Starting phenix.real_space_refine
on Wed Sep 17 10:23:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zsj_60417/09_2025/8zsj_60417.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zsj_60417/09_2025/8zsj_60417.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zsj_60417/09_2025/8zsj_60417.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zsj_60417/09_2025/8zsj_60417.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zsj_60417/09_2025/8zsj_60417.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zsj_60417/09_2025/8zsj_60417.map"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    5166      2.51       5
     N    1390      2.21       5
     O    1502      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8118
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1889
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "B"
      Number of atoms: 2594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2594
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "R"
      Number of atoms: 2200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2200
          Classifications: {'peptide': 282}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 11, 'TRANS': 270}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 91
          Unresolved non-hydrogen angles: 107
          Unresolved non-hydrogen dihedrals: 80
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 46
    Chain: "R"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 32
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1, 'water': 4}
          Link IDs: {None: 4}
  Time building chain proxies: 1.93, per 1000 atoms: 0.24
  Number of scatterers: 8118
  At special positions: 0
  Unit cell: (80.704, 99.008, 133.952, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    1502      8.00
     N    1390      7.00
     C    5166      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 182 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 424.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1948

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      43.0% alpha, 20.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 38
      removed outlier: 3.557A  pdb=" N   GLU A  34 " --> pdb=" O   ARG A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 56
    Processing helix  chain 'A' and resid 95 through 101
      removed outlier: 3.680A  pdb=" N   ASN A 101 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 131
    Processing helix  chain 'A' and resid 145 through 156
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.245A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 183 through 204
      removed outlier: 3.756A  pdb=" N   ILE A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   SER A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 243
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.658A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 23 through 52
      removed outlier: 3.667A  pdb=" N   SER R  28 " --> pdb=" O   ALA R  24 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   LEU R  29 " --> pdb=" O   SER R  25 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   LYS R  52 " --> pdb=" O   ILE R  48 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 56 through 86
      Proline residue:  R  78  - end of helix
    Processing helix  chain 'R' and resid 92 through 127
    Processing helix  chain 'R' and resid 130 through 135
    Processing helix  chain 'R' and resid 136 through 161
      Proline residue:  R 151  - end of helix
    Processing helix  chain 'R' and resid 169 through 179
      removed outlier: 3.777A  pdb=" N   TYR R 173 " --> pdb=" O   GLU R 169 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 187 through 199
    Processing helix  chain 'R' and resid 199 through 230
      removed outlier: 3.549A  pdb=" N   ILE R 205 " --> pdb=" O   ILE R 201 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 247 through 274
      removed outlier: 3.631A  pdb=" N   LYS R 251 " --> pdb=" O   ARG R 247 " (cutoff:3.500A)
      Proline residue:  R 266  - end of helix
    Processing helix  chain 'R' and resid 282 through 305
      removed outlier: 3.522A  pdb=" N   ASN R 286 " --> pdb=" O   PRO R 282 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   TRP R 291 " --> pdb=" O   ASP R 287 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   SER R 297 " --> pdb=" O   GLY R 293 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 308 through 318
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 75
      removed outlier: 6.446A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A  82 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   PHE A  84 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 7.765A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.844A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 9.644A  pdb=" N   ALA A 105 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   ILE A 107 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 8.611A  pdb=" N   ASP A 111 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.520A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.513A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.873A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.416A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.514A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.697A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.156A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.578A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.808A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.401A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.976A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    424 hydrogen bonds defined for protein.
    1218 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.34

  Time building geometry restraints manager: 1.06 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1314
        1.31 -     1.43: 2289
        1.43 -     1.56: 4604
        1.56 -     1.69: 0
        1.69 -     1.81: 87
  Bond restraints: 8294
  Sorted by residual:
  bond pdb=" C   CYS B 294 "
       pdb=" O   CYS B 294 "
    ideal  model  delta    sigma   weight residual
    1.235  1.179  0.056 1.28e-02 6.10e+03 1.94e+01
  bond pdb=" CA  LEU B 308 "
       pdb=" C   LEU B 308 "
    ideal  model  delta    sigma   weight residual
    1.528  1.485  0.043 1.04e-02 9.25e+03 1.72e+01
  bond pdb=" C   LEU B 210 "
       pdb=" O   LEU B 210 "
    ideal  model  delta    sigma   weight residual
    1.236  1.188  0.048 1.22e-02 6.72e+03 1.52e+01
  bond pdb=" CA  LEU B 210 "
       pdb=" C   LEU B 210 "
    ideal  model  delta    sigma   weight residual
    1.524  1.480  0.044 1.23e-02 6.61e+03 1.29e+01
  bond pdb=" CA  GLU A  92 "
       pdb=" CB  GLU A  92 "
    ideal  model  delta    sigma   weight residual
    1.528  1.482  0.046 1.35e-02 5.49e+03 1.16e+01
  ... (remaining 8289 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 10983
        2.08 -     4.17: 242
        4.17 -     6.25: 21
        6.25 -     8.34: 2
        8.34 -    10.42: 3
  Bond angle restraints: 11251
  Sorted by residual:
  angle pdb=" N   PHE A  70 "
        pdb=" CA  PHE A  70 "
        pdb=" C   PHE A  70 "
      ideal   model   delta    sigma   weight residual
     110.30  100.05   10.25 1.50e+00 4.44e-01 4.67e+01
  angle pdb=" C   PHE A  70 "
        pdb=" CA  PHE A  70 "
        pdb=" CB  PHE A  70 "
      ideal   model   delta    sigma   weight residual
     110.06  118.15   -8.09 1.39e+00 5.18e-01 3.39e+01
  angle pdb=" N   VAL A  57 "
        pdb=" CA  VAL A  57 "
        pdb=" C   VAL A  57 "
      ideal   model   delta    sigma   weight residual
     112.17  107.42    4.75 9.50e-01 1.11e+00 2.50e+01
  angle pdb=" N   GLU R 170 "
        pdb=" CA  GLU R 170 "
        pdb=" C   GLU R 170 "
      ideal   model   delta    sigma   weight residual
     111.71  106.56    5.15 1.15e+00 7.56e-01 2.01e+01
  angle pdb=" N   GLY R 167 "
        pdb=" CA  GLY R 167 "
        pdb=" C   GLY R 167 "
      ideal   model   delta    sigma   weight residual
     115.64  109.53    6.11 1.46e+00 4.69e-01 1.75e+01
  ... (remaining 11246 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.07: 4484
       16.07 -    32.13: 371
       32.13 -    48.20: 85
       48.20 -    64.27: 15
       64.27 -    80.34: 8
  Dihedral angle restraints: 4963
    sinusoidal: 1949
      harmonic: 3014
  Sorted by residual:
  dihedral pdb=" CA  HIS R  50 "
           pdb=" C   HIS R  50 "
           pdb=" N   PHE R  51 "
           pdb=" CA  PHE R  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.62  -24.38     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.06   39.94     1      1.00e+01 1.00e-02 2.24e+01
  dihedral pdb=" CG  ARG N  67 "
           pdb=" CD  ARG N  67 "
           pdb=" NE  ARG N  67 "
           pdb=" CZ  ARG N  67 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  131.74  -41.74     2      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 4960 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1063
       0.067 -    0.133: 178
       0.133 -    0.200: 21
       0.200 -    0.266: 3
       0.266 -    0.333: 1
  Chirality restraints: 1266
  Sorted by residual:
  chirality pdb=" CA  THR N  91 "
            pdb=" N   THR N  91 "
            pdb=" C   THR N  91 "
            pdb=" CB  THR N  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.19    0.33 2.00e-01 2.50e+01 2.77e+00
  chirality pdb=" CA  ASP R 287 "
            pdb=" N   ASP R 287 "
            pdb=" C   ASP R 287 "
            pdb=" CB  ASP R 287 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CA  VAL A  57 "
            pdb=" N   VAL A  57 "
            pdb=" C   VAL A  57 "
            pdb=" CB  VAL A  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1263 not shown)

  Planarity restraints: 1429
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG R  83 "    0.418 9.50e-02 1.11e+02   1.88e-01 2.15e+01
        pdb=" NE  ARG R  83 "   -0.025 2.00e-02 2.50e+03
        pdb=" CZ  ARG R  83 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG R  83 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG R  83 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR R 308 "    0.071 5.00e-02 4.00e+02   1.07e-01 1.83e+01
        pdb=" N   PRO R 309 "   -0.185 5.00e-02 4.00e+02
        pdb=" CA  PRO R 309 "    0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO R 309 "    0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG R 312 "    0.383 9.50e-02 1.11e+02   1.72e-01 1.80e+01
        pdb=" NE  ARG R 312 "   -0.022 2.00e-02 2.50e+03
        pdb=" CZ  ARG R 312 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG R 312 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG R 312 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1426 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1105
        2.75 -     3.29: 7970
        3.29 -     3.83: 14027
        3.83 -     4.36: 17110
        4.36 -     4.90: 29488
  Nonbonded interactions: 69700
  Sorted by model distance:
  nonbonded pdb=" OG  SER N   7 "
            pdb=" OG  SER N  21 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OG1 THR R  56 "
            pdb=" OD1 ASN R  59 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OG  SER B 227 "
            pdb=" O   PRO N 100 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OD2 ASP R 103 "
            pdb=" O   HOH R 501 "
     model   vdw
     2.273 3.040
  ... (remaining 69695 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:             2.570
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.950
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
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      :  0.005   0.056   8297  Z= 0.317
  Angle     :  0.684  10.422  11257  Z= 0.444
  Chirality :  0.051   0.333   1266
  Planarity :  0.011   0.188   1429
  Dihedral  : 12.911  80.336   3006
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.16 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.27), residues: 1021
  helix:  2.24 (0.25), residues: 387
  sheet: -0.06 (0.35), residues: 215
  loop : -0.62 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 237 
 TYR   0.010   0.001   TYR R 308 
 PHE   0.018   0.001   PHE R  91 
 TRP   0.017   0.002   TRP R 291 
 HIS   0.004   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 8294)
  covalent geometry    : angle       0.68372 (11251)
  SS BOND              : bond        0.00416 (    3)
  SS BOND              : angle       0.75444 (    6)
  hydrogen bonds       : bond        0.15790 (  424)
  hydrogen bonds       : angle       6.81497 ( 1218)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 178
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASP cc_start: 0.7879 (m-30) cc_final: 0.7577 (m-30)
REVERT: N   53 GLN cc_start: 0.8750 (mp10) cc_final: 0.8533 (mp10)
REVERT: R   95 PHE cc_start: 0.7456 (t80) cc_final: 0.7231 (t80)
REVERT: R  302 MET cc_start: 0.7989 (mtt) cc_final: 0.7758 (mtp)
  outliers start: 1
  outliers final: 1
  residues processed: 178
  average time/residue: 0.6637
  time to fit residues: 124.0163
Evaluate side-chains
  142 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  184 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0370
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A 131 ASN
B  17 GLN
B  44 GLN
B 237 ASN
B 239 ASN
B 259 GLN
B 340 ASN
N   3 GLN
N  35 ASN
N  39 GLN
N  77 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.151018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.116154 restraints weight = 10323.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.52
r_work: 0.3294 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8297  Z= 0.136
  Angle     :  0.540  10.246  11257  Z= 0.288
  Chirality :  0.041   0.160   1266
  Planarity :  0.005   0.071   1429
  Dihedral  :  4.268  26.670   1191
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.45 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.27), residues: 1021
  helix:  2.43 (0.25), residues: 389
  sheet:  0.02 (0.35), residues: 212
  loop : -0.53 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 199 
 TYR   0.011   0.001   TYR A 115 
 PHE   0.013   0.001   PHE R  51 
 TRP   0.017   0.002   TRP B  82 
 HIS   0.005   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 8294)
  covalent geometry    : angle       0.53921 (11251)
  SS BOND              : bond        0.00341 (    3)
  SS BOND              : angle       1.63974 (    6)
  hydrogen bonds       : bond        0.04288 (  424)
  hydrogen bonds       : angle       5.20618 ( 1218)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 153
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ASP cc_start: 0.7748 (m-30) cc_final: 0.7350 (m-30)
REVERT: A   35 LYS cc_start: 0.8667 (ttpt) cc_final: 0.8347 (ptpt)
REVERT: A  151 GLU cc_start: 0.8062 (tp30) cc_final: 0.7839 (tp30)
REVERT: A  169 ARG cc_start: 0.8429 (mtp180) cc_final: 0.7980 (ptp-170)
REVERT: B   59 TYR cc_start: 0.8648 (m-80) cc_final: 0.8233 (m-80)
REVERT: B   75 GLN cc_start: 0.8149 (tt0) cc_final: 0.7909 (tt0)
REVERT: B  134 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6721 (ptm160)
REVERT: N   37 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8588 (m)
REVERT: N   53 GLN cc_start: 0.8548 (mp10) cc_final: 0.8263 (mp10)
REVERT: N  123 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8282 (tm-30)
REVERT: R   95 PHE cc_start: 0.7582 (t80) cc_final: 0.7139 (t80)
REVERT: R  262 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7920 (mp)
REVERT: R  302 MET cc_start: 0.8377 (mtt) cc_final: 0.7995 (mtp)
  outliers start: 14
  outliers final: 3
  residues processed: 157
  average time/residue: 0.6130
  time to fit residues: 101.3301
Evaluate side-chains
  147 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 141
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  262 ILE
Chi-restraints excluded: chain R residue  315 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0570
   chunk 49 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 44 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 75 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 16 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   overall best weight:    1.0700

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

Flipped N/Q/H residues before XYZ refinement:
A  80 ASN
B  17 GLN
B  44 GLN
B  75 GLN
B 237 ASN
B 259 GLN
N  77 ASN
R 296 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.148931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.113716 restraints weight = 10339.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 2.53
r_work: 0.3255 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.1775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8297  Z= 0.164
  Angle     :  0.535   9.795  11257  Z= 0.284
  Chirality :  0.042   0.147   1266
  Planarity :  0.005   0.061   1429
  Dihedral  :  4.339  31.145   1191
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.80 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.27), residues: 1021
  helix:  2.33 (0.25), residues: 397
  sheet: -0.13 (0.34), residues: 217
  loop : -0.46 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 199 
 TYR   0.018   0.001   TYR N  60 
 PHE   0.016   0.001   PHE R  91 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 8294)
  covalent geometry    : angle       0.53392 (11251)
  SS BOND              : bond        0.00485 (    3)
  SS BOND              : angle       1.36455 (    6)
  hydrogen bonds       : bond        0.04115 (  424)
  hydrogen bonds       : angle       4.98941 ( 1218)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 145
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7148 (pm20) cc_final: 0.6907 (pm20)
REVERT: A   15 ASP cc_start: 0.7793 (m-30) cc_final: 0.7366 (m-30)
REVERT: A  151 GLU cc_start: 0.8179 (tp30) cc_final: 0.7862 (tp30)
REVERT: B   19 ARG cc_start: 0.7612 (ttp-110) cc_final: 0.7357 (ttp-110)
REVERT: B   75 GLN cc_start: 0.8222 (tt0) cc_final: 0.7968 (tt0)
REVERT: B  134 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6786 (ptm160)
REVERT: B  219 ARG cc_start: 0.8319 (mtt-85) cc_final: 0.7847 (mtp85)
REVERT: B  325 MET cc_start: 0.8507 (tpp) cc_final: 0.7988 (mmm)
REVERT: N   37 VAL cc_start: 0.8860 (t) cc_final: 0.8596 (m)
REVERT: N   53 GLN cc_start: 0.8557 (mp10) cc_final: 0.8210 (mp10)
REVERT: R  262 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.7920 (mp)
REVERT: R  302 MET cc_start: 0.8358 (mtt) cc_final: 0.7975 (mtp)
  outliers start: 17
  outliers final: 5
  residues processed: 152
  average time/residue: 0.6416
  time to fit residues: 102.6824
Evaluate side-chains
  138 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 131
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ASP
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue  262 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 87 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0870
   chunk 84 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 95 optimal weight:    0.8980
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  44 GLN
B 237 ASN
B 259 GLN
N  77 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.149731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.114776 restraints weight = 10579.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 2.55
r_work: 0.3278 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8297  Z= 0.131
  Angle     :  0.505   9.930  11257  Z= 0.268
  Chirality :  0.041   0.146   1266
  Planarity :  0.004   0.055   1429
  Dihedral  :  4.144  19.274   1190
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.38 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.27), residues: 1021
  helix:  2.37 (0.25), residues: 397
  sheet: -0.09 (0.33), residues: 217
  loop : -0.45 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 199 
 TYR   0.019   0.001   TYR N  60 
 PHE   0.020   0.001   PHE R  91 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8294)
  covalent geometry    : angle       0.50506 (11251)
  SS BOND              : bond        0.00725 (    3)
  SS BOND              : angle       0.77735 (    6)
  hydrogen bonds       : bond        0.03753 (  424)
  hydrogen bonds       : angle       4.78105 ( 1218)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 149
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7150 (pm20) cc_final: 0.6896 (pm20)
REVERT: A   15 ASP cc_start: 0.7806 (m-30) cc_final: 0.7371 (m-30)
REVERT: A   35 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8282 (ptpt)
REVERT: A  151 GLU cc_start: 0.8204 (tp30) cc_final: 0.7901 (tp30)
REVERT: B   75 GLN cc_start: 0.8254 (tt0) cc_final: 0.8023 (tt0)
REVERT: B  134 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6728 (ptm160)
REVERT: B  325 MET cc_start: 0.8488 (tpp) cc_final: 0.7946 (mmm)
REVERT: N   53 GLN cc_start: 0.8517 (mp10) cc_final: 0.8138 (mp10)
REVERT: R  262 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7894 (mp)
REVERT: R  302 MET cc_start: 0.8339 (mtt) cc_final: 0.7960 (mtp)
  outliers start: 23
  outliers final: 6
  residues processed: 163
  average time/residue: 0.5518
  time to fit residues: 95.5344
Evaluate side-chains
  147 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 139
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue  226 ASP
Chi-restraints excluded: chain R residue  262 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 92 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 25 optimal weight:    9.9990
   chunk 32 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
B  17 GLN
B  44 GLN
B 237 ASN
B 259 GLN
N  77 ASN
R  53 GLN
R  55 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.147928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.112781 restraints weight = 10510.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 2.54
r_work: 0.3251 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8297  Z= 0.166
  Angle     :  0.531   9.424  11257  Z= 0.281
  Chirality :  0.042   0.146   1266
  Planarity :  0.004   0.053   1429
  Dihedral  :  4.210  18.756   1190
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.30 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.26), residues: 1021
  helix:  2.32 (0.25), residues: 398
  sheet: -0.14 (0.32), residues: 217
  loop : -0.45 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 199 
 TYR   0.023   0.002   TYR N  60 
 PHE   0.017   0.001   PHE R  91 
 TRP   0.012   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 8294)
  covalent geometry    : angle       0.53125 (11251)
  SS BOND              : bond        0.00490 (    3)
  SS BOND              : angle       0.64612 (    6)
  hydrogen bonds       : bond        0.03860 (  424)
  hydrogen bonds       : angle       4.80955 ( 1218)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7095 (pm20) cc_final: 0.6798 (pm20)
REVERT: A   15 ASP cc_start: 0.7802 (m-30) cc_final: 0.7387 (m-30)
REVERT: A   21 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7574 (ttt180)
REVERT: A  151 GLU cc_start: 0.8222 (tp30) cc_final: 0.7837 (tp30)
REVERT: B   32 GLN cc_start: 0.8261 (tt0) cc_final: 0.8036 (tt0)
REVERT: B   59 TYR cc_start: 0.8659 (m-80) cc_final: 0.8312 (m-80)
REVERT: B   75 GLN cc_start: 0.8281 (tt0) cc_final: 0.8045 (tt0)
REVERT: B  134 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6777 (ptm160)
REVERT: B  325 MET cc_start: 0.8496 (tpp) cc_final: 0.7960 (mmm)
REVERT: N   53 GLN cc_start: 0.8534 (mp10) cc_final: 0.8108 (mp10)
REVERT: R  262 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7889 (mp)
REVERT: R  302 MET cc_start: 0.8360 (mtt) cc_final: 0.7991 (mtp)
  outliers start: 25
  outliers final: 13
  residues processed: 158
  average time/residue: 0.5735
  time to fit residues: 95.7243
Evaluate side-chains
  152 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 136
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ARG
Chi-restraints excluded: chain A residue   83 MET
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue   67 THR
Chi-restraints excluded: chain R residue   74 CYS
Chi-restraints excluded: chain R residue   97 LYS
Chi-restraints excluded: chain R residue  226 ASP
Chi-restraints excluded: chain R residue  262 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 14 optimal weight:    0.0270
   chunk 96 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 84 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 72 optimal weight:    0.0470
   chunk 66 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.4536

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  44 GLN
B 237 ASN
B 259 GLN
N  31 ASN
N  77 ASN
R  53 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.150611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.115706 restraints weight = 10355.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 2.52
r_work: 0.3290 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8297  Z= 0.112
  Angle     :  0.497   9.526  11257  Z= 0.264
  Chirality :  0.040   0.143   1266
  Planarity :  0.004   0.051   1429
  Dihedral  :  4.038  18.058   1190
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.92 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.26), residues: 1021
  helix:  2.40 (0.25), residues: 397
  sheet: -0.04 (0.32), residues: 215
  loop : -0.46 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 199 
 TYR   0.025   0.001   TYR N  60 
 PHE   0.012   0.001   PHE A  74 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 8294)
  covalent geometry    : angle       0.49669 (11251)
  SS BOND              : bond        0.00482 (    3)
  SS BOND              : angle       0.70471 (    6)
  hydrogen bonds       : bond        0.03491 (  424)
  hydrogen bonds       : angle       4.61197 ( 1218)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7128 (pm20) cc_final: 0.6792 (pm20)
REVERT: A   15 ASP cc_start: 0.7804 (m-30) cc_final: 0.7403 (m-30)
REVERT: A  151 GLU cc_start: 0.8211 (tp30) cc_final: 0.7807 (tp30)
REVERT: B   59 TYR cc_start: 0.8688 (m-80) cc_final: 0.8320 (m-80)
REVERT: B   75 GLN cc_start: 0.8296 (tt0) cc_final: 0.8063 (tt0)
REVERT: B  134 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6693 (ptm160)
REVERT: B  155 ASN cc_start: 0.8152 (t0) cc_final: 0.7908 (t0)
REVERT: B  325 MET cc_start: 0.8519 (tpp) cc_final: 0.7980 (mmm)
REVERT: N   43 LYS cc_start: 0.7970 (mtpt) cc_final: 0.7744 (mtpp)
REVERT: N   53 GLN cc_start: 0.8552 (mp10) cc_final: 0.8109 (mp10)
REVERT: N  109 ASP cc_start: 0.8296 (m-30) cc_final: 0.8020 (m-30)
REVERT: R  262 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.7915 (mp)
REVERT: R  302 MET cc_start: 0.8335 (mtt) cc_final: 0.7934 (mtp)
  outliers start: 22
  outliers final: 12
  residues processed: 156
  average time/residue: 0.5559
  time to fit residues: 91.9613
Evaluate side-chains
  154 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue   97 LYS
Chi-restraints excluded: chain R residue  103 ASP
Chi-restraints excluded: chain R residue  226 ASP
Chi-restraints excluded: chain R residue  262 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0060
   chunk 47 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0980
   chunk 69 optimal weight:    0.4980
   chunk 98 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 97 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 62 optimal weight:    0.2980
   overall best weight:    0.2996

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  32 GLN
B  44 GLN
B 237 ASN
B 259 GLN
N  77 ASN
R  53 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.151725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.117045 restraints weight = 10448.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 2.53
r_work: 0.3306 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8297  Z= 0.103
  Angle     :  0.492   9.319  11257  Z= 0.260
  Chirality :  0.040   0.141   1266
  Planarity :  0.004   0.050   1429
  Dihedral  :  3.936  17.679   1190
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.31 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.27), residues: 1021
  helix:  2.43 (0.25), residues: 399
  sheet:  0.05 (0.32), residues: 214
  loop : -0.49 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 199 
 TYR   0.025   0.001   TYR N  60 
 PHE   0.015   0.001   PHE R  91 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 8294)
  covalent geometry    : angle       0.49224 (11251)
  SS BOND              : bond        0.00226 (    3)
  SS BOND              : angle       0.53298 (    6)
  hydrogen bonds       : bond        0.03346 (  424)
  hydrogen bonds       : angle       4.50690 ( 1218)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7130 (pm20) cc_final: 0.6789 (pm20)
REVERT: A   15 ASP cc_start: 0.7794 (m-30) cc_final: 0.7397 (m-30)
REVERT: A  151 GLU cc_start: 0.8175 (tp30) cc_final: 0.7781 (tp30)
REVERT: B   59 TYR cc_start: 0.8685 (m-80) cc_final: 0.8291 (m-80)
REVERT: B   75 GLN cc_start: 0.8311 (tt0) cc_final: 0.8100 (tt0)
REVERT: B  134 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6657 (ptm160)
REVERT: B  155 ASN cc_start: 0.8139 (t0) cc_final: 0.7890 (t0)
REVERT: B  325 MET cc_start: 0.8505 (tpp) cc_final: 0.7971 (mmm)
REVERT: N   43 LYS cc_start: 0.7931 (mtpt) cc_final: 0.7709 (mtpp)
REVERT: N   53 GLN cc_start: 0.8530 (mp10) cc_final: 0.8075 (mp10)
REVERT: N   59 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.8220 (p)
REVERT: R  262 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7925 (mp)
REVERT: R  302 MET cc_start: 0.8317 (mtt) cc_final: 0.7931 (mtp)
  outliers start: 20
  outliers final: 8
  residues processed: 158
  average time/residue: 0.5568
  time to fit residues: 93.0462
Evaluate side-chains
  156 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 145
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain R residue   74 CYS
Chi-restraints excluded: chain R residue  226 ASP
Chi-restraints excluded: chain R residue  262 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 88 optimal weight:   10.0000
   chunk 67 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
A 131 ASN
B  17 GLN
B  44 GLN
B 259 GLN
N  77 ASN
R  53 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.146474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.111019 restraints weight = 10563.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 2.54
r_work: 0.3221 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8297  Z= 0.231
  Angle     :  0.577   9.366  11257  Z= 0.305
  Chirality :  0.043   0.140   1266
  Planarity :  0.005   0.051   1429
  Dihedral  :  4.221  18.011   1190
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.42 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.26), residues: 1021
  helix:  2.23 (0.25), residues: 400
  sheet: -0.21 (0.32), residues: 222
  loop : -0.51 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 199 
 TYR   0.027   0.002   TYR N  60 
 PHE   0.011   0.002   PHE R  91 
 TRP   0.013   0.002   TRP B 211 
 HIS   0.004   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 ( 8294)
  covalent geometry    : angle       0.57688 (11251)
  SS BOND              : bond        0.00379 (    3)
  SS BOND              : angle       0.64850 (    6)
  hydrogen bonds       : bond        0.04002 (  424)
  hydrogen bonds       : angle       4.79650 ( 1218)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7145 (pm20) cc_final: 0.6799 (pm20)
REVERT: A   15 ASP cc_start: 0.7801 (m-30) cc_final: 0.7409 (m-30)
REVERT: A  151 GLU cc_start: 0.8224 (tp30) cc_final: 0.7822 (tp30)
REVERT: B   59 TYR cc_start: 0.8670 (m-80) cc_final: 0.8311 (m-80)
REVERT: B   75 GLN cc_start: 0.8299 (tt0) cc_final: 0.8022 (tt0)
REVERT: B  134 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6865 (ptm160)
REVERT: B  219 ARG cc_start: 0.8334 (mtt-85) cc_final: 0.7882 (mtp85)
REVERT: B  262 MET cc_start: 0.8413 (tpt) cc_final: 0.8174 (tpp)
REVERT: B  325 MET cc_start: 0.8534 (tpp) cc_final: 0.8054 (mmm)
REVERT: N   53 GLN cc_start: 0.8586 (mp10) cc_final: 0.8107 (mp10)
REVERT: R  262 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7998 (mp)
REVERT: R  302 MET cc_start: 0.8376 (mtt) cc_final: 0.8015 (mtp)
  outliers start: 22
  outliers final: 10
  residues processed: 152
  average time/residue: 0.5787
  time to fit residues: 92.8081
Evaluate side-chains
  146 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   95 TYR
Chi-restraints excluded: chain R residue   74 CYS
Chi-restraints excluded: chain R residue  226 ASP
Chi-restraints excluded: chain R residue  262 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 80 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 88 optimal weight:    4.9990
   chunk 92 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 79 optimal weight:    0.2980
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  32 GLN
B  44 GLN
B 259 GLN
N  77 ASN
R  53 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.149470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.114512 restraints weight = 10465.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 2.53
r_work: 0.3275 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8297  Z= 0.131
  Angle     :  0.531   9.075  11257  Z= 0.280
  Chirality :  0.041   0.141   1266
  Planarity :  0.004   0.051   1429
  Dihedral  :  4.096  17.779   1190
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 19.88 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.26), residues: 1021
  helix:  2.31 (0.25), residues: 399
  sheet: -0.12 (0.32), residues: 219
  loop : -0.49 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG N 105 
 TYR   0.015   0.001   TYR N  60 
 PHE   0.018   0.001   PHE R  91 
 TRP   0.013   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8294)
  covalent geometry    : angle       0.53053 (11251)
  SS BOND              : bond        0.00317 (    3)
  SS BOND              : angle       0.70048 (    6)
  hydrogen bonds       : bond        0.03598 (  424)
  hydrogen bonds       : angle       4.63301 ( 1218)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7133 (pm20) cc_final: 0.6790 (pm20)
REVERT: A   15 ASP cc_start: 0.7810 (m-30) cc_final: 0.7400 (m-30)
REVERT: A  151 GLU cc_start: 0.8205 (tp30) cc_final: 0.7809 (tp30)
REVERT: A  169 ARG cc_start: 0.8473 (mtp180) cc_final: 0.8036 (ptp90)
REVERT: B   75 GLN cc_start: 0.8312 (tt0) cc_final: 0.7995 (tt0)
REVERT: B  134 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6718 (ptm160)
REVERT: B  155 ASN cc_start: 0.8123 (t0) cc_final: 0.7871 (t0)
REVERT: B  262 MET cc_start: 0.8317 (tpt) cc_final: 0.8086 (tpp)
REVERT: B  325 MET cc_start: 0.8511 (tpp) cc_final: 0.8050 (mmm)
REVERT: N   43 LYS cc_start: 0.8019 (mtpt) cc_final: 0.7798 (mtpp)
REVERT: N   53 GLN cc_start: 0.8577 (mp10) cc_final: 0.8102 (mp10)
REVERT: N  109 ASP cc_start: 0.8200 (m-30) cc_final: 0.7848 (m-30)
REVERT: R  262 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7898 (mp)
REVERT: R  302 MET cc_start: 0.8332 (mtt) cc_final: 0.7973 (mtp)
  outliers start: 20
  outliers final: 13
  residues processed: 153
  average time/residue: 0.5463
  time to fit residues: 88.5475
Evaluate side-chains
  152 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   95 TYR
Chi-restraints excluded: chain R residue   74 CYS
Chi-restraints excluded: chain R residue  103 ASP
Chi-restraints excluded: chain R residue  226 ASP
Chi-restraints excluded: chain R residue  262 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 35 optimal weight:    0.0070
   chunk 11 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 53 optimal weight:    8.9990
   chunk 13 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 68 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.7000

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  32 GLN
B  44 GLN
B 259 GLN
N  77 ASN
R  53 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.149498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.114621 restraints weight = 10419.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 2.52
r_work: 0.3271 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8297  Z= 0.134
  Angle     :  0.536   9.155  11257  Z= 0.282
  Chirality :  0.041   0.143   1266
  Planarity :  0.005   0.065   1429
  Dihedral  :  4.094  17.808   1190
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 20.23 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.26), residues: 1021
  helix:  2.30 (0.25), residues: 398
  sheet: -0.09 (0.32), residues: 219
  loop : -0.51 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG N 105 
 TYR   0.028   0.002   TYR R 172 
 PHE   0.012   0.001   PHE B 234 
 TRP   0.013   0.002   TRP B  82 
 HIS   0.005   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8294)
  covalent geometry    : angle       0.53609 (11251)
  SS BOND              : bond        0.00299 (    3)
  SS BOND              : angle       0.63858 (    6)
  hydrogen bonds       : bond        0.03604 (  424)
  hydrogen bonds       : angle       4.63098 ( 1218)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7129 (pm20) cc_final: 0.6783 (pm20)
REVERT: A   15 ASP cc_start: 0.7814 (m-30) cc_final: 0.7419 (m-30)
REVERT: A  151 GLU cc_start: 0.8199 (tp30) cc_final: 0.7802 (tp30)
REVERT: A  169 ARG cc_start: 0.8486 (mtp180) cc_final: 0.8050 (ptp90)
REVERT: B   75 GLN cc_start: 0.8289 (tt0) cc_final: 0.8061 (tt0)
REVERT: B  134 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6710 (ptm160)
REVERT: B  155 ASN cc_start: 0.8072 (t0) cc_final: 0.7817 (t0)
REVERT: B  262 MET cc_start: 0.8322 (tpt) cc_final: 0.8092 (tpp)
REVERT: B  325 MET cc_start: 0.8514 (tpp) cc_final: 0.8053 (mmm)
REVERT: N   43 LYS cc_start: 0.8007 (mtpt) cc_final: 0.7785 (mtpp)
REVERT: N   53 GLN cc_start: 0.8574 (mp10) cc_final: 0.8098 (mp10)
REVERT: N  109 ASP cc_start: 0.8186 (m-30) cc_final: 0.7822 (m-30)
REVERT: R  262 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7892 (mp)
REVERT: R  302 MET cc_start: 0.8341 (mtt) cc_final: 0.8027 (mtp)
  outliers start: 17
  outliers final: 14
  residues processed: 147
  average time/residue: 0.5715
  time to fit residues: 88.9042
Evaluate side-chains
  151 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLU
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   95 TYR
Chi-restraints excluded: chain R residue   74 CYS
Chi-restraints excluded: chain R residue  103 ASP
Chi-restraints excluded: chain R residue  226 ASP
Chi-restraints excluded: chain R residue  262 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0060
   chunk 98 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 83 optimal weight:    0.5980
   chunk 75 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0970
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
B  17 GLN
B  32 GLN
B  44 GLN
B 259 GLN
N  77 ASN
R  53 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.150390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.115630 restraints weight = 10511.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.53
r_work: 0.3285 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3148 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8297  Z= 0.119
  Angle     :  0.527   9.230  11257  Z= 0.277
  Chirality :  0.040   0.145   1266
  Planarity :  0.005   0.062   1429
  Dihedral  :  4.041  17.772   1190
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 20.35 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.26), residues: 1021
  helix:  2.33 (0.25), residues: 398
  sheet:  0.01 (0.32), residues: 213
  loop : -0.53 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG N 105 
 TYR   0.025   0.001   TYR R 172 
 PHE   0.017   0.001   PHE R  91 
 TRP   0.014   0.002   TRP B  82 
 HIS   0.005   0.001   HIS R  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8294)
  covalent geometry    : angle       0.52658 (11251)
  SS BOND              : bond        0.00263 (    3)
  SS BOND              : angle       0.63832 (    6)
  hydrogen bonds       : bond        0.03512 (  424)
  hydrogen bonds       : angle       4.58003 ( 1218)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3643.79 seconds
wall clock time: 62 minutes 38.80 seconds (3758.80 seconds total)