Starting phenix.real_space_refine
on Fri Aug 22 17:53:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ge7_29959/08_2025/8ge7_29959.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ge7_29959/08_2025/8ge7_29959.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ge7_29959/08_2025/8ge7_29959.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ge7_29959/08_2025/8ge7_29959.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ge7_29959/08_2025/8ge7_29959.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ge7_29959/08_2025/8ge7_29959.map"
  }
  resolution = 3.4
  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=  -0.001 sd=   0.033
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      42      5.16       5
     C    4245      2.51       5
     N    1143      2.21       5
     O    1187      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6617
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1717
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1717
          Classifications: {'peptide': 230}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PTRANS': 5, 'TRANS': 224}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 198
          Unresolved non-hydrogen angles: 237
          Unresolved non-hydrogen dihedrals: 161
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 6, 'ASN:plan1': 1, 'GLU:plan': 13, 'ASP:plan': 9, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 134
    Chain: "B"
      Number of atoms: 2446
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2446
          Classifications: {'peptide': 331}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 5, 'TRANS': 325}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 98
          Unresolved non-hydrogen angles: 119
          Unresolved non-hydrogen dihedrals: 77
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 6, 'GLU:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 77
    Chain: "G"
      Number of atoms: 349
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 349
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 65
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "R"
      Number of atoms: 2090
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2090
          Classifications: {'peptide': 282}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 7, 'TRANS': 274}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 182
          Unresolved non-hydrogen angles: 226
          Unresolved non-hydrogen dihedrals: 149
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLU:plan': 9, 'TRP:plan': 1, 'ASP:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 3, 'HIS:plan': 2, 'GLN:plan1': 3}
          Unresolved non-hydrogen planarities: 103
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.88, per 1000 atoms: 0.28
  Number of scatterers: 6617
  At special positions: 0
  Unit cell: (69.96, 98.58, 129.32, 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      42     16.00
     O    1187      8.00
     N    1143      7.00
     C    4245      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " 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: 0.64
  Conformation dependent library (CDL) restraints added in 380.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1696

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      48.7% alpha, 18.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 40
      removed outlier: 3.799A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   THR A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 51
      No H-bonds generated for 'chain 'A' and resid 49 through 51'
    Processing helix  chain 'A' and resid 52 through 60
      removed outlier: 3.633A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.006A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.957A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 7 through 25
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.714A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 12 through 24
      removed outlier: 3.569A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 31 through 61
    Processing helix  chain 'R' and resid 66 through 96
      removed outlier: 3.664A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.525A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 5.240A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      removed outlier: 4.303A  pdb=" N   LEU R 167 " --> pdb=" O   LEU R 163 " (cutoff:3.500A)
      Proline residue:  R 168  - end of helix
      removed outlier: 3.868A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 3.695A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 4.004A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 3.755A  pdb=" N   ASN R 318 " --> pdb=" O   ILE R 314 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 6.433A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 7.775A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.792A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.511A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.043A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.226A  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: 6.614A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.317A  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: 6.841A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.941A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.262A  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: 6.879A  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: 6.850A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.521A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.267A  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: 6.711A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.786A  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: 5.613A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    391 hydrogen bonds defined for protein.
    1137 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: 1.12

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2142
        1.34 -     1.46: 1573
        1.46 -     1.58: 2984
        1.58 -     1.70: 0
        1.70 -     1.81: 58
  Bond restraints: 6757
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.449 -0.052 2.00e-02 2.50e+03 6.63e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.566 -0.043 2.00e-02 2.50e+03 4.70e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.437 -0.043 2.00e-02 2.50e+03 4.67e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 2.00e-02 2.50e+03 4.36e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" NAN G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.451  1.484 -0.033 2.00e-02 2.50e+03 2.72e+00
  ... (remaining 6752 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 8833
        1.13 -     2.26: 308
        2.26 -     3.39: 62
        3.39 -     4.52: 13
        4.52 -     5.65: 10
  Bond angle restraints: 9226
  Sorted by residual:
  angle pdb=" C   HIS B 183 "
        pdb=" N   THR B 184 "
        pdb=" CA  THR B 184 "
      ideal   model   delta    sigma   weight residual
     122.79  118.37    4.42 1.70e+00 3.46e-01 6.76e+00
  angle pdb=" N   GLN A 227 "
        pdb=" CA  GLN A 227 "
        pdb=" C   GLN A 227 "
      ideal   model   delta    sigma   weight residual
     111.81  108.60    3.21 1.44e+00 4.82e-01 4.98e+00
  angle pdb=" CA  GLU G  47 "
        pdb=" CB  GLU G  47 "
        pdb=" CG  GLU G  47 "
      ideal   model   delta    sigma   weight residual
     114.10  118.54   -4.44 2.00e+00 2.50e-01 4.92e+00
  angle pdb=" C   TYR B  59 "
        pdb=" N   ALA B  60 "
        pdb=" CA  ALA B  60 "
      ideal   model   delta    sigma   weight residual
     121.75  118.36    3.39 1.73e+00 3.34e-01 3.84e+00
  angle pdb=" N   PHE B 335 "
        pdb=" CA  PHE B 335 "
        pdb=" C   PHE B 335 "
      ideal   model   delta    sigma   weight residual
     109.24  112.41   -3.17 1.63e+00 3.76e-01 3.79e+00
  ... (remaining 9221 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.98: 3557
       15.98 -    31.95: 292
       31.95 -    47.93: 68
       47.93 -    63.90: 9
       63.90 -    79.88: 3
  Dihedral angle restraints: 3929
    sinusoidal: 1319
      harmonic: 2610
  Sorted by residual:
  dihedral pdb=" CA  THR B 165 "
           pdb=" C   THR B 165 "
           pdb=" N   CYS B 166 "
           pdb=" CA  CYS B 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.02   21.98     0      5.00e+00 4.00e-02 1.93e+01
  dihedral pdb=" CA  ASP B 291 "
           pdb=" C   ASP B 291 "
           pdb=" N   PHE B 292 "
           pdb=" CA  PHE B 292 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.87  -19.13     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  TRP B 332 "
           pdb=" C   TRP B 332 "
           pdb=" N   ASP B 333 "
           pdb=" CA  ASP B 333 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.73   18.27     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 3926 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 757
       0.034 -    0.069: 248
       0.069 -    0.103: 71
       0.103 -    0.137: 22
       0.137 -    0.171: 1
  Chirality restraints: 1099
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.57   -0.17 2.00e-01 2.50e+01 7.33e-01
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.54e-01
  chirality pdb=" CA  VAL B 327 "
            pdb=" N   VAL B 327 "
            pdb=" C   VAL B 327 "
            pdb=" CB  VAL B 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.17e-01
  ... (remaining 1096 not shown)

  Planarity restraints: 1163
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN G  59 "    0.024 5.00e-02 4.00e+02   3.59e-02 2.07e+00
        pdb=" N   PRO G  60 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO G  60 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO G  60 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR G  52 "   -0.021 5.00e-02 4.00e+02   3.24e-02 1.67e+00
        pdb=" N   PRO G  53 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO G  53 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO G  53 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 320 "   -0.020 5.00e-02 4.00e+02   3.04e-02 1.48e+00
        pdb=" N   PRO A 321 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 321 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 321 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1160 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 488
        2.74 -     3.28: 6779
        3.28 -     3.82: 11192
        3.82 -     4.36: 12602
        4.36 -     4.90: 22962
  Nonbonded interactions: 54023
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 281 "
            pdb=" O   HIS G  44 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" NZ  LYS A 233 "
            pdb=" OD2 ASP B 228 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" OD1 ASP B 247 "
            pdb=" OG1 THR B 249 "
     model   vdw
     2.226 3.040
  ... (remaining 54018 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=0.00 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:             1.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.620
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6758  Z= 0.150
  Angle     :  0.532   5.652   9228  Z= 0.295
  Chirality :  0.039   0.171   1099
  Planarity :  0.004   0.039   1163
  Dihedral  : 12.646  79.878   2230
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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:  0.95 (0.28), residues: 877
  helix:  2.16 (0.26), residues: 389
  sheet:  0.22 (0.42), residues: 155
  loop : -1.03 (0.30), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 347 
 TYR   0.019   0.001   TYR B  59 
 PHE   0.015   0.001   PHE B 234 
 TRP   0.013   0.001   TRP R  99 
 HIS   0.012   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 6757)
  covalent geometry    : angle       0.53224 ( 9226)
  SS BOND              : bond        0.00351 (    1)
  SS BOND              : angle       1.09807 (    2)
  hydrogen bonds       : bond        0.15968 (  391)
  hydrogen bonds       : angle       6.10427 ( 1137)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0743
  time to fit residues: 10.5821
Evaluate side-chains
  81 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0270
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    0.0050
   overall best weight:    0.5052

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
G  18 GLN
R 231 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.145749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.128547 restraints weight = 9262.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 1.88
r_work: 0.3498 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3382
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3382 r_free = 0.3382    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3382 r_free = 0.3382    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3382
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.0926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6758  Z= 0.129
  Angle     :  0.504   5.382   9228  Z= 0.280
  Chirality :  0.040   0.146   1099
  Planarity :  0.004   0.034   1163
  Dihedral  :  4.655  32.801    969
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  8.98 %
    Favored  : 90.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.28), residues: 877
  helix:  2.31 (0.26), residues: 388
  sheet:  0.24 (0.36), residues: 179
  loop : -1.03 (0.32), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 347 
 TYR   0.013   0.001   TYR B  59 
 PHE   0.018   0.001   PHE B 199 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.008   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6757)
  covalent geometry    : angle       0.50448 ( 9226)
  SS BOND              : bond        0.00331 (    1)
  SS BOND              : angle       0.31872 (    2)
  hydrogen bonds       : bond        0.04364 (  391)
  hydrogen bonds       : angle       4.51589 ( 1137)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8785 (tp40) cc_final: 0.8492 (tp40)
REVERT: A  343 ASP cc_start: 0.7936 (m-30) cc_final: 0.7601 (m-30)
REVERT: G   18 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8443 (tp40)
  outliers start: 4
  outliers final: 3
  residues processed: 93
  average time/residue: 0.0771
  time to fit residues: 10.0178
Evaluate side-chains
  86 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain G residue   18 GLN
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 72 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 225 HIS
B 237 ASN
R 231 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.148525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.130489 restraints weight = 9754.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 2.03
r_work: 0.3464 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3349
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3349
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6758  Z= 0.147
  Angle     :  0.488   5.420   9228  Z= 0.270
  Chirality :  0.040   0.145   1099
  Planarity :  0.003   0.036   1163
  Dihedral  :  4.629  31.001    969
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 11.18 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.28), residues: 877
  helix:  2.34 (0.26), residues: 388
  sheet:  0.10 (0.37), residues: 180
  loop : -1.08 (0.32), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  49 
 TYR   0.013   0.001   TYR B  59 
 PHE   0.017   0.001   PHE B 199 
 TRP   0.013   0.001   TRP B 211 
 HIS   0.005   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 6757)
  covalent geometry    : angle       0.48840 ( 9226)
  SS BOND              : bond        0.00307 (    1)
  SS BOND              : angle       0.24369 (    2)
  hydrogen bonds       : bond        0.04190 (  391)
  hydrogen bonds       : angle       4.31954 ( 1137)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8773 (tp40) cc_final: 0.8515 (tp40)
REVERT: A  317 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.7980 (ptp90)
REVERT: A  343 ASP cc_start: 0.7984 (m-30) cc_final: 0.7623 (m-30)
REVERT: B  246 ASP cc_start: 0.7983 (m-30) cc_final: 0.7626 (m-30)
REVERT: G   47 GLU cc_start: 0.8738 (pp20) cc_final: 0.8057 (pp20)
  outliers start: 8
  outliers final: 5
  residues processed: 95
  average time/residue: 0.0813
  time to fit residues: 10.5736
Evaluate side-chains
  89 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 76 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0010
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.149708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.131547 restraints weight = 9869.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 2.09
r_work: 0.3461 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3351
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3351 r_free = 0.3351    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3351 r_free = 0.3351    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3351
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6758  Z= 0.124
  Angle     :  0.461   5.391   9228  Z= 0.256
  Chirality :  0.039   0.135   1099
  Planarity :  0.003   0.035   1163
  Dihedral  :  4.498  28.330    969
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 12.13 %
    Favored  : 86.14 %
  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:  1.14 (0.28), residues: 877
  helix:  2.46 (0.26), residues: 388
  sheet:  0.14 (0.37), residues: 179
  loop : -1.11 (0.32), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 251 
 TYR   0.011   0.001   TYR R 199 
 PHE   0.016   0.001   PHE B 199 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6757)
  covalent geometry    : angle       0.46073 ( 9226)
  SS BOND              : bond        0.00285 (    1)
  SS BOND              : angle       0.18090 (    2)
  hydrogen bonds       : bond        0.03871 (  391)
  hydrogen bonds       : angle       4.15281 ( 1137)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8787 (tp40) cc_final: 0.8557 (tp40)
REVERT: A  317 ARG cc_start: 0.8269 (mtm-85) cc_final: 0.8035 (ptp-170)
REVERT: A  343 ASP cc_start: 0.7947 (m-30) cc_final: 0.7578 (m-30)
REVERT: B  117 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8329 (tt)
REVERT: G   47 GLU cc_start: 0.8682 (pp20) cc_final: 0.8049 (pp20)
  outliers start: 11
  outliers final: 6
  residues processed: 101
  average time/residue: 0.0783
  time to fit residues: 10.8137
Evaluate side-chains
  91 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 86 optimal weight:    0.5980
   chunk 75 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0980
   chunk 63 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.147482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.130284 restraints weight = 9760.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 1.92
r_work: 0.3487 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3342 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3371
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3371 r_free = 0.3371    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3371 r_free = 0.3371    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3371
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.1425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6758  Z= 0.125
  Angle     :  0.462   5.537   9228  Z= 0.255
  Chirality :  0.039   0.173   1099
  Planarity :  0.003   0.034   1163
  Dihedral  :  4.480  29.489    969
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.07 %
    Favored  : 85.20 %
  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:  1.15 (0.28), residues: 877
  helix:  2.51 (0.26), residues: 388
  sheet:  0.08 (0.37), residues: 179
  loop : -1.13 (0.32), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 251 
 TYR   0.012   0.001   TYR B  59 
 PHE   0.016   0.001   PHE B 199 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6757)
  covalent geometry    : angle       0.46220 ( 9226)
  SS BOND              : bond        0.00187 (    1)
  SS BOND              : angle       0.13583 (    2)
  hydrogen bonds       : bond        0.03771 (  391)
  hydrogen bonds       : angle       4.06040 ( 1137)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8749 (tp40) cc_final: 0.8532 (tp40)
REVERT: A  317 ARG cc_start: 0.8270 (mtm-85) cc_final: 0.7982 (ptp90)
REVERT: A  343 ASP cc_start: 0.7972 (m-30) cc_final: 0.7587 (m-30)
REVERT: B   59 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.8244 (m-80)
REVERT: B  117 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8253 (tt)
REVERT: B  228 ASP cc_start: 0.7454 (p0) cc_final: 0.6869 (p0)
REVERT: B  246 ASP cc_start: 0.7566 (m-30) cc_final: 0.7207 (m-30)
REVERT: G   47 GLU cc_start: 0.8746 (pp20) cc_final: 0.8130 (pp20)
  outliers start: 11
  outliers final: 6
  residues processed: 97
  average time/residue: 0.0806
  time to fit residues: 10.7900
Evaluate side-chains
  90 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0770
   chunk 47 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0060
   chunk 26 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.4354

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.148613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.130911 restraints weight = 9708.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 1.98
r_work: 0.3501 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3384
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3384 r_free = 0.3384    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3384 r_free = 0.3384    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3384
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6758  Z= 0.107
  Angle     :  0.444   6.643   9228  Z= 0.245
  Chirality :  0.039   0.167   1099
  Planarity :  0.003   0.034   1163
  Dihedral  :  4.361  28.648    969
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 14.17 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.19 (0.28), residues: 877
  helix:  2.61 (0.26), residues: 388
  sheet: -0.12 (0.36), residues: 186
  loop : -1.06 (0.33), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 251 
 TYR   0.009   0.001   TYR R 199 
 PHE   0.016   0.001   PHE B 199 
 TRP   0.011   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 6757)
  covalent geometry    : angle       0.44380 ( 9226)
  SS BOND              : bond        0.00123 (    1)
  SS BOND              : angle       0.17845 (    2)
  hydrogen bonds       : bond        0.03561 (  391)
  hydrogen bonds       : angle       3.94437 ( 1137)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8723 (tp40) cc_final: 0.8508 (tp40)
REVERT: A  343 ASP cc_start: 0.7904 (m-30) cc_final: 0.7510 (m-30)
REVERT: B   59 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.8174 (m-80)
REVERT: B  117 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8225 (tt)
REVERT: R  232 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8835 (ttmt)
  outliers start: 9
  outliers final: 5
  residues processed: 97
  average time/residue: 0.0819
  time to fit residues: 10.8469
Evaluate side-chains
  92 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.133530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.114955 restraints weight = 10260.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 2.18
r_work: 0.3268 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3292
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3292
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6758  Z= 0.146
  Angle     :  0.471   6.230   9228  Z= 0.261
  Chirality :  0.040   0.182   1099
  Planarity :  0.003   0.034   1163
  Dihedral  :  4.450  28.547    969
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.49 %
    Favored  : 83.46 %
  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:  1.14 (0.28), residues: 877
  helix:  2.54 (0.26), residues: 388
  sheet: -0.18 (0.36), residues: 186
  loop : -1.02 (0.33), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 228 
 TYR   0.012   0.001   TYR R 199 
 PHE   0.016   0.001   PHE B 199 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 6757)
  covalent geometry    : angle       0.47086 ( 9226)
  SS BOND              : bond        0.00160 (    1)
  SS BOND              : angle       0.07278 (    2)
  hydrogen bonds       : bond        0.03792 (  391)
  hydrogen bonds       : angle       4.00188 ( 1137)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8694 (tp40) cc_final: 0.8491 (tp40)
REVERT: B   59 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.8071 (m-80)
REVERT: B  117 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8056 (tt)
  outliers start: 13
  outliers final: 9
  residues processed: 96
  average time/residue: 0.0651
  time to fit residues: 8.9157
Evaluate side-chains
  96 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0770
   chunk 43 optimal weight:    0.0270
   chunk 65 optimal weight:    0.6980
   chunk 75 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.136238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.117574 restraints weight = 10311.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.21
r_work: 0.3303 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3324
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3324 r_free = 0.3324    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3324 r_free = 0.3324    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3324
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6758  Z= 0.109
  Angle     :  0.454   6.089   9228  Z= 0.249
  Chirality :  0.039   0.170   1099
  Planarity :  0.003   0.033   1163
  Dihedral  :  4.316  27.416    969
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.28 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.22 (0.29), residues: 877
  helix:  2.63 (0.26), residues: 388
  sheet: -0.14 (0.37), residues: 186
  loop : -1.01 (0.33), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 231 
 TYR   0.009   0.001   TYR R 199 
 PHE   0.015   0.001   PHE B 199 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 6757)
  covalent geometry    : angle       0.45384 ( 9226)
  SS BOND              : bond        0.00112 (    1)
  SS BOND              : angle       0.15745 (    2)
  hydrogen bonds       : bond        0.03520 (  391)
  hydrogen bonds       : angle       3.90070 ( 1137)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8675 (tp40) cc_final: 0.8472 (tp40)
REVERT: A  343 ASP cc_start: 0.7968 (m-30) cc_final: 0.7707 (m-30)
REVERT: B   45 MET cc_start: 0.7527 (mtt) cc_final: 0.7249 (mtt)
REVERT: B   59 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7992 (m-80)
REVERT: B  117 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8007 (tt)
REVERT: R  231 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7980 (mp10)
  outliers start: 12
  outliers final: 6
  residues processed: 97
  average time/residue: 0.0739
  time to fit residues: 10.0976
Evaluate side-chains
  94 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  231 GLN
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 86 optimal weight:    0.4980
   chunk 64 optimal weight:    3.9990
   chunk 84 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
R 231 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.133634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.114388 restraints weight = 10427.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 2.24
r_work: 0.3247 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3269
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3269
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6758  Z= 0.177
  Angle     :  0.503   6.161   9228  Z= 0.279
  Chirality :  0.041   0.189   1099
  Planarity :  0.003   0.034   1163
  Dihedral  :  4.498  27.644    969
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.59 %
    Favored  : 82.68 %
  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 (0.29), residues: 877
  helix:  2.50 (0.26), residues: 392
  sheet: -0.27 (0.37), residues: 186
  loop : -0.97 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 228 
 TYR   0.013   0.001   TYR R 199 
 PHE   0.017   0.002   PHE B 199 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 6757)
  covalent geometry    : angle       0.50326 ( 9226)
  SS BOND              : bond        0.00184 (    1)
  SS BOND              : angle       0.10533 (    2)
  hydrogen bonds       : bond        0.03928 (  391)
  hydrogen bonds       : angle       4.04016 ( 1137)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  343 ASP cc_start: 0.8091 (m-30) cc_final: 0.7789 (m-30)
REVERT: B   59 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.8136 (m-80)
REVERT: B  117 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8067 (tt)
REVERT: R  140 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7740 (mttm)
REVERT: R  231 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.8042 (mp10)
  outliers start: 11
  outliers final: 7
  residues processed: 89
  average time/residue: 0.0755
  time to fit residues: 9.4595
Evaluate side-chains
  91 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  231 GLN
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0870
   chunk 60 optimal weight:    0.0470
   overall best weight:    0.5456

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.134143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.115321 restraints weight = 10281.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 2.22
r_work: 0.3275 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3297
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3297 r_free = 0.3297    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3297 r_free = 0.3297    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3297
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6758  Z= 0.122
  Angle     :  0.476   6.208   9228  Z= 0.261
  Chirality :  0.040   0.177   1099
  Planarity :  0.003   0.034   1163
  Dihedral  :  4.404  27.147    969
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.59 %
    Favored  : 82.68 %
  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:  1.15 (0.29), residues: 877
  helix:  2.54 (0.26), residues: 392
  sheet: -0.30 (0.37), residues: 186
  loop : -0.97 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 228 
 TYR   0.011   0.001   TYR R 199 
 PHE   0.016   0.001   PHE B 199 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6757)
  covalent geometry    : angle       0.47568 ( 9226)
  SS BOND              : bond        0.00158 (    1)
  SS BOND              : angle       0.08284 (    2)
  hydrogen bonds       : bond        0.03679 (  391)
  hydrogen bonds       : angle       3.96846 ( 1137)

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

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

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1754 Ramachandran restraints generated.
    877 Oldfield, 0 Emsley, 877 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  343 ASP cc_start: 0.8040 (m-30) cc_final: 0.7754 (m-30)
REVERT: B   59 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.8022 (m-80)
REVERT: B  117 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8034 (tt)
REVERT: R  231 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8026 (mp10)
REVERT: R  279 MET cc_start: 0.8107 (mmp) cc_final: 0.7850 (mmp)
  outliers start: 11
  outliers final: 7
  residues processed: 90
  average time/residue: 0.0766
  time to fit residues: 9.7273
Evaluate side-chains
  93 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain G residue   16 VAL
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  231 GLN
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 59 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 82 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
R 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.133212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.114458 restraints weight = 10210.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 2.19
r_work: 0.3269 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3290
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3290
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6758  Z= 0.149
  Angle     :  0.489   6.522   9228  Z= 0.269
  Chirality :  0.040   0.179   1099
  Planarity :  0.003   0.034   1163
  Dihedral  :  4.432  27.184    969
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.75 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.29), residues: 877
  helix:  2.51 (0.26), residues: 392
  sheet: -0.31 (0.36), residues: 186
  loop : -0.97 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 231 
 TYR   0.011   0.001   TYR R 199 
 PHE   0.016   0.001   PHE B 199 
 TRP   0.012   0.001   TRP B 211 
 HIS   0.003   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6757)
  covalent geometry    : angle       0.48939 ( 9226)
  SS BOND              : bond        0.00172 (    1)
  SS BOND              : angle       0.07609 (    2)
  hydrogen bonds       : bond        0.03766 (  391)
  hydrogen bonds       : angle       3.98464 ( 1137)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1712.37 seconds
wall clock time: 30 minutes 12.88 seconds (1812.88 seconds total)