Starting phenix.real_space_refine
on Mon Apr 28 19:32:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f4d_31448/04_2025/7f4d_31448.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f4d_31448/04_2025/7f4d_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_31448/04_2025/7f4d_31448.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f4d_31448/04_2025/7f4d_31448.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f4d_31448/04_2025/7f4d_31448.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f4d_31448/04_2025/7f4d_31448.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2}
          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: 4.74, per 1000 atoms: 0.59
  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: 1.74
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 1.03
  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: 2.52

  Time building geometry restraints manager: 2.10 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:             0.510
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.330
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (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
 TRP   0.058   0.009   TRP A 281 
 HIS   0.016   0.004   HIS R 153 
 PHE   0.030   0.005   PHE A 246 
 TYR   0.048   0.007   TYR R  74 
 ARG   0.053   0.005   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14781 (  463)
  hydrogen bonds       : angle       7.19128 ( 1299)
  SS BOND              : bond        0.00388 (    2)
  SS BOND              : angle       1.23694 (    4)
  covalent geometry    : bond        0.00936 ( 8203)
  covalent geometry    : angle       1.06561 (11113)

*********************** 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  : 0.941 
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: 1.2668
  time to fit residues: 331.0275
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  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 75 optimal weight:    0.3980
   chunk 42 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 40 optimal weight:    7.9990
   chunk 78 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 58 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
G  18 GLN
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.087224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.066530 restraints weight = 17705.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 3.17
r_work: 0.2899 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8205  Z= 0.152
  Angle     :  0.678   8.253  11117  Z= 0.355
  Chirality :  0.042   0.145   1275
  Planarity :  0.004   0.040   1413
  Dihedral  :  5.350  24.717   1120
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 11.41 %
    Favored  : 86.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.26), residues: 1014
  helix:  1.71 (0.24), residues: 403
  sheet: -0.40 (0.35), residues: 210
  loop : -0.46 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP B 339 
 HIS   0.003   0.001   HIS R 260 
 PHE   0.017   0.002   PHE G  61 
 TYR   0.018   0.002   TYR N  95 
 ARG   0.006   0.001   ARG G  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04507 (  463)
  hydrogen bonds       : angle       5.21061 ( 1299)
  SS BOND              : bond        0.00278 (    2)
  SS BOND              : angle       0.86141 (    4)
  covalent geometry    : bond        0.00334 ( 8203)
  covalent geometry    : angle       0.67776 (11113)

*********************** 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: 16
    poor density    : 184
  time to evaluate  : 1.074 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   22 GLU cc_start: 0.8478 (tt0) cc_final: 0.7979 (tm-30)
REVERT: G   36 ASP cc_start: 0.8574 (m-30) cc_final: 0.8357 (m-30)
REVERT: G   48 ASP cc_start: 0.8752 (t0) cc_final: 0.8515 (t0)
REVERT: G   58 GLU cc_start: 0.8771 (mp0) cc_final: 0.8547 (pm20)
REVERT: A   16 ASP cc_start: 0.9027 (t0) cc_final: 0.8748 (t0)
REVERT: A  221 MET cc_start: 0.9083 (ttm) cc_final: 0.8845 (ttm)
REVERT: A  268 GLU cc_start: 0.9056 (tt0) cc_final: 0.8805 (tt0)
REVERT: A  271 ASN cc_start: 0.9101 (m-40) cc_final: 0.8810 (m-40)
REVERT: A  327 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8738 (pm20)
REVERT: A  378 ASP cc_start: 0.8475 (m-30) cc_final: 0.7931 (m-30)
REVERT: N   33 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8211 (tmtp)
REVERT: N   46 GLU cc_start: 0.8325 (tt0) cc_final: 0.7634 (tt0)
REVERT: N   73 ASP cc_start: 0.8227 (t0) cc_final: 0.7767 (t0)
REVERT: N   76 LYS cc_start: 0.9304 (mtpp) cc_final: 0.9097 (mtpp)
REVERT: N   82 GLN cc_start: 0.9034 (tp40) cc_final: 0.8767 (tp40)
REVERT: N   83 MET cc_start: 0.9091 (mtm) cc_final: 0.8772 (mtp)
REVERT: N   87 LYS cc_start: 0.8483 (mttp) cc_final: 0.8250 (ptpt)
REVERT: N   90 ASP cc_start: 0.8823 (m-30) cc_final: 0.8359 (m-30)
REVERT: N  107 CYS cc_start: 0.8308 (m) cc_final: 0.7907 (m)
REVERT: N  120 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8791 (mm110)
REVERT: B   32 GLN cc_start: 0.9189 (mt0) cc_final: 0.8935 (pt0)
REVERT: B  172 GLU cc_start: 0.8473 (pp20) cc_final: 0.8165 (pp20)
REVERT: B  186 ASP cc_start: 0.7320 (t0) cc_final: 0.6664 (t0)
REVERT: B  188 MET cc_start: 0.8627 (mmm) cc_final: 0.8162 (mmm)
REVERT: B  189 SER cc_start: 0.9274 (t) cc_final: 0.9067 (p)
REVERT: B  217 MET cc_start: 0.8797 (ptm) cc_final: 0.8353 (pmm)
REVERT: B  262 MET cc_start: 0.8799 (tpp) cc_final: 0.8102 (ttm)
REVERT: B  267 ASP cc_start: 0.9059 (p0) cc_final: 0.8766 (p0)
REVERT: B  275 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8503 (m)
REVERT: B  277 SER cc_start: 0.9275 (t) cc_final: 0.8977 (t)
REVERT: R   56 ASN cc_start: 0.9009 (m-40) cc_final: 0.8809 (m110)
REVERT: R  126 SER cc_start: 0.8701 (t) cc_final: 0.8469 (m)
REVERT: R  226 LYS cc_start: 0.7971 (mttt) cc_final: 0.7710 (mmmt)
REVERT: R  238 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7988 (ttmt)
REVERT: R  290 ASN cc_start: 0.8052 (t0) cc_final: 0.7818 (t0)
REVERT: R  303 GLN cc_start: 0.8154 (mm110) cc_final: 0.7653 (mm-40)
REVERT: M   11 LYS cc_start: 0.9200 (mppt) cc_final: 0.8896 (mmmm)
  outliers start: 16
  outliers final: 3
  residues processed: 192
  average time/residue: 1.1328
  time to fit residues: 230.9258
Evaluate side-chains
  161 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 155
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 GLU
Chi-restraints excluded: chain N residue   33 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 41 optimal weight:   10.0000
   chunk 62 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 33 optimal weight:    0.4980
   chunk 95 optimal weight:   10.0000
   chunk 0 optimal weight:   20.0000
   chunk 98 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
G  18 GLN
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.087134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.066393 restraints weight = 17772.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 3.15
r_work: 0.2892 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8205  Z= 0.146
  Angle     :  0.620   7.685  11117  Z= 0.320
  Chirality :  0.041   0.153   1275
  Planarity :  0.004   0.046   1413
  Dihedral  :  4.763  25.608   1120
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 14.52 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.26), residues: 1014
  helix:  2.13 (0.24), residues: 408
  sheet: -0.46 (0.34), residues: 203
  loop : -0.44 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 169 
 HIS   0.005   0.001   HIS M   6 
 PHE   0.016   0.002   PHE G  61 
 TYR   0.016   0.002   TYR N  95 
 ARG   0.010   0.001   ARG R  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04044 (  463)
  hydrogen bonds       : angle       4.85570 ( 1299)
  SS BOND              : bond        0.00173 (    2)
  SS BOND              : angle       0.62500 (    4)
  covalent geometry    : bond        0.00325 ( 8203)
  covalent geometry    : angle       0.61965 (11113)

*********************** 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
  192 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 170
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   17 GLU cc_start: 0.9097 (pt0) cc_final: 0.8845 (tm-30)
REVERT: G   21 MET cc_start: 0.8931 (mmp) cc_final: 0.8396 (mmp)
REVERT: G   22 GLU cc_start: 0.8442 (tt0) cc_final: 0.7916 (tm-30)
REVERT: G   26 ASP cc_start: 0.9061 (t0) cc_final: 0.8810 (t0)
REVERT: G   29 LYS cc_start: 0.9129 (mmmt) cc_final: 0.8871 (mmmt)
REVERT: G   36 ASP cc_start: 0.8584 (m-30) cc_final: 0.8366 (m-30)
REVERT: G   48 ASP cc_start: 0.8678 (t0) cc_final: 0.8416 (t0)
REVERT: G   58 GLU cc_start: 0.8698 (mp0) cc_final: 0.8208 (pm20)
REVERT: A  268 GLU cc_start: 0.9094 (tt0) cc_final: 0.8811 (tt0)
REVERT: A  271 ASN cc_start: 0.9048 (m-40) cc_final: 0.8665 (m110)
REVERT: A  327 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8751 (pm20)
REVERT: A  378 ASP cc_start: 0.8533 (m-30) cc_final: 0.8139 (m-30)
REVERT: N   33 LYS cc_start: 0.8596 (tttm) cc_final: 0.8008 (tmtp)
REVERT: N   46 GLU cc_start: 0.8428 (tt0) cc_final: 0.7753 (tt0)
REVERT: N   73 ASP cc_start: 0.8172 (t0) cc_final: 0.7569 (t0)
REVERT: N   80 TYR cc_start: 0.8184 (m-80) cc_final: 0.7863 (m-80)
REVERT: N   82 GLN cc_start: 0.8968 (tp40) cc_final: 0.8697 (tp40)
REVERT: N   87 LYS cc_start: 0.8592 (mttp) cc_final: 0.8334 (ptpt)
REVERT: N   90 ASP cc_start: 0.8800 (m-30) cc_final: 0.8002 (m-30)
REVERT: N  107 CYS cc_start: 0.8238 (m) cc_final: 0.7743 (m)
REVERT: B   32 GLN cc_start: 0.9196 (mt0) cc_final: 0.8950 (pt0)
REVERT: B  105 TYR cc_start: 0.9201 (OUTLIER) cc_final: 0.8774 (m-80)
REVERT: B  172 GLU cc_start: 0.8587 (pp20) cc_final: 0.8236 (pp20)
REVERT: B  186 ASP cc_start: 0.7153 (t0) cc_final: 0.6426 (t0)
REVERT: B  188 MET cc_start: 0.8422 (mmm) cc_final: 0.7937 (mmm)
REVERT: B  189 SER cc_start: 0.9356 (t) cc_final: 0.9092 (p)
REVERT: B  217 MET cc_start: 0.8814 (ptm) cc_final: 0.8539 (ppp)
REVERT: B  262 MET cc_start: 0.8831 (tpp) cc_final: 0.7864 (ttm)
REVERT: B  275 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8380 (m)
REVERT: B  277 SER cc_start: 0.9427 (t) cc_final: 0.9192 (t)
REVERT: R  126 SER cc_start: 0.8631 (t) cc_final: 0.8388 (m)
REVERT: R  184 ASP cc_start: 0.9306 (t0) cc_final: 0.9064 (p0)
REVERT: R  226 LYS cc_start: 0.8074 (mttt) cc_final: 0.7720 (mmmt)
REVERT: R  238 LYS cc_start: 0.8263 (ttmt) cc_final: 0.7870 (ttpp)
REVERT: R  303 GLN cc_start: 0.8160 (mm110) cc_final: 0.7724 (mm-40)
REVERT: M   11 LYS cc_start: 0.9192 (mppt) cc_final: 0.8938 (mppt)
  outliers start: 22
  outliers final: 5
  residues processed: 181
  average time/residue: 1.1118
  time to fit residues: 214.2731
Evaluate side-chains
  158 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 150
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain A residue  327 GLU
Chi-restraints excluded: chain N residue   99 CYS
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 3 optimal weight:    7.9990
   chunk 68 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   chunk 77 optimal weight:    8.9990
   chunk 79 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 1 optimal weight:    9.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3435 r_free = 0.3435 target = 0.085523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.063760 restraints weight = 17882.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 3.17
r_work: 0.2827 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.3598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8205  Z= 0.213
  Angle     :  0.642   8.380  11117  Z= 0.328
  Chirality :  0.042   0.167   1275
  Planarity :  0.004   0.033   1413
  Dihedral  :  4.720  25.122   1120
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 15.78 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.27), residues: 1014
  helix:  2.27 (0.24), residues: 407
  sheet: -0.71 (0.33), residues: 217
  loop : -0.21 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 339 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.017   0.002   PHE G  61 
 TYR   0.018   0.002   TYR N  95 
 ARG   0.008   0.000   ARG R  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04060 (  463)
  hydrogen bonds       : angle       4.77443 ( 1299)
  SS BOND              : bond        0.00086 (    2)
  SS BOND              : angle       0.49207 (    4)
  covalent geometry    : bond        0.00483 ( 8203)
  covalent geometry    : angle       0.64235 (11113)

*********************** 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
  184 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 160
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   21 MET cc_start: 0.8984 (mmp) cc_final: 0.8468 (mmp)
REVERT: G   22 GLU cc_start: 0.8453 (tt0) cc_final: 0.7948 (tm-30)
REVERT: G   25 ILE cc_start: 0.8282 (pt) cc_final: 0.7998 (pt)
REVERT: G   26 ASP cc_start: 0.9120 (t0) cc_final: 0.8885 (t0)
REVERT: G   36 ASP cc_start: 0.8651 (m-30) cc_final: 0.8429 (m-30)
REVERT: G   48 ASP cc_start: 0.8699 (t0) cc_final: 0.8472 (t0)
REVERT: G   58 GLU cc_start: 0.8428 (mp0) cc_final: 0.8218 (pm20)
REVERT: A  268 GLU cc_start: 0.9090 (tt0) cc_final: 0.8816 (tt0)
REVERT: A  271 ASN cc_start: 0.9052 (m-40) cc_final: 0.8670 (m110)
REVERT: A  327 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8740 (pm20)
REVERT: A  378 ASP cc_start: 0.8539 (m-30) cc_final: 0.8210 (m-30)
REVERT: N    3 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7235 (tm130)
REVERT: N   33 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7846 (tmtp)
REVERT: N   46 GLU cc_start: 0.8501 (tt0) cc_final: 0.7788 (tt0)
REVERT: N   73 ASP cc_start: 0.8322 (t0) cc_final: 0.8058 (t0)
REVERT: N   80 TYR cc_start: 0.8093 (m-80) cc_final: 0.7742 (m-80)
REVERT: N   82 GLN cc_start: 0.8994 (tp40) cc_final: 0.8532 (tp40)
REVERT: N  107 CYS cc_start: 0.8343 (m) cc_final: 0.7942 (m)
REVERT: B   32 GLN cc_start: 0.9158 (mt0) cc_final: 0.8908 (pt0)
REVERT: B  105 TYR cc_start: 0.9288 (OUTLIER) cc_final: 0.8643 (m-80)
REVERT: B  172 GLU cc_start: 0.8690 (pp20) cc_final: 0.8310 (pp20)
REVERT: B  186 ASP cc_start: 0.7132 (t0) cc_final: 0.6863 (t0)
REVERT: B  188 MET cc_start: 0.8475 (mmm) cc_final: 0.8090 (mmm)
REVERT: B  189 SER cc_start: 0.9269 (t) cc_final: 0.8961 (p)
REVERT: B  217 MET cc_start: 0.8867 (ptm) cc_final: 0.8541 (ppp)
REVERT: B  262 MET cc_start: 0.8926 (tpp) cc_final: 0.8027 (ttm)
REVERT: B  275 SER cc_start: 0.8820 (OUTLIER) cc_final: 0.8374 (m)
REVERT: R  126 SER cc_start: 0.8675 (t) cc_final: 0.8398 (m)
REVERT: R  184 ASP cc_start: 0.9265 (t0) cc_final: 0.8999 (p0)
REVERT: R  226 LYS cc_start: 0.8165 (mttt) cc_final: 0.7785 (mmmt)
REVERT: R  238 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8131 (ttpp)
REVERT: R  303 GLN cc_start: 0.7949 (mm110) cc_final: 0.7558 (mm-40)
REVERT: M    5 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8231 (tt0)
REVERT: M   11 LYS cc_start: 0.9202 (mppt) cc_final: 0.8883 (mppt)
  outliers start: 24
  outliers final: 9
  residues processed: 172
  average time/residue: 1.1514
  time to fit residues: 210.3810
Evaluate side-chains
  163 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain A residue  264 ASN
Chi-restraints excluded: chain A residue  327 GLU
Chi-restraints excluded: chain N residue    3 GLN
Chi-restraints excluded: chain N residue   33 LYS
Chi-restraints excluded: chain N residue   65 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
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 58 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 40 optimal weight:   20.0000
   chunk 34 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 97 optimal weight:    7.9990
   chunk 4 optimal weight:    7.9990
   chunk 22 optimal weight:   10.0000
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3471 r_free = 0.3471 target = 0.087577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.066405 restraints weight = 17588.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 3.13
r_work: 0.2888 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.3868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8205  Z= 0.136
  Angle     :  0.605   9.299  11117  Z= 0.309
  Chirality :  0.041   0.149   1275
  Planarity :  0.004   0.034   1413
  Dihedral  :  4.513  24.236   1120
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.82 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.27), residues: 1014
  helix:  2.57 (0.24), residues: 401
  sheet: -0.71 (0.34), residues: 211
  loop : -0.17 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.012   0.001   PHE G  61 
 TYR   0.017   0.001   TYR N  95 
 ARG   0.006   0.000   ARG G  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03722 (  463)
  hydrogen bonds       : angle       4.66507 ( 1299)
  SS BOND              : bond        0.00201 (    2)
  SS BOND              : angle       0.81241 (    4)
  covalent geometry    : bond        0.00306 ( 8203)
  covalent geometry    : angle       0.60469 (11113)

*********************** 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
  191 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8590 (mtm110) cc_final: 0.8300 (mtm110)
REVERT: G   22 GLU cc_start: 0.8467 (tt0) cc_final: 0.7961 (tm-30)
REVERT: G   26 ASP cc_start: 0.9146 (t0) cc_final: 0.8940 (t0)
REVERT: G   29 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8732 (mmtt)
REVERT: G   32 LYS cc_start: 0.8960 (ttmm) cc_final: 0.8666 (tppp)
REVERT: G   36 ASP cc_start: 0.8634 (m-30) cc_final: 0.8301 (m-30)
REVERT: A  268 GLU cc_start: 0.9057 (tt0) cc_final: 0.8708 (tt0)
REVERT: A  271 ASN cc_start: 0.9029 (m-40) cc_final: 0.8645 (m110)
REVERT: A  292 ASN cc_start: 0.9035 (t0) cc_final: 0.8827 (t0)
REVERT: A  378 ASP cc_start: 0.8536 (m-30) cc_final: 0.8219 (m-30)
REVERT: N    3 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7298 (tm130)
REVERT: N   33 LYS cc_start: 0.8364 (tttm) cc_final: 0.8001 (tttm)
REVERT: N   46 GLU cc_start: 0.8517 (tt0) cc_final: 0.7962 (tt0)
REVERT: N   73 ASP cc_start: 0.8293 (t0) cc_final: 0.8004 (t0)
REVERT: N   80 TYR cc_start: 0.8090 (m-80) cc_final: 0.7720 (m-80)
REVERT: N   82 GLN cc_start: 0.8981 (tp40) cc_final: 0.8586 (tp40)
REVERT: N   87 LYS cc_start: 0.8555 (mttp) cc_final: 0.8341 (mttp)
REVERT: N  107 CYS cc_start: 0.8292 (m) cc_final: 0.7736 (m)
REVERT: B  105 TYR cc_start: 0.9219 (OUTLIER) cc_final: 0.8587 (m-80)
REVERT: B  172 GLU cc_start: 0.8692 (pp20) cc_final: 0.8375 (pp20)
REVERT: B  186 ASP cc_start: 0.7172 (t0) cc_final: 0.6372 (t0)
REVERT: B  188 MET cc_start: 0.8423 (mmm) cc_final: 0.7916 (mmm)
REVERT: B  189 SER cc_start: 0.9335 (t) cc_final: 0.9045 (p)
REVERT: B  209 LYS cc_start: 0.8143 (mttm) cc_final: 0.7879 (mttm)
REVERT: B  217 MET cc_start: 0.8868 (ptm) cc_final: 0.8599 (ppp)
REVERT: B  275 SER cc_start: 0.8796 (OUTLIER) cc_final: 0.8329 (m)
REVERT: B  325 MET cc_start: 0.9092 (tpp) cc_final: 0.8678 (mmm)
REVERT: R  126 SER cc_start: 0.8598 (t) cc_final: 0.8321 (m)
REVERT: R  184 ASP cc_start: 0.9275 (t0) cc_final: 0.9044 (p0)
REVERT: R  226 LYS cc_start: 0.8155 (mttt) cc_final: 0.7768 (mmmt)
REVERT: R  238 LYS cc_start: 0.8361 (ttmt) cc_final: 0.8084 (tttm)
REVERT: R  303 GLN cc_start: 0.7771 (mm110) cc_final: 0.7363 (mm-40)
REVERT: M    5 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8613 (tt0)
REVERT: M   11 LYS cc_start: 0.9238 (mppt) cc_final: 0.8819 (mmmm)
  outliers start: 25
  outliers final: 9
  residues processed: 182
  average time/residue: 1.0037
  time to fit residues: 195.2267
Evaluate side-chains
  164 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue    3 GLN
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  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue  188 VAL
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3422 r_free = 0.3422 target = 0.084889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.064311 restraints weight = 17992.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 3.10
r_work: 0.2852 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.4059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8205  Z= 0.169
  Angle     :  0.648   8.878  11117  Z= 0.327
  Chirality :  0.042   0.170   1275
  Planarity :  0.004   0.034   1413
  Dihedral  :  4.482  24.290   1120
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 17.97 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.27), residues: 1014
  helix:  2.62 (0.24), residues: 402
  sheet: -0.76 (0.34), residues: 215
  loop : -0.06 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 339 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.012   0.002   PHE N  29 
 TYR   0.028   0.002   TYR R 183 
 ARG   0.007   0.000   ARG N 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03794 (  463)
  hydrogen bonds       : angle       4.65680 ( 1299)
  SS BOND              : bond        0.00123 (    2)
  SS BOND              : angle       0.66725 (    4)
  covalent geometry    : bond        0.00387 ( 8203)
  covalent geometry    : angle       0.64803 (11113)

*********************** 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
  187 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 159
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
REVERT: G   22 GLU cc_start: 0.8486 (tt0) cc_final: 0.7960 (tm-30)
REVERT: G   29 LYS cc_start: 0.9061 (mmtt) cc_final: 0.8817 (mmtt)
REVERT: G   32 LYS cc_start: 0.8985 (ttmm) cc_final: 0.8708 (tppp)
REVERT: G   36 ASP cc_start: 0.8681 (m-30) cc_final: 0.8362 (m-30)
REVERT: A  268 GLU cc_start: 0.9096 (tt0) cc_final: 0.8789 (tt0)
REVERT: A  271 ASN cc_start: 0.9083 (m-40) cc_final: 0.8711 (m110)
REVERT: A  292 ASN cc_start: 0.9117 (t0) cc_final: 0.8916 (t0)
REVERT: A  378 ASP cc_start: 0.8559 (m-30) cc_final: 0.8246 (m-30)
REVERT: N   33 LYS cc_start: 0.8445 (tttm) cc_final: 0.7656 (tmtp)
REVERT: N   46 GLU cc_start: 0.8612 (tt0) cc_final: 0.8140 (tt0)
REVERT: N   73 ASP cc_start: 0.8344 (t0) cc_final: 0.7936 (t0)
REVERT: N   80 TYR cc_start: 0.8129 (m-80) cc_final: 0.7788 (m-80)
REVERT: N   82 GLN cc_start: 0.9046 (tp40) cc_final: 0.8613 (tp40)
REVERT: B    9 GLN cc_start: 0.9232 (mm-40) cc_final: 0.9000 (mm-40)
REVERT: B  105 TYR cc_start: 0.9267 (OUTLIER) cc_final: 0.8633 (m-80)
REVERT: B  172 GLU cc_start: 0.8704 (pp20) cc_final: 0.8415 (pp20)
REVERT: B  186 ASP cc_start: 0.7268 (t0) cc_final: 0.7006 (t0)
REVERT: B  188 MET cc_start: 0.8435 (mmm) cc_final: 0.8066 (mmm)
REVERT: B  189 SER cc_start: 0.9347 (t) cc_final: 0.9078 (p)
REVERT: B  209 LYS cc_start: 0.8383 (mttm) cc_final: 0.8111 (mttm)
REVERT: B  217 MET cc_start: 0.8906 (ptm) cc_final: 0.8669 (ppp)
REVERT: B  262 MET cc_start: 0.8702 (tpp) cc_final: 0.8000 (ttm)
REVERT: B  275 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8543 (m)
REVERT: B  325 MET cc_start: 0.9130 (tpp) cc_final: 0.8720 (mmm)
REVERT: R  126 SER cc_start: 0.8728 (t) cc_final: 0.8448 (m)
REVERT: R  184 ASP cc_start: 0.9228 (t0) cc_final: 0.9010 (p0)
REVERT: R  226 LYS cc_start: 0.8206 (mttt) cc_final: 0.7832 (mmmt)
REVERT: R  238 LYS cc_start: 0.8572 (ttmt) cc_final: 0.8206 (tttm)
REVERT: R  303 GLN cc_start: 0.7794 (mm110) cc_final: 0.7439 (mm-40)
REVERT: M    5 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8687 (tt0)
REVERT: M   11 LYS cc_start: 0.9286 (mppt) cc_final: 0.8882 (mmmm)
  outliers start: 28
  outliers final: 10
  residues processed: 177
  average time/residue: 1.0832
  time to fit residues: 204.5745
Evaluate side-chains
  164 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain A residue  264 ASN
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  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
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  305 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:   10.0000
   chunk 24 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
N   3 GLN
N  39 GLN
B  36 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.086172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.064820 restraints weight = 17866.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 3.15
r_work: 0.2843 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.4220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8205  Z= 0.186
  Angle     :  0.678   9.674  11117  Z= 0.340
  Chirality :  0.042   0.165   1275
  Planarity :  0.004   0.037   1413
  Dihedral  :  4.548  22.544   1120
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 19.47 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.27), residues: 1014
  helix:  2.49 (0.24), residues: 403
  sheet: -0.75 (0.34), residues: 215
  loop : -0.07 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 339 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.013   0.002   PHE G  61 
 TYR   0.022   0.002   TYR G  40 
 ARG   0.008   0.000   ARG G  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03906 (  463)
  hydrogen bonds       : angle       4.70486 ( 1299)
  SS BOND              : bond        0.00096 (    2)
  SS BOND              : angle       0.64080 (    4)
  covalent geometry    : bond        0.00426 ( 8203)
  covalent geometry    : angle       0.67758 (11113)

*********************** 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
  185 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 161
  time to evaluate  : 0.920 
Fit side-chains
REVERT: G   13 ARG cc_start: 0.8621 (mtm110) cc_final: 0.8388 (mtm110)
REVERT: G   17 GLU cc_start: 0.9131 (tp30) cc_final: 0.8886 (tp30)
REVERT: G   20 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8224 (mtmm)
REVERT: G   22 GLU cc_start: 0.8466 (tt0) cc_final: 0.7979 (tm-30)
REVERT: G   29 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8779 (mmtt)
REVERT: G   32 LYS cc_start: 0.8955 (ttmm) cc_final: 0.8709 (tppp)
REVERT: G   36 ASP cc_start: 0.8665 (m-30) cc_final: 0.8335 (m-30)
REVERT: A  268 GLU cc_start: 0.9106 (tt0) cc_final: 0.8799 (tt0)
REVERT: A  271 ASN cc_start: 0.9085 (m-40) cc_final: 0.8711 (m110)
REVERT: A  378 ASP cc_start: 0.8530 (m-30) cc_final: 0.8207 (m-30)
REVERT: N    3 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7211 (tm130)
REVERT: N    7 SER cc_start: 0.8941 (m) cc_final: 0.8730 (p)
REVERT: N   33 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7505 (tmtp)
REVERT: N   46 GLU cc_start: 0.8557 (tt0) cc_final: 0.8148 (tt0)
REVERT: N   73 ASP cc_start: 0.8168 (t0) cc_final: 0.7613 (t0)
REVERT: N   80 TYR cc_start: 0.8000 (m-80) cc_final: 0.7736 (m-80)
REVERT: N   82 GLN cc_start: 0.8948 (tp40) cc_final: 0.8504 (tp40)
REVERT: B   30 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8378 (tp)
REVERT: B   31 SER cc_start: 0.9421 (t) cc_final: 0.9147 (p)
REVERT: B  105 TYR cc_start: 0.9288 (OUTLIER) cc_final: 0.8536 (m-80)
REVERT: B  172 GLU cc_start: 0.8733 (pp20) cc_final: 0.8458 (pp20)
REVERT: B  186 ASP cc_start: 0.7163 (t0) cc_final: 0.6907 (t0)
REVERT: B  188 MET cc_start: 0.8449 (mmm) cc_final: 0.8128 (mmm)
REVERT: B  189 SER cc_start: 0.9269 (t) cc_final: 0.8962 (p)
REVERT: B  209 LYS cc_start: 0.8261 (mttm) cc_final: 0.7997 (mttm)
REVERT: B  217 MET cc_start: 0.8944 (ptm) cc_final: 0.8659 (ppp)
REVERT: B  262 MET cc_start: 0.8721 (tpp) cc_final: 0.7915 (ttm)
REVERT: B  275 SER cc_start: 0.8844 (OUTLIER) cc_final: 0.8398 (m)
REVERT: B  325 MET cc_start: 0.9114 (tpp) cc_final: 0.8732 (mmm)
REVERT: R  126 SER cc_start: 0.8669 (t) cc_final: 0.8373 (m)
REVERT: R  184 ASP cc_start: 0.9297 (t0) cc_final: 0.8936 (p0)
REVERT: R  226 LYS cc_start: 0.8113 (mttt) cc_final: 0.7794 (mmmt)
REVERT: R  238 LYS cc_start: 0.8516 (ttmt) cc_final: 0.8145 (tttm)
REVERT: M    5 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8433 (tt0)
REVERT: M   11 LYS cc_start: 0.9252 (mppt) cc_final: 0.8843 (mmmm)
  outliers start: 24
  outliers final: 12
  residues processed: 174
  average time/residue: 1.1684
  time to fit residues: 216.0218
Evaluate side-chains
  168 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 151
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   16 VAL
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   30 LEU
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
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  305 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 74 optimal weight:   10.0000
   chunk 80 optimal weight:    2.9990
   chunk 4 optimal weight:    0.2980
   chunk 89 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 2 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 95 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 49 optimal weight:    6.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
N   3 GLN
N  39 GLN
B  36 ASN
B 266 HIS
** R  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.085415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.065054 restraints weight = 18083.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 3.10
r_work: 0.2869 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.4362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8205  Z= 0.156
  Angle     :  0.683  10.246  11117  Z= 0.345
  Chirality :  0.042   0.200   1275
  Planarity :  0.004   0.035   1413
  Dihedral  :  4.477  21.852   1120
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 19.70 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.27), residues: 1014
  helix:  2.48 (0.25), residues: 403
  sheet: -0.69 (0.34), residues: 228
  loop :  0.03 (0.34), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.012   0.001   PHE N  29 
 TYR   0.023   0.002   TYR G  40 
 ARG   0.008   0.000   ARG N 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03795 (  463)
  hydrogen bonds       : angle       4.68227 ( 1299)
  SS BOND              : bond        0.00140 (    2)
  SS BOND              : angle       0.70867 (    4)
  covalent geometry    : bond        0.00359 ( 8203)
  covalent geometry    : angle       0.68323 (11113)

*********************** 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
  185 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 161
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8589 (mtm110) cc_final: 0.8364 (mtm110)
REVERT: G   22 GLU cc_start: 0.8492 (tt0) cc_final: 0.7936 (tm-30)
REVERT: G   29 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8851 (mmtt)
REVERT: G   36 ASP cc_start: 0.8694 (m-30) cc_final: 0.8415 (t0)
REVERT: A  268 GLU cc_start: 0.9090 (tt0) cc_final: 0.8776 (tt0)
REVERT: A  271 ASN cc_start: 0.9076 (m-40) cc_final: 0.8716 (m110)
REVERT: A  292 ASN cc_start: 0.9087 (t0) cc_final: 0.8827 (t0)
REVERT: A  378 ASP cc_start: 0.8535 (m-30) cc_final: 0.8238 (m-30)
REVERT: N    3 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7313 (tm130)
REVERT: N    7 SER cc_start: 0.8928 (m) cc_final: 0.8704 (p)
REVERT: N   33 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7668 (tmtp)
REVERT: N   46 GLU cc_start: 0.8662 (tt0) cc_final: 0.8059 (tt0)
REVERT: N   73 ASP cc_start: 0.8179 (t0) cc_final: 0.7793 (t0)
REVERT: N   80 TYR cc_start: 0.7944 (m-80) cc_final: 0.7621 (m-80)
REVERT: N   82 GLN cc_start: 0.8955 (tp40) cc_final: 0.8478 (tp40)
REVERT: N  107 CYS cc_start: 0.8286 (m) cc_final: 0.7743 (m)
REVERT: B   31 SER cc_start: 0.9389 (t) cc_final: 0.9120 (p)
REVERT: B  105 TYR cc_start: 0.9269 (OUTLIER) cc_final: 0.8635 (m-80)
REVERT: B  172 GLU cc_start: 0.8710 (pp20) cc_final: 0.8424 (pp20)
REVERT: B  186 ASP cc_start: 0.7305 (t0) cc_final: 0.7048 (t0)
REVERT: B  188 MET cc_start: 0.8393 (mmm) cc_final: 0.8095 (mmm)
REVERT: B  189 SER cc_start: 0.9278 (t) cc_final: 0.9007 (p)
REVERT: B  209 LYS cc_start: 0.8331 (mttm) cc_final: 0.8078 (mttm)
REVERT: B  217 MET cc_start: 0.8915 (ptm) cc_final: 0.8691 (ppp)
REVERT: B  225 HIS cc_start: 0.8353 (OUTLIER) cc_final: 0.7116 (t-90)
REVERT: B  262 MET cc_start: 0.8697 (tpp) cc_final: 0.8009 (ttm)
REVERT: B  275 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8522 (m)
REVERT: B  325 MET cc_start: 0.9099 (tpp) cc_final: 0.8664 (mmm)
REVERT: R  184 ASP cc_start: 0.9169 (t0) cc_final: 0.8865 (p0)
REVERT: R  226 LYS cc_start: 0.8137 (mttt) cc_final: 0.7840 (mmmt)
REVERT: R  238 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8230 (tttm)
REVERT: M    5 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8371 (tt0)
REVERT: M   11 LYS cc_start: 0.9311 (mppt) cc_final: 0.8913 (mmmm)
  outliers start: 24
  outliers final: 13
  residues processed: 175
  average time/residue: 1.0606
  time to fit residues: 197.8410
Evaluate side-chains
  168 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 149
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain G residue   16 VAL
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   43 ILE
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain R residue  238 LYS
Chi-restraints excluded: chain R residue  301 HIS
Chi-restraints excluded: chain R residue  305 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 50 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 86 optimal weight:    6.9990
   chunk 66 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 76 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
N   3 GLN
N  39 GLN
** R  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 219 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.085950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.065225 restraints weight = 18506.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 3.17
r_work: 0.2873 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.4544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8205  Z= 0.150
  Angle     :  0.701  10.967  11117  Z= 0.348
  Chirality :  0.042   0.267   1275
  Planarity :  0.004   0.038   1413
  Dihedral  :  4.436  21.309   1120
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 21.20 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.27), residues: 1014
  helix:  2.51 (0.25), residues: 403
  sheet: -0.61 (0.33), residues: 242
  loop :  0.03 (0.34), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.012   0.001   PHE N  29 
 TYR   0.023   0.001   TYR G  40 
 ARG   0.009   0.000   ARG N 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03748 (  463)
  hydrogen bonds       : angle       4.63960 ( 1299)
  SS BOND              : bond        0.00182 (    2)
  SS BOND              : angle       0.78354 (    4)
  covalent geometry    : bond        0.00348 ( 8203)
  covalent geometry    : angle       0.70115 (11113)

*********************** 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
  173 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
REVERT: G   13 ARG cc_start: 0.8588 (mtm110) cc_final: 0.8332 (mtm110)
REVERT: G   17 GLU cc_start: 0.9136 (tp30) cc_final: 0.8865 (tp30)
REVERT: G   20 LYS cc_start: 0.8823 (mtmt) cc_final: 0.8150 (mtmm)
REVERT: G   22 GLU cc_start: 0.8517 (tt0) cc_final: 0.8112 (tm-30)
REVERT: G   29 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8800 (mmtt)
REVERT: A  268 GLU cc_start: 0.9068 (tt0) cc_final: 0.8746 (tt0)
REVERT: A  271 ASN cc_start: 0.9076 (m-40) cc_final: 0.8741 (m110)
REVERT: A  292 ASN cc_start: 0.9058 (t0) cc_final: 0.8804 (t0)
REVERT: A  378 ASP cc_start: 0.8539 (m-30) cc_final: 0.8237 (m-30)
REVERT: N    3 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7340 (tm130)
REVERT: N    7 SER cc_start: 0.8823 (m) cc_final: 0.8608 (p)
REVERT: N   33 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7661 (tmtp)
REVERT: N   46 GLU cc_start: 0.8648 (tt0) cc_final: 0.8056 (tt0)
REVERT: N   73 ASP cc_start: 0.8181 (t0) cc_final: 0.7842 (t0)
REVERT: N   80 TYR cc_start: 0.7894 (m-80) cc_final: 0.7652 (m-80)
REVERT: N   82 GLN cc_start: 0.8951 (tp40) cc_final: 0.8434 (tp40)
REVERT: N   87 LYS cc_start: 0.8846 (ptpt) cc_final: 0.8582 (ptpp)
REVERT: B   31 SER cc_start: 0.9395 (t) cc_final: 0.9128 (p)
REVERT: B  105 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.8628 (m-80)
REVERT: B  172 GLU cc_start: 0.8721 (pp20) cc_final: 0.8433 (pp20)
REVERT: B  186 ASP cc_start: 0.7316 (t0) cc_final: 0.6846 (t0)
REVERT: B  188 MET cc_start: 0.8374 (mmm) cc_final: 0.8063 (mmm)
REVERT: B  189 SER cc_start: 0.9276 (t) cc_final: 0.9013 (p)
REVERT: B  217 MET cc_start: 0.8879 (ptm) cc_final: 0.8667 (ppp)
REVERT: B  225 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.7115 (t-90)
REVERT: B  246 ASP cc_start: 0.9087 (m-30) cc_final: 0.8572 (m-30)
REVERT: B  262 MET cc_start: 0.8681 (tpp) cc_final: 0.8002 (ttm)
REVERT: B  275 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8502 (m)
REVERT: B  325 MET cc_start: 0.9079 (tpp) cc_final: 0.8646 (mmm)
REVERT: R  183 TYR cc_start: 0.9188 (p90) cc_final: 0.8937 (p90)
REVERT: R  184 ASP cc_start: 0.9250 (t0) cc_final: 0.8924 (p0)
REVERT: R  226 LYS cc_start: 0.8103 (mttt) cc_final: 0.7814 (mmmt)
REVERT: R  238 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8247 (tttm)
REVERT: M    5 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8299 (tt0)
REVERT: M   11 LYS cc_start: 0.9299 (mppt) cc_final: 0.8905 (mmmm)
  outliers start: 20
  outliers final: 11
  residues processed: 164
  average time/residue: 1.2178
  time to fit residues: 212.5800
Evaluate side-chains
  164 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain N residue    3 GLN
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  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0010
   chunk 82 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   chunk 98 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   overall best weight:    1.5992

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

Flipped N/Q/H residues before XYZ refinement:
N   3 GLN
N  39 GLN
** R  56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.085763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.064688 restraints weight = 18163.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 3.15
r_work: 0.2856 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.4542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8205  Z= 0.182
  Angle     :  0.726  12.141  11117  Z= 0.364
  Chirality :  0.042   0.188   1275
  Planarity :  0.004   0.039   1413
  Dihedral  :  4.493  20.969   1120
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 21.66 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.27), residues: 1014
  helix:  2.46 (0.25), residues: 403
  sheet: -0.70 (0.34), residues: 229
  loop : -0.07 (0.33), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 339 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.012   0.002   PHE N  29 
 TYR   0.023   0.002   TYR G  40 
 ARG   0.009   0.000   ARG N 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03833 (  463)
  hydrogen bonds       : angle       4.67848 ( 1299)
  SS BOND              : bond        0.00088 (    2)
  SS BOND              : angle       0.71129 (    4)
  covalent geometry    : bond        0.00421 ( 8203)
  covalent geometry    : angle       0.72602 (11113)

********************** 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
  168 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 149
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   22 GLU cc_start: 0.8450 (tt0) cc_final: 0.8185 (tm-30)
REVERT: G   27 ARG cc_start: 0.8289 (mtt90) cc_final: 0.6757 (mtt90)
REVERT: G   29 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8811 (tppt)
REVERT: G   32 LYS cc_start: 0.9373 (tppp) cc_final: 0.8699 (tptp)
REVERT: A  268 GLU cc_start: 0.9083 (tt0) cc_final: 0.8787 (tt0)
REVERT: A  271 ASN cc_start: 0.9032 (m-40) cc_final: 0.8681 (m110)
REVERT: A  292 ASN cc_start: 0.9078 (t0) cc_final: 0.8813 (t0)
REVERT: A  378 ASP cc_start: 0.8554 (m-30) cc_final: 0.8253 (m-30)
REVERT: N    3 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7345 (tm130)
REVERT: N    7 SER cc_start: 0.8914 (m) cc_final: 0.8658 (p)
REVERT: N   33 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7554 (tmtp)
REVERT: N   46 GLU cc_start: 0.8516 (tt0) cc_final: 0.8033 (tt0)
REVERT: N   73 ASP cc_start: 0.8141 (t0) cc_final: 0.7777 (t0)
REVERT: N   80 TYR cc_start: 0.7894 (m-80) cc_final: 0.7690 (m-80)
REVERT: N   82 GLN cc_start: 0.8927 (tp40) cc_final: 0.8425 (tp40)
REVERT: N  107 CYS cc_start: 0.8279 (m) cc_final: 0.7693 (m)
REVERT: N  123 GLN cc_start: 0.8952 (tp40) cc_final: 0.8593 (mm-40)
REVERT: B   31 SER cc_start: 0.9382 (t) cc_final: 0.9119 (p)
REVERT: B  105 TYR cc_start: 0.9280 (OUTLIER) cc_final: 0.8647 (m-80)
REVERT: B  172 GLU cc_start: 0.8748 (pp20) cc_final: 0.8472 (pp20)
REVERT: B  186 ASP cc_start: 0.7191 (t0) cc_final: 0.6706 (t0)
REVERT: B  188 MET cc_start: 0.8395 (mmm) cc_final: 0.8080 (mmm)
REVERT: B  189 SER cc_start: 0.9263 (t) cc_final: 0.8948 (p)
REVERT: B  217 MET cc_start: 0.8856 (ptm) cc_final: 0.8519 (ppp)
REVERT: B  262 MET cc_start: 0.8638 (tpp) cc_final: 0.8014 (ttm)
REVERT: B  275 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8477 (m)
REVERT: B  325 MET cc_start: 0.9043 (tpp) cc_final: 0.8638 (mmm)
REVERT: R   73 MET cc_start: 0.8370 (ttp) cc_final: 0.8128 (tmm)
REVERT: R  183 TYR cc_start: 0.9170 (p90) cc_final: 0.8904 (p90)
REVERT: R  184 ASP cc_start: 0.9286 (t0) cc_final: 0.8924 (p0)
REVERT: R  226 LYS cc_start: 0.8092 (mttt) cc_final: 0.7796 (mmmt)
REVERT: R  238 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8250 (tttm)
REVERT: M    5 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8325 (tt0)
REVERT: M   11 LYS cc_start: 0.9302 (mppt) cc_final: 0.8917 (mmmm)
  outliers start: 19
  outliers final: 14
  residues processed: 159
  average time/residue: 1.1094
  time to fit residues: 187.7808
Evaluate side-chains
  164 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue    9 ILE
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain G residue   36 ASP
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  225 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0470
   chunk 99 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    1.6086

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

Flipped N/Q/H residues before XYZ refinement:
N   3 GLN
N  39 GLN
B  36 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.085774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.065075 restraints weight = 18188.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 3.09
r_work: 0.2858 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.4601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8205  Z= 0.184
  Angle     :  0.740  12.347  11117  Z= 0.368
  Chirality :  0.043   0.195   1275
  Planarity :  0.004   0.036   1413
  Dihedral  :  4.533  22.722   1120
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 22.24 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.27), residues: 1014
  helix:  2.41 (0.25), residues: 403
  sheet: -0.71 (0.34), residues: 228
  loop : -0.09 (0.33), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 339 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.013   0.001   PHE N  29 
 TYR   0.023   0.002   TYR G  40 
 ARG   0.011   0.000   ARG G  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03850 (  463)
  hydrogen bonds       : angle       4.70824 ( 1299)
  SS BOND              : bond        0.00131 (    2)
  SS BOND              : angle       0.69243 (    4)
  covalent geometry    : bond        0.00427 ( 8203)
  covalent geometry    : angle       0.73977 (11113)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5866.51 seconds
wall clock time: 101 minutes 22.78 seconds (6082.78 seconds total)