVERT: A  271 ASN cc_start: 0.9074 (m-40) cc_final: 0.8674 (m110)
REVERT: A  378 ASP cc_start: 0.8574 (m-30) cc_final: 0.8255 (m-30)
REVERT: N   33 LYS cc_start: 0.8646 (tttm) cc_final: 0.8080 (tmtp)
REVERT: N   46 GLU cc_start: 0.8442 (tt0) cc_final: 0.7715 (tt0)
REVERT: N   73 ASP cc_start: 0.8236 (t0) cc_final: 0.7641 (OUTLIER)
REVERT: N   76 LYS cc_start: 0.9374 (mtpp) cc_final: 0.9143 (mtpp)
REVERT: N   80 TYR cc_start: 0.8194 (m-80) cc_final: 0.7828 (m-80)
REVERT: N   82 GLN cc_start: 0.9048 (tp40) cc_final: 0.8790 (tp40)
REVERT: N   87 LYS cc_start: 0.8641 (mttp) cc_final: 0.8362 (ptpt)
REVERT: N   90 ASP cc_start: 0.8832 (m-30) cc_final: 0.8138 (m-30)
REVERT: N  107 CYS cc_start: 0.8279 (m) cc_final: 0.7961 (m)
REVERT: N  120 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8971 (mm-40)
REVERT: B   32 GLN cc_start: 0.9198 (mt0) cc_final: 0.8915 (pt0)
REVERT: B   89 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8208 (mmtm)
REVERT: B  105 TYR cc_start: 0.9295 (OUTLIER) cc_final: 0.8616 (m-80)
REVERT: B  172 GLU cc_start: 0.8643 (pp20) cc_final: 0.8301 (pp20)
REVERT: B  186 ASP cc_start: 0.7208 (t0) cc_final: 0.6484 (t0)
REVERT: B  188 MET cc_start: 0.8536 (mmm) cc_final: 0.8040 (mmm)
REVERT: B  189 SER cc_start: 0.9236 (t) cc_final: 0.8937 (p)
REVERT: B  217 MET cc_start: 0.8856 (ptm) cc_final: 0.8480 (ppp)
REVERT: B  262 MET cc_start: 0.8862 (tpp) cc_final: 0.8262 (ttm)
REVERT: B  275 SER cc_start: 0.8909 (OUTLIER) cc_final: 0.8483 (m)
REVERT: B  277 SER cc_start: 0.9496 (t) cc_final: 0.9269 (t)
REVERT: R  126 SER cc_start: 0.8676 (t) cc_final: 0.8396 (m)
REVERT: R  184 ASP cc_start: 0.9291 (t0) cc_final: 0.9067 (p0)
REVERT: R  226 LYS cc_start: 0.8076 (mttt) cc_final: 0.7749 (mmmt)
REVERT: R  238 LYS cc_start: 0.8335 (ttmt) cc_final: 0.7918 (ttpp)
REVERT: R  290 ASN cc_start: 0.8114 (t0) cc_final: 0.7881 (t0)
REVERT: R  303 GLN cc_start: 0.8211 (mm110) cc_final: 0.7746 (mm-40)
REVERT: M   11 LYS cc_start: 0.9205 (mppt) cc_final: 0.8932 (mppt)
  outliers start: 24
  outliers final: 7
  residues processed: 180
  average time/residue: 0.5356
  time to fit residues: 102.3670
Evaluate side-chains
  158 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 148
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  188 VAL
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  301 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 45 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 79 optimal weight:    5.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  18 GLN
N   3 GLN
B  36 ASN
B 132 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.087389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.065907 restraints weight = 18251.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3022 rms_B_bonded: 3.26
r_work: 0.2861 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8205  Z= 0.140
  Angle     :  0.617   8.921  11117  Z= 0.316
  Chirality :  0.041   0.181   1275
  Planarity :  0.004   0.052   1413
  Dihedral  :  4.604  24.726   1120
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.09 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.27), residues: 1014
  helix:  2.28 (0.24), residues: 409
  sheet: -0.69 (0.34), residues: 211
  loop : -0.38 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG R  67 
 TYR   0.016   0.001   TYR N  95 
 PHE   0.013   0.001   PHE G  61 
 TRP   0.018   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B  54 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.14 ( 8203)
  covalent geometry    : angle       0.61748 /  0.32 (11113)
  SS BOND              : bond        0.00130 /  0.07 (    2)
  SS BOND              : angle       0.52858 /  0.27 (    4)
  hydrogen bonds       : bond        0.03774 /  2.54 (  463)
  hydrogen bonds       : angle       4.69540 /  3.23 ( 1299)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 161
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   21 MET cc_start: 0.8980 (mmp) cc_final: 0.8171 (mmp)
REVERT: G   22 GLU cc_start: 0.8449 (tt0) cc_final: 0.7946 (tm-30)
REVERT: G   25 ILE cc_start: 0.8205 (pt) cc_final: 0.7917 (pt)
REVERT: G   26 ASP cc_start: 0.9105 (t0) cc_final: 0.8872 (t0)
REVERT: G   32 LYS cc_start: 0.8880 (ttmm) cc_final: 0.8672 (tppp)
REVERT: G   36 ASP cc_start: 0.8589 (m-30) cc_final: 0.8325 (m-30)
REVERT: G   58 GLU cc_start: 0.8428 (mp0) cc_final: 0.8215 (pm20)
REVERT: A  209 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8078 (tp30)
REVERT: A  268 GLU cc_start: 0.9095 (tt0) cc_final: 0.8760 (tt0)
REVERT: A  271 ASN cc_start: 0.8994 (m-40) cc_final: 0.8656 (m110)
REVERT: A  378 ASP cc_start: 0.8555 (m-30) cc_final: 0.8226 (m-30)
REVERT: N    3 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7068 (tm130)
REVERT: N   33 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7873 (tttm)
REVERT: N   46 GLU cc_start: 0.8479 (tt0) cc_final: 0.7828 (tt0)
REVERT: N   73 ASP cc_start: 0.8125 (t0) cc_final: 0.7619 (t0)
REVERT: N   76 LYS cc_start: 0.9408 (mtpp) cc_final: 0.9184 (mtpp)
REVERT: N   80 TYR cc_start: 0.8121 (m-80) cc_final: 0.7776 (m-80)
REVERT: N   82 GLN cc_start: 0.8977 (tp40) cc_final: 0.8511 (tp40)
REVERT: B  105 TYR cc_start: 0.9248 (OUTLIER) cc_final: 0.8591 (m-80)
REVERT: B  172 GLU cc_start: 0.8686 (pp20) cc_final: 0.8299 (pp20)
REVERT: B  186 ASP cc_start: 0.7080 (t0) cc_final: 0.6432 (t0)
REVERT: B  188 MET cc_start: 0.8401 (mmm) cc_final: 0.7918 (mmm)
REVERT: B  189 SER cc_start: 0.9347 (t) cc_final: 0.9049 (p)
REVERT: B  217 MET cc_start: 0.8850 (ptm) cc_final: 0.8545 (ppp)
REVERT: B  262 MET cc_start: 0.8890 (tpp) cc_final: 0.7572 (ttm)
REVERT: B  275 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8411 (m)
REVERT: R  126 SER cc_start: 0.8599 (t) cc_final: 0.8315 (m)
REVERT: R  184 ASP cc_start: 0.9277 (t0) cc_final: 0.8997 (p0)
REVERT: R  226 LYS cc_start: 0.8087 (mttt) cc_final: 0.7758 (mmmt)
REVERT: R  238 LYS cc_start: 0.8287 (ttmt) cc_final: 0.8012 (tttm)
REVERT: R  290 ASN cc_start: 0.8106 (t0) cc_final: 0.7895 (t0)
REVERT: R  303 GLN cc_start: 0.8164 (mm110) cc_final: 0.7728 (mm-40)
REVERT: M    5 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8185 (tt0)
REVERT: M   11 LYS cc_start: 0.9208 (mppt) cc_final: 0.8809 (mmmm)
  outliers start: 22
  outliers final: 5
  residues processed: 173
  average time/residue: 0.5536
  time to fit residues: 101.9005
Evaluate side-chains
  158 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 148
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   33 LYS
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  188 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 77 optimal weight:    7.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  18 GLN
N  39 GLN
B  36 ASN
** R  56 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 = 0.3412 r_free = 0.3412 target = 0.084398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.062681 restraints weight = 18138.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 3.15
r_work: 0.2789 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.3809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   8205  Z= 0.249
  Angle     :  0.649   8.396  11117  Z= 0.334
  Chirality :  0.043   0.157   1275
  Planarity :  0.004   0.033   1413
  Dihedral  :  4.705  24.381   1120
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 15.90 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.27), residues: 1014
  helix:  2.45 (0.24), residues: 401
  sheet: -0.84 (0.34), residues: 221
  loop : -0.22 (0.33), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG R  67 
 TYR   0.019   0.002   TYR B 264 
 PHE   0.017   0.002   PHE G  61 
 TRP   0.014   0.002   TRP B 339 
 HIS   0.005   0.001   HIS B 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00563 /  0.25 ( 8203)
  covalent geometry    : angle       0.64904 /  0.33 (11113)
  SS BOND              : bond        0.00052 /  0.03 (    2)
  SS BOND              : angle       0.65167 /  0.34 (    4)
  hydrogen bonds       : bond        0.04070 /  2.71 (  463)
  hydrogen bonds       : angle       4.76047 /  3.29 ( 1299)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 151
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8636 (mtm110) cc_final: 0.8428 (mtm110)
REVERT: G   17 GLU cc_start: 0.8874 (tp30) cc_final: 0.8333 (tp30)
REVERT: G   21 MET cc_start: 0.8750 (mmp) cc_final: 0.8350 (mmp)
REVERT: G   22 GLU cc_start: 0.8500 (tt0) cc_final: 0.7948 (tm-30)
REVERT: G   58 GLU cc_start: 0.8420 (mp0) cc_final: 0.8206 (pm20)
REVERT: A  209 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8158 (tp30)
REVERT: A  268 GLU cc_start: 0.9113 (tt0) cc_final: 0.8841 (tt0)
REVERT: A  271 ASN cc_start: 0.9063 (m-40) cc_final: 0.8654 (m110)
REVERT: A  378 ASP cc_start: 0.8558 (m-30) cc_final: 0.8250 (m-30)
REVERT: N    3 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7403 (tm-30)
REVERT: N   33 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7813 (tttm)
REVERT: N   46 GLU cc_start: 0.8552 (tt0) cc_final: 0.7981 (tt0)
REVERT: N   73 ASP cc_start: 0.8226 (t0) cc_final: 0.7580 (t0)
REVERT: N   80 TYR cc_start: 0.8196 (m-80) cc_final: 0.7870 (m-80)
REVERT: N   82 GLN cc_start: 0.8962 (tp40) cc_final: 0.8555 (tp40)
REVERT: N   90 ASP cc_start: 0.8820 (m-30) cc_final: 0.8308 (m-30)
REVERT: N  107 CYS cc_start: 0.8339 (m) cc_final: 0.7618 (m)
REVERT: B    9 GLN cc_start: 0.9238 (mm-40) cc_final: 0.9026 (mm-40)
REVERT: B   10 GLU cc_start: 0.9359 (mt-10) cc_final: 0.9155 (mp0)
REVERT: B  105 TYR cc_start: 0.9332 (OUTLIER) cc_final: 0.8553 (m-80)
REVERT: B  172 GLU cc_start: 0.8740 (pp20) cc_final: 0.8370 (pp20)
REVERT: B  188 MET cc_start: 0.8486 (mmm) cc_final: 0.8143 (mmm)
REVERT: B  189 SER cc_start: 0.9281 (t) cc_final: 0.8998 (p)
REVERT: B  217 MET cc_start: 0.8889 (ptm) cc_final: 0.8559 (ppp)
REVERT: B  262 MET cc_start: 0.8898 (tpp) cc_final: 0.7788 (ttm)
REVERT: B  275 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8444 (m)
REVERT: R  126 SER cc_start: 0.8693 (t) cc_final: 0.8399 (m)
REVERT: R  184 ASP cc_start: 0.9310 (t0) cc_final: 0.9032 (p0)
REVERT: R  226 LYS cc_start: 0.8146 (mttt) cc_final: 0.7810 (mmmt)
REVERT: R  238 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8206 (tttm)
REVERT: R  290 ASN cc_start: 0.8207 (t0) cc_final: 0.7947 (t0)
REVERT: R  303 GLN cc_start: 0.8229 (mm110) cc_final: 0.7850 (mm-40)
REVERT: M    5 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8647 (tt0)
REVERT: M   11 LYS cc_start: 0.9265 (mppt) cc_final: 0.8951 (mppt)
  outliers start: 31
  outliers final: 10
  residues processed: 170
  average time/residue: 0.5413
  time to fit residues: 97.9956
Evaluate side-chains
  163 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   33 LYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain R residue  188 VAL
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  301 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0570
   chunk 28 optimal weight:    8.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.6900

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  18 GLN
A  31 GLN
N   3 GLN
N  39 GLN
B  36 ASN
** R  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.085843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.065410 restraints weight = 17886.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 3.08
r_work: 0.2877 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.4082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8205  Z= 0.132
  Angle     :  0.617   9.017  11117  Z= 0.315
  Chirality :  0.041   0.175   1275
  Planarity :  0.004   0.036   1413
  Dihedral  :  4.493  23.559   1120
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 18.09 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.27), residues: 1014
  helix:  2.62 (0.24), residues: 402
  sheet: -0.80 (0.34), residues: 213
  loop : -0.24 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG N 105 
 TYR   0.016   0.001   TYR N  95 
 PHE   0.011   0.001   PHE G  61 
 TRP   0.017   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B  54 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.13 ( 8203)
  covalent geometry    : angle       0.61733 /  0.31 (11113)
  SS BOND              : bond        0.00244 /  0.12 (    2)
  SS BOND              : angle       0.79349 /  0.39 (    4)
  hydrogen bonds       : bond        0.03670 /  2.45 (  463)
  hydrogen bonds       : angle       4.63198 /  3.21 ( 1299)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 164
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   14 LYS cc_start: 0.9387 (mppt) cc_final: 0.9093 (mmpt)
REVERT: G   17 GLU cc_start: 0.8942 (tp30) cc_final: 0.8313 (tp30)
REVERT: G   21 MET cc_start: 0.8770 (mmp) cc_final: 0.8309 (mmp)
REVERT: G   22 GLU cc_start: 0.8544 (tt0) cc_final: 0.7946 (tm-30)
REVERT: G   32 LYS cc_start: 0.8916 (ttmm) cc_final: 0.8706 (tppp)
REVERT: G   36 ASP cc_start: 0.8575 (m-30) cc_final: 0.8313 (m-30)
REVERT: A  209 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8044 (tp30)
REVERT: A  268 GLU cc_start: 0.9081 (tt0) cc_final: 0.8749 (tt0)
REVERT: A  271 ASN cc_start: 0.9020 (m-40) cc_final: 0.8637 (m110)
REVERT: A  378 ASP cc_start: 0.8574 (m-30) cc_final: 0.8267 (m-30)
REVERT: N    3 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7438 (tm-30)
REVERT: N   33 LYS cc_start: 0.8290 (tttm) cc_final: 0.7742 (tttm)
REVERT: N   43 LYS cc_start: 0.9231 (mtpm) cc_final: 0.8670 (mptt)
REVERT: N   46 GLU cc_start: 0.8562 (tt0) cc_final: 0.8119 (tt0)
REVERT: N   73 ASP cc_start: 0.8299 (t0) cc_final: 0.7925 (t0)
REVERT: N   76 LYS cc_start: 0.9397 (mtpp) cc_final: 0.9089 (mtmm)
REVERT: N   80 TYR cc_start: 0.8126 (m-80) cc_final: 0.7431 (m-80)
REVERT: N   82 GLN cc_start: 0.8963 (tp40) cc_final: 0.8477 (tp40)
REVERT: B    9 GLN cc_start: 0.9250 (mm-40) cc_final: 0.9006 (mm-40)
REVERT: B   31 SER cc_start: 0.9427 (t) cc_final: 0.9142 (p)
REVERT: B  105 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.8593 (m-80)
REVERT: B  172 GLU cc_start: 0.8732 (pp20) cc_final: 0.8446 (pp20)
REVERT: B  188 MET cc_start: 0.8324 (mmm) cc_final: 0.7945 (mmm)
REVERT: B  189 SER cc_start: 0.9337 (t) cc_final: 0.9065 (p)
REVERT: B  209 LYS cc_start: 0.8207 (mttm) cc_final: 0.7947 (mttm)
REVERT: B  217 MET cc_start: 0.8859 (ptm) cc_final: 0.8590 (ppp)
REVERT: B  262 MET cc_start: 0.8895 (tpp) cc_final: 0.7469 (ttm)
REVERT: B  275 SER cc_start: 0.8864 (OUTLIER) cc_final: 0.8409 (m)
REVERT: B  325 MET cc_start: 0.9069 (tpp) cc_final: 0.8615 (mmm)
REVERT: R  126 SER cc_start: 0.8674 (t) cc_final: 0.8391 (m)
REVERT: R  184 ASP cc_start: 0.9281 (t0) cc_final: 0.9045 (p0)
REVERT: R  226 LYS cc_start: 0.8142 (mttt) cc_final: 0.7795 (mmmt)
REVERT: R  238 LYS cc_start: 0.8497 (ttmt) cc_final: 0.8125 (tttm)
REVERT: R  290 ASN cc_start: 0.8205 (t0) cc_final: 0.7949 (t0)
REVERT: R  303 GLN cc_start: 0.7786 (mm110) cc_final: 0.7409 (mm-40)
REVERT: M    5 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8683 (tt0)
REVERT: M   11 LYS cc_start: 0.9295 (mppt) cc_final: 0.8887 (mmmm)
  outliers start: 20
  outliers final: 9
  residues processed: 177
  average time/residue: 0.5139
  time to fit residues: 96.8955
Evaluate side-chains
  166 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 153
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue  188 VAL
Chi-restraints excluded: chain R residue  304 GLU
Chi-restraints excluded: chain R residue  305 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9980
   chunk 54 optimal weight:    0.1980
   chunk 41 optimal weight:   10.0000
   chunk 83 optimal weight:    1.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  18 GLN
N   3 GLN
N  39 GLN
** R  56 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 = 0.3435 r_free = 0.3435 target = 0.085495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.065170 restraints weight = 18170.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 3.10
r_work: 0.2874 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.4282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8205  Z= 0.147
  Angle     :  0.645   9.362  11117  Z= 0.326
  Chirality :  0.041   0.171   1275
  Planarity :  0.004   0.036   1413
  Dihedral  :  4.433  22.147   1120
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 19.47 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.27), residues: 1014
  helix:  2.69 (0.25), residues: 403
  sheet: -0.75 (0.35), residues: 215
  loop : -0.21 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G  13 
 TYR   0.022   0.002   TYR G  40 
 PHE   0.010   0.001   PHE A 376 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 225 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.15 ( 8203)
  covalent geometry    : angle       0.64451 /  0.33 (11113)
  SS BOND              : bond        0.00194 /  0.10 (    2)
  SS BOND              : angle       0.82253 /  0.42 (    4)
  hydrogen bonds       : bond        0.03708 /  2.47 (  463)
  hydrogen bonds       : angle       4.58682 /  3.18 ( 1299)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 160
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8640 (mtm110) cc_final: 0.8430 (mtm110)
REVERT: G   22 GLU cc_start: 0.8547 (tt0) cc_final: 0.7886 (tm-30)
REVERT: G   24 ASN cc_start: 0.8290 (p0) cc_final: 0.7997 (p0)
REVERT: G   32 LYS cc_start: 0.8916 (ttmm) cc_final: 0.8706 (tppp)
REVERT: G   36 ASP cc_start: 0.8574 (m-30) cc_final: 0.8297 (m-30)
REVERT: A  209 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8090 (tp30)
REVERT: A  268 GLU cc_start: 0.9085 (tt0) cc_final: 0.8749 (tt0)
REVERT: A  271 ASN cc_start: 0.9025 (m-40) cc_final: 0.8657 (m110)
REVERT: A  378 ASP cc_start: 0.8564 (m-30) cc_final: 0.8255 (m-30)
REVERT: N    3 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7552 (tm-30)
REVERT: N   33 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7682 (tmtp)
REVERT: N   46 GLU cc_start: 0.8629 (tt0) cc_final: 0.8005 (tt0)
REVERT: N   73 ASP cc_start: 0.8292 (t0) cc_final: 0.8042 (t0)
REVERT: N   80 TYR cc_start: 0.8047 (m-80) cc_final: 0.7736 (m-80)
REVERT: N   82 GLN cc_start: 0.8909 (tp40) cc_final: 0.8478 (tp40)
REVERT: N  106 ASP cc_start: 0.8721 (p0) cc_final: 0.8513 (p0)
REVERT: B    9 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8977 (mm-40)
REVERT: B   31 SER cc_start: 0.9406 (t) cc_final: 0.9121 (p)
REVERT: B  105 TYR cc_start: 0.9264 (OUTLIER) cc_final: 0.8606 (m-80)
REVERT: B  172 GLU cc_start: 0.8729 (pp20) cc_final: 0.8450 (pp20)
REVERT: B  188 MET cc_start: 0.8334 (mmm) cc_final: 0.7943 (mmm)
REVERT: B  189 SER cc_start: 0.9345 (t) cc_final: 0.9068 (p)
REVERT: B  209 LYS cc_start: 0.8204 (mttm) cc_final: 0.7937 (mttm)
REVERT: B  217 MET cc_start: 0.8868 (ptm) cc_final: 0.8626 (ppp)
REVERT: B  262 MET cc_start: 0.8670 (tpp) cc_final: 0.7615 (ttm)
REVERT: B  275 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8399 (m)
REVERT: B  325 MET cc_start: 0.9086 (tpp) cc_final: 0.8679 (mmm)
REVERT: R   73 MET cc_start: 0.8584 (ptp) cc_final: 0.8345 (ttp)
REVERT: R  126 SER cc_start: 0.8656 (t) cc_final: 0.8369 (m)
REVERT: R  184 ASP cc_start: 0.9328 (t0) cc_final: 0.9038 (p0)
REVERT: R  226 LYS cc_start: 0.8120 (mttt) cc_final: 0.7805 (mmmt)
REVERT: R  238 LYS cc_start: 0.8498 (ttmt) cc_final: 0.8139 (tttm)
REVERT: R  290 ASN cc_start: 0.8211 (t0) cc_final: 0.7956 (t0)
REVERT: R  303 GLN cc_start: 0.7791 (mm110) cc_final: 0.7376 (mm-40)
REVERT: M    5 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8478 (tt0)
REVERT: M   11 LYS cc_start: 0.9269 (mppt) cc_final: 0.8865 (mmmm)
  outliers start: 20
  outliers final: 8
  residues processed: 172
  average time/residue: 0.5416
  time to fit residues: 98.9528
Evaluate side-chains
  163 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 150
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   33 LYS
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  301 HIS
Chi-restraints excluded: chain R residue  305 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 42 optimal weight:    9.9990
   chunk 73 optimal weight:    7.9990
   chunk 63 optimal weight:    0.0980
   chunk 60 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0670
   chunk 11 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0470
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 87 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.3416

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  18 GLN
N  39 GLN
B  32 GLN
R 219 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.087652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.067548 restraints weight = 18130.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 3.13
r_work: 0.2928 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.4510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8205  Z= 0.127
  Angle     :  0.645   9.940  11117  Z= 0.326
  Chirality :  0.041   0.172   1275
  Planarity :  0.004   0.037   1413
  Dihedral  :  4.317  20.919   1120
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 20.16 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.27), residues: 1014
  helix:  2.71 (0.25), residues: 403
  sheet: -0.62 (0.34), residues: 225
  loop : -0.16 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG N 105 
 TYR   0.023   0.001   TYR G  40 
 PHE   0.012   0.001   PHE A 376 
 TRP   0.015   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B  54 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.13 ( 8203)
  covalent geometry    : angle       0.64516 /  0.33 (11113)
  SS BOND              : bond        0.00227 /  0.12 (    2)
  SS BOND              : angle       0.75489 /  0.38 (    4)
  hydrogen bonds       : bond        0.03625 /  2.42 (  463)
  hydrogen bonds       : angle       4.47257 /  3.09 ( 1299)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 167
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8593 (mtm110) cc_final: 0.8232 (mtm110)
REVERT: G   14 LYS cc_start: 0.9378 (mppt) cc_final: 0.9038 (mmpt)
REVERT: G   22 GLU cc_start: 0.8517 (tt0) cc_final: 0.7930 (tm-30)
REVERT: G   29 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8658 (tppt)
REVERT: A  209 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8016 (tp30)
REVERT: A  268 GLU cc_start: 0.9045 (tt0) cc_final: 0.8710 (tt0)
REVERT: A  271 ASN cc_start: 0.9016 (m-40) cc_final: 0.8691 (m110)
REVERT: A  278 ASN cc_start: 0.8855 (m-40) cc_final: 0.8628 (m-40)
REVERT: A  378 ASP cc_start: 0.8565 (m-30) cc_final: 0.8258 (m-30)
REVERT: N    3 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7440 (mm-40)
REVERT: N    6 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6775 (mt-10)
REVERT: N   33 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7854 (tmtp)
REVERT: N   46 GLU cc_start: 0.8636 (tt0) cc_final: 0.8056 (tt0)
REVERT: N   73 ASP cc_start: 0.8247 (t0) cc_final: 0.7768 (t0)
REVERT: N   76 LYS cc_start: 0.9342 (mtpp) cc_final: 0.9120 (mtmm)
REVERT: N   80 TYR cc_start: 0.7964 (m-80) cc_final: 0.7449 (m-80)
REVERT: N   82 GLN cc_start: 0.8869 (tp40) cc_final: 0.8407 (tp40)
REVERT: N  106 ASP cc_start: 0.8707 (p0) cc_final: 0.8505 (p0)
REVERT: N  107 CYS cc_start: 0.7988 (m) cc_final: 0.7473 (m)
REVERT: B    9 GLN cc_start: 0.9285 (mm-40) cc_final: 0.9004 (mm-40)
REVERT: B   31 SER cc_start: 0.9421 (t) cc_final: 0.9139 (p)
REVERT: B  105 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.8559 (m-80)
REVERT: B  172 GLU cc_start: 0.8702 (pp20) cc_final: 0.8407 (pp20)
REVERT: B  188 MET cc_start: 0.8222 (mmm) cc_final: 0.7859 (mmm)
REVERT: B  189 SER cc_start: 0.9263 (t) cc_final: 0.9024 (p)
REVERT: B  209 LYS cc_start: 0.8106 (mttm) cc_final: 0.7877 (mttm)
REVERT: B  217 MET cc_start: 0.8911 (ptm) cc_final: 0.8696 (ppp)
REVERT: B  246 ASP cc_start: 0.8936 (m-30) cc_final: 0.8441 (m-30)
REVERT: B  262 MET cc_start: 0.8720 (tpp) cc_final: 0.7673 (ttm)
REVERT: B  275 SER cc_start: 0.8837 (OUTLIER) cc_final: 0.8369 (m)
REVERT: B  325 MET cc_start: 0.8993 (tpp) cc_final: 0.8549 (mmm)
REVERT: R   73 MET cc_start: 0.8551 (ptp) cc_final: 0.8272 (ttp)
REVERT: R  126 SER cc_start: 0.8608 (t) cc_final: 0.8302 (m)
REVERT: R  184 ASP cc_start: 0.9179 (t0) cc_final: 0.8895 (p0)
REVERT: R  226 LYS cc_start: 0.7973 (mttt) cc_final: 0.7763 (mmmt)
REVERT: R  238 LYS cc_start: 0.8515 (ttmt) cc_final: 0.8186 (tttm)
REVERT: R  290 ASN cc_start: 0.8256 (t0) cc_final: 0.8023 (t0)
REVERT: M    5 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8429 (tt0)
REVERT: M   11 LYS cc_start: 0.9284 (mppt) cc_final: 0.8895 (mmmm)
  outliers start: 16
  outliers final: 8
  residues processed: 177
  average time/residue: 0.4799
  time to fit residues: 90.6899
Evaluate side-chains
  163 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 150
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   33 LYS
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue  301 HIS
Chi-restraints excluded: chain R residue  305 LEU
Chi-restraints excluded: chain R residue  308 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 93 optimal weight:    0.0980
   chunk 56 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 40 optimal weight:    9.9990
   chunk 57 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   overall best weight:    2.2188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
N   3 GLN
N  39 GLN
B  32 GLN
** B  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.084998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.063666 restraints weight = 18323.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 3.13
r_work: 0.2836 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.4505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8205  Z= 0.220
  Angle     :  0.728  11.956  11117  Z= 0.363
  Chirality :  0.043   0.183   1275
  Planarity :  0.004   0.037   1413
  Dihedral  :  4.547  21.382   1120
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 21.43 %
    Favored  : 76.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.27), residues: 1014
  helix:  2.56 (0.25), residues: 403
  sheet: -0.70 (0.35), residues: 215
  loop : -0.20 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG N 105 
 TYR   0.022   0.002   TYR G  40 
 PHE   0.013   0.002   PHE G  61 
 TRP   0.011   0.002   TRP A 234 
 HIS   0.004   0.001   HIS R 209 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00503 /  0.22 ( 8203)
  covalent geometry    : angle       0.72835 /  0.36 (11113)
  SS BOND              : bond        0.00028 /  0.01 (    2)
  SS BOND              : angle       0.62455 /  0.32 (    4)
  hydrogen bonds       : bond        0.03924 /  2.61 (  463)
  hydrogen bonds       : angle       4.62216 /  3.21 ( 1299)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 153
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   14 LYS cc_start: 0.9405 (mppt) cc_final: 0.9091 (mmpt)
REVERT: G   22 GLU cc_start: 0.8531 (tt0) cc_final: 0.7934 (tm-30)
REVERT: A  209 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8112 (tp30)
REVERT: A  268 GLU cc_start: 0.9091 (tt0) cc_final: 0.8786 (tt0)
REVERT: A  271 ASN cc_start: 0.9046 (m-40) cc_final: 0.8702 (m110)
REVERT: A  378 ASP cc_start: 0.8541 (m-30) cc_final: 0.8221 (m-30)
REVERT: N    3 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8047 (tm-30)
REVERT: N   33 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7858 (tttp)
REVERT: N   46 GLU cc_start: 0.8636 (tt0) cc_final: 0.8037 (tt0)
REVERT: N   73 ASP cc_start: 0.8286 (t0) cc_final: 0.7686 (t0)
REVERT: N   76 LYS cc_start: 0.9377 (mtpp) cc_final: 0.9120 (mtmm)
REVERT: N   80 TYR cc_start: 0.8114 (m-80) cc_final: 0.7602 (m-80)
REVERT: N   82 GLN cc_start: 0.8865 (tp40) cc_final: 0.8397 (tp40)
REVERT: N  107 CYS cc_start: 0.7965 (m) cc_final: 0.7427 (m)
REVERT: B   31 SER cc_start: 0.9424 (t) cc_final: 0.9119 (p)
REVERT: B  105 TYR cc_start: 0.9304 (OUTLIER) cc_final: 0.8633 (m-80)
REVERT: B  172 GLU cc_start: 0.8732 (pp20) cc_final: 0.8437 (pp20)
REVERT: B  188 MET cc_start: 0.8399 (mmm) cc_final: 0.8104 (mmm)
REVERT: B  189 SER cc_start: 0.9328 (t) cc_final: 0.8997 (p)
REVERT: B  209 LYS cc_start: 0.8337 (mttm) cc_final: 0.8065 (mttm)
REVERT: B  217 MET cc_start: 0.8899 (ptm) cc_final: 0.8627 (ppp)
REVERT: B  262 MET cc_start: 0.8756 (tpp) cc_final: 0.7725 (ttm)
REVERT: B  275 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8427 (m)
REVERT: B  325 MET cc_start: 0.9149 (tpp) cc_final: 0.8783 (mmm)
REVERT: R   73 MET cc_start: 0.8460 (ptp) cc_final: 0.8221 (ttp)
REVERT: R  126 SER cc_start: 0.8667 (t) cc_final: 0.8364 (m)
REVERT: R  183 TYR cc_start: 0.9160 (p90) cc_final: 0.8914 (p90)
REVERT: R  184 ASP cc_start: 0.9311 (t0) cc_final: 0.8948 (p0)
REVERT: R  226 LYS cc_start: 0.8116 (mttt) cc_final: 0.7806 (mmmt)
REVERT: R  238 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8144 (tttm)
REVERT: R  290 ASN cc_start: 0.8253 (t0) cc_final: 0.8012 (t0)
REVERT: M    5 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8302 (tt0)
REVERT: M   11 LYS cc_start: 0.9308 (mppt) cc_final: 0.8927 (mmmm)
  outliers start: 19
  outliers final: 8
  residues processed: 164
  average time/residue: 0.4913
  time to fit residues: 85.8234
Evaluate side-chains
  157 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   33 LYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue  284 LEU
Chi-restraints excluded: chain R residue  301 HIS
Chi-restraints excluded: chain R residue  308 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 73 optimal weight:    0.1980
   chunk 61 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 24 optimal weight:    9.9990
   chunk 20 optimal weight:    0.2980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
N   3 GLN
N  39 GLN
B  32 GLN
B  36 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.087138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.066666 restraints weight = 18272.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 3.13
r_work: 0.2911 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.4683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8205  Z= 0.144
  Angle     :  0.723  11.278  11117  Z= 0.364
  Chirality :  0.042   0.193   1275
  Planarity :  0.004   0.037   1413
  Dihedral  :  4.444  24.244   1120
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 22.70 %
    Favored  : 75.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.27), residues: 1014
  helix:  2.54 (0.25), residues: 403
  sheet: -0.68 (0.35), residues: 214
  loop : -0.25 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG N 105 
 TYR   0.023   0.002   TYR G  40 
 PHE   0.012   0.001   PHE N  29 
 TRP   0.016   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B  54 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.14 ( 8203)
  covalent geometry    : angle       0.72284 /  0.36 (11113)
  SS BOND              : bond        0.00241 /  0.12 (    2)
  SS BOND              : angle       0.87663 /  0.46 (    4)
  hydrogen bonds       : bond        0.03684 /  2.46 (  463)
  hydrogen bonds       : angle       4.59821 /  3.17 ( 1299)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 155
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8570 (mtm110) cc_final: 0.8325 (mtm110)
REVERT: G   14 LYS cc_start: 0.9411 (mppt) cc_final: 0.9047 (mmpt)
REVERT: G   20 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8216 (mtmm)
REVERT: G   22 GLU cc_start: 0.8506 (tt0) cc_final: 0.7909 (tm-30)
REVERT: G   27 ARG cc_start: 0.8360 (mtt90) cc_final: 0.7729 (mtt90)
REVERT: G   29 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8650 (tppt)
REVERT: G   48 ASP cc_start: 0.8808 (t0) cc_final: 0.8542 (t0)
REVERT: A  209 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8086 (tp30)
REVERT: A  268 GLU cc_start: 0.9069 (tt0) cc_final: 0.8749 (tt0)
REVERT: A  271 ASN cc_start: 0.9031 (m-40) cc_final: 0.8735 (m-40)
REVERT: A  378 ASP cc_start: 0.8556 (m-30) cc_final: 0.8249 (m-30)
REVERT: N    3 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7879 (tm-30)
REVERT: N    5 GLN cc_start: 0.8615 (mp10) cc_final: 0.7963 (mp10)
REVERT: N   33 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7832 (tmtp)
REVERT: N   38 ARG cc_start: 0.8757 (ptm160) cc_final: 0.8553 (mtm180)
REVERT: N   46 GLU cc_start: 0.8612 (tt0) cc_final: 0.8022 (tt0)
REVERT: N   73 ASP cc_start: 0.8275 (t0) cc_final: 0.7699 (t0)
REVERT: N   76 LYS cc_start: 0.9297 (mtpp) cc_final: 0.9012 (mtmm)
REVERT: N   80 TYR cc_start: 0.8018 (m-80) cc_final: 0.7479 (m-80)
REVERT: N   82 GLN cc_start: 0.8843 (tp40) cc_final: 0.8381 (tp40)
REVERT: N  107 CYS cc_start: 0.8249 (m) cc_final: 0.7622 (m)
REVERT: N  123 GLN cc_start: 0.9012 (tp40) cc_final: 0.8682 (mm-40)
REVERT: B   31 SER cc_start: 0.9466 (t) cc_final: 0.9165 (p)
REVERT: B  105 TYR cc_start: 0.9222 (OUTLIER) cc_final: 0.8616 (m-80)
REVERT: B  172 GLU cc_start: 0.8719 (pp20) cc_final: 0.8425 (pp20)
REVERT: B  188 MET cc_start: 0.8307 (mmm) cc_final: 0.7940 (mmm)
REVERT: B  189 SER cc_start: 0.9315 (t) cc_final: 0.9051 (p)
REVERT: B  217 MET cc_start: 0.8879 (ptm) cc_final: 0.8656 (ppp)
REVERT: B  246 ASP cc_start: 0.9030 (m-30) cc_final: 0.8451 (m-30)
REVERT: B  262 MET cc_start: 0.8770 (tpp) cc_final: 0.7791 (ttm)
REVERT: B  275 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8494 (m)
REVERT: B  280 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8539 (mtpp)
REVERT: B  325 MET cc_start: 0.8941 (tpp) cc_final: 0.8474 (mmm)
REVERT: R   73 MET cc_start: 0.8454 (ptp) cc_final: 0.8175 (ttp)
REVERT: R  183 TYR cc_start: 0.9139 (p90) cc_final: 0.8883 (p90)
REVERT: R  184 ASP cc_start: 0.9248 (t0) cc_final: 0.8919 (p0)
REVERT: R  226 LYS cc_start: 0.8035 (mttt) cc_final: 0.7783 (mmmt)
REVERT: R  238 LYS cc_start: 0.8558 (ttmt) cc_final: 0.8247 (tttm)
REVERT: R  290 ASN cc_start: 0.8307 (t0) cc_final: 0.8062 (t0)
REVERT: M    5 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8309 (tt0)
REVERT: M   11 LYS cc_start: 0.9339 (mppt) cc_final: 0.8941 (mmmm)
  outliers start: 15
  outliers final: 6
  residues processed: 163
  average time/residue: 0.4839
  time to fit residues: 83.9801
Evaluate side-chains
  158 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain G residue   36 ASP
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   33 LYS
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue  301 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 10 optimal weight:    8.9990
   chunk 50 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 44 optimal weight:    0.4980
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  44 HIS
N   3 GLN
N  39 GLN
B  36 ASN
R  66 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.087199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.066698 restraints weight = 18138.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 3.11
r_work: 0.2912 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.4777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8205  Z= 0.145
  Angle     :  0.721  11.456  11117  Z= 0.359
  Chirality :  0.042   0.203   1275
  Planarity :  0.004   0.037   1413
  Dihedral  :  4.413  25.415   1120
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 22.70 %
    Favored  : 75.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.27), residues: 1014
  helix:  2.55 (0.25), residues: 403
  sheet: -0.60 (0.35), residues: 212
  loop : -0.21 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG N 105 
 TYR   0.016   0.001   TYR N  95 
 PHE   0.013   0.001   PHE N  29 
 TRP   0.014   0.002   TRP B 169 
 HIS   0.007   0.001   HIS G  44 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.15 ( 8203)
  covalent geometry    : angle       0.72047 /  0.36 (11113)
  SS BOND              : bond        0.00195 /  0.10 (    2)
  SS BOND              : angle       0.82804 /  0.42 (    4)
  hydrogen bonds       : bond        0.03661 /  2.42 (  463)
  hydrogen bonds       : angle       4.58774 /  3.16 ( 1299)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2681.33 seconds
wall clock time: 46 minutes 33.73 seconds (2793.73 seconds total)