Starting phenix.real_space_refine
on Mon Apr 28 21:03:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lgm_63068/04_2025/9lgm_63068.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lgm_63068/04_2025/9lgm_63068.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lgm_63068/04_2025/9lgm_63068.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lgm_63068/04_2025/9lgm_63068.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lgm_63068/04_2025/9lgm_63068.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lgm_63068/04_2025/9lgm_63068.cif"
  }
  resolution = 2.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.019
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      50      5.16       5
     C    5107      2.51       5
     N    1395      2.21       5
     O    1509      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8061
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1919
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1919
          Classifications: {'peptide': 239}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 6, 'TRANS': 232}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 59
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 32
    Chain: "B"
      Number of atoms: 2533
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2533
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 79
          Unresolved non-hydrogen dihedrals: 55
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 8, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 55
    Chain: "C"
      Number of atoms: 393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 393
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "N"
      Number of atoms: 963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 963
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "R"
      Number of atoms: 2253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2253
          Classifications: {'peptide': 289}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 12, 'TRANS': 276}
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 110
          Unresolved non-hydrogen dihedrals: 81
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 65
  Time building chain proxies: 5.23, per 1000 atoms: 0.65
  Number of scatterers: 8061
  At special positions: 0
  Unit cell: (75.92, 100.88, 131.04, 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      50     16.00
     O    1509      8.00
     N    1395      7.00
     C    5107      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  90 " - pdb=" SG  CYS R 168 " 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: 1.97
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1968

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 11 sheets defined
      44.5% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 39
    Processing helix  chain 'A' and resid 52 through 60
      removed outlier: 3.514A  pdb=" N   MET A  60 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 238
      removed outlier: 3.510A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 269
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 297 through 302
      removed outlier: 4.175A  pdb=" N   TYR A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 308
      removed outlier: 3.550A  pdb=" N   ALA A 306 " --> pdb=" O   PRO A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 342
      removed outlier: 3.502A  pdb=" N   PHE A 335 " --> pdb=" O   ILE A 331 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   SER A 342 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 381
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.501A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 24
      removed outlier: 3.600A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 45 through 48
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.712A  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 18 through 48
      removed outlier: 3.746A  pdb=" N   LEU R  32 " --> pdb=" O   ILE R  28 " (cutoff:3.500A)
      Proline residue:  R  33  - end of helix
    Processing helix  chain 'R' and resid 50 through 80
      removed outlier: 4.070A  pdb=" N   VAL R  54 " --> pdb=" O   ASN R  50 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   TYR R  55 " --> pdb=" O   GLU R  51 " (cutoff:3.500A)
      Proline residue:  R  71  - end of helix
    Processing helix  chain 'R' and resid 86 through 121
      removed outlier: 5.027A  pdb=" N   ILE R 101 " --> pdb=" O   PHE R  97 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   TYR R 102 " --> pdb=" O   TYR R  98 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 130 through 150
    Processing helix  chain 'R' and resid 150 through 155
    Processing helix  chain 'R' and resid 155 through 163
    Processing helix  chain 'R' and resid 175 through 189
      removed outlier: 3.857A  pdb=" N   TRP R 180 " --> pdb=" O   GLY R 176 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 190 through 211
    Processing helix  chain 'R' and resid 215 through 254
      removed outlier: 3.777A  pdb=" N   VAL R 233 " --> pdb=" O   LEU R 229 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU R 234 " --> pdb=" O   ILE R 230 " (cutoff:3.500A)
      Proline residue:  R 239  - end of helix
    Processing helix  chain 'R' and resid 258 through 276
      removed outlier: 4.235A  pdb=" N   SER R 266 " --> pdb=" O   GLU R 262 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   ALA R 267 " --> pdb=" O   ARG R 263 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   SER R 276 " --> pdb=" O   LEU R 272 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 277 through 287
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 290 through 300
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.482A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 7.644A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.443A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   PHE A 280 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ASN A 282 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.642A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.649A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.678A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.758A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.039A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.515A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 7.149A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.032A  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: 4.495A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.410A  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: 6.644A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.661A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.498A  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: 6.865A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 18 through 19

    439 hydrogen bonds defined for protein.
    1254 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.33

  Time building geometry restraints manager: 2.35 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: 2664
        1.34 -     1.46: 1586
        1.46 -     1.58: 3921
        1.58 -     1.69: 0
        1.69 -     1.81: 67
  Bond restraints: 8238
  Sorted by residual:
  bond pdb=" C   LEU R  70 "
       pdb=" N   PRO R  71 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.025 1.28e-02 6.10e+03 3.71e+00
  bond pdb=" C   VAL R 188 "
       pdb=" O   VAL R 188 "
    ideal  model  delta    sigma   weight residual
    1.242  1.230  0.012 1.17e-02 7.31e+03 1.12e+00
  bond pdb=" CB  GLU A 289 "
       pdb=" CG  GLU A 289 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.07e+00
  bond pdb=" CG  ARG A  38 "
       pdb=" CD  ARG A  38 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.031 3.00e-02 1.11e+03 1.05e+00
  bond pdb=" N   PHE R 169 "
       pdb=" CA  PHE R 169 "
    ideal  model  delta    sigma   weight residual
    1.457  1.469 -0.012 1.29e-02 6.01e+03 8.73e-01
  ... (remaining 8233 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 10996
        1.79 -     3.59: 160
        3.59 -     5.38: 36
        5.38 -     7.17: 11
        7.17 -     8.97: 1
  Bond angle restraints: 11204
  Sorted by residual:
  angle pdb=" C   HIS R  80 "
        pdb=" CA  HIS R  80 "
        pdb=" CB  HIS R  80 "
      ideal   model   delta    sigma   weight residual
     115.79  109.09    6.70 1.19e+00 7.06e-01 3.17e+01
  angle pdb=" N   VAL R 280 "
        pdb=" CA  VAL R 280 "
        pdb=" C   VAL R 280 "
      ideal   model   delta    sigma   weight residual
     111.81  108.32    3.49 8.60e-01 1.35e+00 1.65e+01
  angle pdb=" N   ILE A  62 "
        pdb=" CA  ILE A  62 "
        pdb=" C   ILE A  62 "
      ideal   model   delta    sigma   weight residual
     112.96  109.49    3.47 1.00e+00 1.00e+00 1.21e+01
  angle pdb=" N   ARG A  38 "
        pdb=" CA  ARG A  38 "
        pdb=" CB  ARG A  38 "
      ideal   model   delta    sigma   weight residual
     110.16  114.57   -4.41 1.48e+00 4.57e-01 8.87e+00
  angle pdb=" C   PHE R 169 "
        pdb=" CA  PHE R 169 "
        pdb=" CB  PHE R 169 "
      ideal   model   delta    sigma   weight residual
     110.42  115.64   -5.22 1.99e+00 2.53e-01 6.89e+00
  ... (remaining 11199 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 4251
       17.92 -    35.85: 420
       35.85 -    53.77: 137
       53.77 -    71.70: 30
       71.70 -    89.62: 10
  Dihedral angle restraints: 4848
    sinusoidal: 1798
      harmonic: 3050
  Sorted by residual:
  dihedral pdb=" CB  CYS R  90 "
           pdb=" SG  CYS R  90 "
           pdb=" SG  CYS R 168 "
           pdb=" CB  CYS R 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -175.62   89.62     1      1.00e+01 1.00e-02 9.54e+01
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.72   18.28     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  PHE B 151 "
           pdb=" C   PHE B 151 "
           pdb=" N   LEU B 152 "
           pdb=" CA  LEU B 152 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.08   17.92     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 4845 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 814
       0.034 -    0.067: 310
       0.067 -    0.101: 106
       0.101 -    0.135: 35
       0.135 -    0.169: 1
  Chirality restraints: 1266
  Sorted by residual:
  chirality pdb=" CB  ILE R 232 "
            pdb=" CA  ILE R 232 "
            pdb=" CG1 ILE R 232 "
            pdb=" CG2 ILE R 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.81   -0.17 2.00e-01 2.50e+01 7.11e-01
  chirality pdb=" CA  ILE B 273 "
            pdb=" N   ILE B 273 "
            pdb=" C   ILE B 273 "
            pdb=" CB  ILE B 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.24e-01
  chirality pdb=" CA  PRO B 236 "
            pdb=" N   PRO B 236 "
            pdb=" C   PRO B 236 "
            pdb=" CB  PRO B 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.22e-01
  ... (remaining 1263 not shown)

  Planarity restraints: 1444
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.035 5.00e-02 4.00e+02   5.31e-02 4.50e+00
        pdb=" N   PRO B 236 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 196 "    0.011 2.00e-02 2.50e+03   2.11e-02 4.46e+00
        pdb=" C   THR B 196 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   THR B 196 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ARG B 197 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 159 "   -0.005 2.00e-02 2.50e+03   1.32e-02 3.05e+00
        pdb=" CG  PHE R 159 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 159 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 159 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 159 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 159 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 159 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1441 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 80
        2.60 -     3.18: 7063
        3.18 -     3.75: 13399
        3.75 -     4.33: 18867
        4.33 -     4.90: 30843
  Nonbonded interactions: 70252
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 313 "
            pdb=" N   ARG B 314 "
     model   vdw
     2.028 3.120
  nonbonded pdb=" OD1 ASN A 269 "
            pdb=" OD2 ASP N 106 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" NH2 ARG A 232 "
            pdb=" OD1 ASP B 228 "
     model   vdw
     2.162 3.120
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" CD1 ILE R 101 "
            pdb=" CG2 THR R 275 "
     model   vdw
     2.224 3.880
  ... (remaining 70247 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.770
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.230
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
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      :  0.004   0.031   8239  Z= 0.176
  Angle     :  0.605   8.967  11206  Z= 0.327
  Chirality :  0.042   0.169   1266
  Planarity :  0.004   0.053   1444
  Dihedral  : 16.710  88.756   2877
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 26.43 %
    Favored  : 73.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.27), residues: 1037
  helix:  1.91 (0.25), residues: 408
  sheet: -0.44 (0.35), residues: 231
  loop : -0.54 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 234 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.027   0.002   PHE R 159 
 TYR   0.009   0.001   TYR A 329 
 ARG   0.014   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18218 (  439)
  hydrogen bonds       : angle       6.52562 ( 1254)
  SS BOND              : bond        0.00048 (    1)
  SS BOND              : angle       0.74864 (    2)
  covalent geometry    : bond        0.00398 ( 8238)
  covalent geometry    : angle       0.60544 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 183
  time to evaluate  : 0.870 
Fit side-chains
REVERT: A   38 ARG cc_start: 0.7101 (mpp80) cc_final: 0.6771 (mpp80)
REVERT: A  252 ASP cc_start: 0.8095 (t70) cc_final: 0.7834 (t70)
REVERT: A  312 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6911 (mm-30)
REVERT: R  209 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7497 (ttp80)
REVERT: R  277 LEU cc_start: 0.8190 (mm) cc_final: 0.7892 (mt)
  outliers start: 2
  outliers final: 6
  residues processed: 185
  average time/residue: 1.5310
  time to fit residues: 298.5572
Evaluate side-chains
  179 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 173
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  313 ASN
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue  101 ILE
Chi-restraints excluded: chain R residue  250 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 79 optimal weight:    0.3980
   chunk 30 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 91 optimal weight:    0.1980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 ASN
R  58 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.124510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.109185 restraints weight = 11301.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 1.74
r_work: 0.3276 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   8239  Z= 0.215
  Angle     :  0.582   6.805  11206  Z= 0.309
  Chirality :  0.044   0.164   1266
  Planarity :  0.004   0.054   1444
  Dihedral  :  5.295  53.805   1149
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 21.31 %
    Favored  : 73.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.26), residues: 1037
  helix:  2.06 (0.25), residues: 413
  sheet: -0.74 (0.32), residues: 229
  loop : -0.46 (0.32), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 234 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.016   0.002   PHE R 107 
 TYR   0.014   0.001   TYR A 329 
 ARG   0.007   0.001   ARG A 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04825 (  439)
  hydrogen bonds       : angle       4.91757 ( 1254)
  SS BOND              : bond        0.00161 (    1)
  SS BOND              : angle       0.54413 (    2)
  covalent geometry    : bond        0.00500 ( 8238)
  covalent geometry    : angle       0.58219 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 204
  time to evaluate  : 1.338 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7274 (mp-120)
REVERT: A   34 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8187 (tttp)
REVERT: A  269 ASN cc_start: 0.8356 (t0) cc_final: 0.8074 (t160)
REVERT: A  312 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7215 (mm-30)
REVERT: A  368 ASP cc_start: 0.7985 (m-30) cc_final: 0.7754 (m-30)
REVERT: A  370 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7514 (ttp80)
REVERT: B   59 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.6888 (m-80)
REVERT: B  215 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6777 (mp0)
REVERT: N   39 GLN cc_start: 0.8617 (tt0) cc_final: 0.8332 (tp40)
REVERT: N  108 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7211 (m-80)
REVERT: R   49 ARG cc_start: 0.7746 (mmp-170) cc_final: 0.7373 (mmp-170)
REVERT: R  174 MET cc_start: 0.6973 (tpt) cc_final: 0.6615 (mmm)
REVERT: R  209 ARG cc_start: 0.8396 (ttp80) cc_final: 0.7909 (ttp80)
REVERT: R  277 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8040 (mt)
  outliers start: 43
  outliers final: 16
  residues processed: 228
  average time/residue: 1.2977
  time to fit residues: 312.5973
Evaluate side-chains
  219 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 196
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  370 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  130 ARG
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  244 LEU
Chi-restraints excluded: chain R residue  275 THR
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 84 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.124915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.109592 restraints weight = 11410.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.74
r_work: 0.3274 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.1302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8239  Z= 0.192
  Angle     :  0.554   6.764  11206  Z= 0.293
  Chirality :  0.043   0.141   1266
  Planarity :  0.004   0.053   1444
  Dihedral  :  4.870  50.903   1141
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 21.19 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.27), residues: 1037
  helix:  2.12 (0.25), residues: 414
  sheet: -0.64 (0.33), residues: 232
  loop : -0.38 (0.33), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 234 
 HIS   0.011   0.001   HIS A 220 
 PHE   0.018   0.002   PHE R 159 
 TYR   0.016   0.001   TYR A 329 
 ARG   0.008   0.001   ARG A 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04363 (  439)
  hydrogen bonds       : angle       4.77722 ( 1254)
  SS BOND              : bond        0.00170 (    1)
  SS BOND              : angle       0.52993 (    2)
  covalent geometry    : bond        0.00450 ( 8238)
  covalent geometry    : angle       0.55421 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 202
  time to evaluate  : 0.985 
Fit side-chains
REVERT: A   31 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7295 (mp-120)
REVERT: A  223 ASP cc_start: 0.8096 (t0) cc_final: 0.7790 (t70)
REVERT: A  269 ASN cc_start: 0.8362 (t0) cc_final: 0.8080 (t160)
REVERT: A  312 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7189 (mm-30)
REVERT: A  320 GLU cc_start: 0.8153 (tt0) cc_final: 0.7799 (tt0)
REVERT: A  328 LYS cc_start: 0.8324 (mtpt) cc_final: 0.8040 (mtmm)
REVERT: B   15 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7659 (mptp)
REVERT: B   59 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7028 (m-80)
REVERT: B  215 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6704 (mp0)
REVERT: B  336 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8192 (mt)
REVERT: B  340 ASN cc_start: 0.8121 (t0) cc_final: 0.7899 (t0)
REVERT: N  108 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7164 (m-80)
REVERT: R  174 MET cc_start: 0.6965 (tpt) cc_final: 0.6643 (mmm)
REVERT: R  209 ARG cc_start: 0.8390 (ttp80) cc_final: 0.7924 (ttp80)
REVERT: R  277 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8008 (mt)
  outliers start: 51
  outliers final: 24
  residues processed: 230
  average time/residue: 1.3327
  time to fit residues: 323.9566
Evaluate side-chains
  230 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 199
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ASP
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue  101 ILE
Chi-restraints excluded: chain R residue  130 ARG
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain R residue  275 THR
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 92 optimal weight:    0.4980
   chunk 63 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 62 optimal weight:    0.3980
   chunk 32 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0870
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 GLN
** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.126035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.110700 restraints weight = 11443.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 1.75
r_work: 0.3292 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8239  Z= 0.142
  Angle     :  0.523   6.729  11206  Z= 0.277
  Chirality :  0.041   0.133   1266
  Planarity :  0.004   0.052   1444
  Dihedral  :  4.698  46.951   1141
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  5.95 %
    Allowed  : 22.14 %
    Favored  : 71.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.27), residues: 1037
  helix:  2.27 (0.25), residues: 413
  sheet: -0.65 (0.34), residues: 218
  loop : -0.42 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.010   0.001   HIS A 220 
 PHE   0.020   0.001   PHE R 159 
 TYR   0.016   0.001   TYR R 268 
 ARG   0.008   0.001   ARG R 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03919 (  439)
  hydrogen bonds       : angle       4.57669 ( 1254)
  SS BOND              : bond        0.00060 (    1)
  SS BOND              : angle       0.29355 (    2)
  covalent geometry    : bond        0.00327 ( 8238)
  covalent geometry    : angle       0.52258 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 201
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7324 (mp-120)
REVERT: A   34 LYS cc_start: 0.8468 (tttm) cc_final: 0.8220 (tttm)
REVERT: A  223 ASP cc_start: 0.8087 (t0) cc_final: 0.7782 (t70)
REVERT: A  283 LYS cc_start: 0.8123 (mttt) cc_final: 0.7896 (mttt)
REVERT: A  312 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7165 (mm-30)
REVERT: A  328 LYS cc_start: 0.8331 (mtpt) cc_final: 0.8031 (mtmm)
REVERT: A  337 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7502 (ttm170)
REVERT: A  358 ASP cc_start: 0.8065 (t70) cc_final: 0.7756 (t0)
REVERT: B   10 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6981 (tm-30)
REVERT: B   15 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7663 (mptp)
REVERT: B   57 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8455 (pttt)
REVERT: B   59 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7039 (m-80)
REVERT: B  212 ASP cc_start: 0.8097 (t70) cc_final: 0.7075 (t70)
REVERT: B  215 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6677 (mp0)
REVERT: B  336 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8137 (mt)
REVERT: N   39 GLN cc_start: 0.8557 (tt0) cc_final: 0.8312 (tp40)
REVERT: R   49 ARG cc_start: 0.7788 (mmp-170) cc_final: 0.7545 (mmp-170)
  outliers start: 50
  outliers final: 26
  residues processed: 226
  average time/residue: 1.4567
  time to fit residues: 347.0314
Evaluate side-chains
  239 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 205
  time to evaluate  : 1.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   77 PHE
Chi-restraints excluded: chain R residue  101 ILE
Chi-restraints excluded: chain R residue  130 ARG
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  275 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 91 optimal weight:    0.6980
   chunk 73 optimal weight:    0.3980
   chunk 8 optimal weight:    0.6980
   chunk 90 optimal weight:    0.6980
   chunk 31 optimal weight:    0.4980
   chunk 18 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
B 340 ASN
N  31 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.125403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.110235 restraints weight = 11360.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.69
r_work: 0.3294 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3155 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8239  Z= 0.163
  Angle     :  0.534   6.728  11206  Z= 0.281
  Chirality :  0.042   0.133   1266
  Planarity :  0.004   0.052   1444
  Dihedral  :  4.677  46.257   1141
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 23.33 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.27), residues: 1037
  helix:  2.28 (0.25), residues: 413
  sheet: -0.69 (0.34), residues: 220
  loop : -0.39 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.010   0.001   HIS A 220 
 PHE   0.019   0.002   PHE R 159 
 TYR   0.029   0.002   TYR R 268 
 ARG   0.008   0.001   ARG A 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03947 (  439)
  hydrogen bonds       : angle       4.52226 ( 1254)
  SS BOND              : bond        0.00108 (    1)
  SS BOND              : angle       0.27501 (    2)
  covalent geometry    : bond        0.00378 ( 8238)
  covalent geometry    : angle       0.53451 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 197
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7553 (mm-30)
REVERT: A   31 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7426 (mp-120)
REVERT: A   34 LYS cc_start: 0.8501 (tttm) cc_final: 0.8238 (tttm)
REVERT: A  223 ASP cc_start: 0.8085 (t0) cc_final: 0.7798 (t70)
REVERT: A  312 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7130 (mm-30)
REVERT: A  328 LYS cc_start: 0.8341 (mtpt) cc_final: 0.8032 (mtmm)
REVERT: A  337 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7470 (ttm170)
REVERT: A  358 ASP cc_start: 0.8031 (t70) cc_final: 0.7729 (t0)
REVERT: B   10 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6985 (tm-30)
REVERT: B   15 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7663 (mptp)
REVERT: B   59 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.6878 (m-80)
REVERT: B   75 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7843 (tp40)
REVERT: B  215 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6630 (mp0)
REVERT: B  336 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8271 (mt)
REVERT: N   39 GLN cc_start: 0.8573 (tt0) cc_final: 0.8331 (tp40)
REVERT: N  108 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7312 (m-80)
REVERT: R   49 ARG cc_start: 0.7785 (mmp-170) cc_final: 0.7555 (mmp-170)
REVERT: R  170 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6601 (tm-30)
REVERT: R  174 MET cc_start: 0.6729 (mmm) cc_final: 0.6508 (mmt)
  outliers start: 49
  outliers final: 25
  residues processed: 225
  average time/residue: 1.3847
  time to fit residues: 328.7128
Evaluate side-chains
  230 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 196
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   77 PHE
Chi-restraints excluded: chain R residue  101 ILE
Chi-restraints excluded: chain R residue  130 ARG
Chi-restraints excluded: chain R residue  170 GLU
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  275 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 57 optimal weight:    0.5980
   chunk 91 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A  50 ASN
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 347 HIS
** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
R 290 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.124218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.108999 restraints weight = 11316.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 1.69
r_work: 0.3272 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.1696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8239  Z= 0.214
  Angle     :  0.567   6.765  11206  Z= 0.299
  Chirality :  0.043   0.139   1266
  Planarity :  0.004   0.053   1444
  Dihedral  :  4.792  45.111   1141
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 23.45 %
    Favored  : 70.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.27), residues: 1037
  helix:  2.20 (0.25), residues: 413
  sheet: -0.75 (0.34), residues: 220
  loop : -0.41 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 234 
 HIS   0.010   0.001   HIS A 220 
 PHE   0.019   0.002   PHE R 159 
 TYR   0.026   0.002   TYR R 268 
 ARG   0.006   0.000   ARG A 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04181 (  439)
  hydrogen bonds       : angle       4.61318 ( 1254)
  SS BOND              : bond        0.00158 (    1)
  SS BOND              : angle       0.34534 (    2)
  covalent geometry    : bond        0.00503 ( 8238)
  covalent geometry    : angle       0.56739 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 202
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7385 (mp-120)
REVERT: A   34 LYS cc_start: 0.8501 (tttm) cc_final: 0.8261 (tttm)
REVERT: A   50 ASN cc_start: 0.7249 (OUTLIER) cc_final: 0.7013 (p0)
REVERT: A  211 LYS cc_start: 0.8430 (mtmm) cc_final: 0.8079 (mtmm)
REVERT: A  223 ASP cc_start: 0.8106 (t0) cc_final: 0.7805 (t70)
REVERT: A  283 LYS cc_start: 0.8231 (mttt) cc_final: 0.7982 (mttt)
REVERT: A  312 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7094 (mm-30)
REVERT: A  328 LYS cc_start: 0.8352 (mtpt) cc_final: 0.8040 (mtmm)
REVERT: A  337 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7501 (ttm170)
REVERT: A  358 ASP cc_start: 0.8045 (t70) cc_final: 0.7714 (t0)
REVERT: B   10 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7000 (tm-30)
REVERT: B   15 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7647 (mptp)
REVERT: B   59 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.6947 (m-80)
REVERT: B   75 GLN cc_start: 0.8431 (mm-40) cc_final: 0.7881 (tp40)
REVERT: B  212 ASP cc_start: 0.8096 (t70) cc_final: 0.7086 (t70)
REVERT: B  215 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6880 (mp0)
REVERT: B  336 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8274 (mt)
REVERT: N  108 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7402 (m-80)
REVERT: R  170 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6671 (tm-30)
REVERT: R  174 MET cc_start: 0.6766 (mmm) cc_final: 0.6524 (mmt)
REVERT: R  277 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8032 (mt)
  outliers start: 52
  outliers final: 26
  residues processed: 230
  average time/residue: 1.2735
  time to fit residues: 309.0581
Evaluate side-chains
  235 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 198
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   50 ASN
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   77 PHE
Chi-restraints excluded: chain R residue  101 ILE
Chi-restraints excluded: chain R residue  130 ARG
Chi-restraints excluded: chain R residue  170 GLU
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  275 THR
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 55 optimal weight:    0.5980
   chunk 68 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 96 optimal weight:    0.6980
   chunk 95 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  50 ASN
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 347 HIS
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.124623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.109412 restraints weight = 11350.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 1.69
r_work: 0.3287 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8239  Z= 0.185
  Angle     :  0.558   7.973  11206  Z= 0.293
  Chirality :  0.042   0.137   1266
  Planarity :  0.004   0.053   1444
  Dihedral  :  4.745  44.358   1141
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 23.81 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.27), residues: 1037
  helix:  2.13 (0.25), residues: 416
  sheet: -0.75 (0.34), residues: 220
  loop : -0.37 (0.33), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 234 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.025   0.002   PHE R 159 
 TYR   0.024   0.002   TYR R 268 
 ARG   0.008   0.000   ARG A 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04044 (  439)
  hydrogen bonds       : angle       4.57378 ( 1254)
  SS BOND              : bond        0.00092 (    1)
  SS BOND              : angle       0.34874 (    2)
  covalent geometry    : bond        0.00435 ( 8238)
  covalent geometry    : angle       0.55771 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 193
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7368 (mp-120)
REVERT: A   34 LYS cc_start: 0.8502 (tttm) cc_final: 0.8242 (tttm)
REVERT: A   50 ASN cc_start: 0.7555 (OUTLIER) cc_final: 0.7288 (p0)
REVERT: A  223 ASP cc_start: 0.8083 (t0) cc_final: 0.7776 (t70)
REVERT: A  245 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8155 (mp)
REVERT: A  312 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7105 (mm-30)
REVERT: A  328 LYS cc_start: 0.8361 (mtpt) cc_final: 0.8053 (mtmm)
REVERT: A  337 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7469 (ttm170)
REVERT: A  358 ASP cc_start: 0.8029 (t70) cc_final: 0.7707 (t0)
REVERT: B   10 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7005 (tm-30)
REVERT: B   15 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7666 (mptp)
REVERT: B   57 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8392 (pttt)
REVERT: B   59 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.6858 (m-80)
REVERT: B   75 GLN cc_start: 0.8420 (mm-40) cc_final: 0.7824 (tp40)
REVERT: B  215 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6769 (mp0)
REVERT: B  336 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8266 (mt)
REVERT: N   39 GLN cc_start: 0.8593 (tt0) cc_final: 0.8382 (tp40)
REVERT: N  108 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7360 (m-80)
REVERT: R  170 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6656 (tm-30)
  outliers start: 52
  outliers final: 25
  residues processed: 219
  average time/residue: 1.3198
  time to fit residues: 304.6011
Evaluate side-chains
  231 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 194
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue   50 ASN
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  379 ARG
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   77 PHE
Chi-restraints excluded: chain R residue  130 ARG
Chi-restraints excluded: chain R residue  170 GLU
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  275 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 76 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 72 optimal weight:    0.7980
   chunk 37 optimal weight:    0.4980
   chunk 83 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A  50 ASN
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 347 HIS
B  88 ASN
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
R  85 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.124912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.109959 restraints weight = 11453.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 1.67
r_work: 0.3286 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.1804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8239  Z= 0.178
  Angle     :  0.562   8.567  11206  Z= 0.296
  Chirality :  0.042   0.183   1266
  Planarity :  0.004   0.052   1444
  Dihedral  :  4.727  43.622   1141
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 24.76 %
    Favored  : 69.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.27), residues: 1037
  helix:  2.14 (0.25), residues: 416
  sheet: -0.76 (0.34), residues: 220
  loop : -0.38 (0.33), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.018   0.002   PHE R 159 
 TYR   0.024   0.002   TYR R 268 
 ARG   0.007   0.000   ARG A 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04013 (  439)
  hydrogen bonds       : angle       4.55640 ( 1254)
  SS BOND              : bond        0.00102 (    1)
  SS BOND              : angle       0.20696 (    2)
  covalent geometry    : bond        0.00419 ( 8238)
  covalent geometry    : angle       0.56156 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 194
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7466 (mp-120)
REVERT: A   34 LYS cc_start: 0.8509 (tttm) cc_final: 0.8248 (tttm)
REVERT: A  223 ASP cc_start: 0.8091 (t0) cc_final: 0.7785 (t70)
REVERT: A  245 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8151 (mp)
REVERT: A  283 LYS cc_start: 0.8173 (mttt) cc_final: 0.7959 (mttt)
REVERT: A  312 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7107 (mm-30)
REVERT: A  328 LYS cc_start: 0.8343 (mtpt) cc_final: 0.8035 (mtmm)
REVERT: A  337 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7468 (ttm170)
REVERT: A  358 ASP cc_start: 0.8026 (t70) cc_final: 0.7719 (t0)
REVERT: B   10 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7038 (tm-30)
REVERT: B   15 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7688 (mptp)
REVERT: B   57 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8393 (pttt)
REVERT: B   59 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.6900 (m-80)
REVERT: B   75 GLN cc_start: 0.8453 (mm-40) cc_final: 0.7881 (tp40)
REVERT: B  212 ASP cc_start: 0.8079 (t70) cc_final: 0.6981 (t70)
REVERT: B  215 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6736 (mp0)
REVERT: B  336 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8276 (mt)
REVERT: N   39 GLN cc_start: 0.8593 (tt0) cc_final: 0.8379 (tp40)
REVERT: R   72 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7884 (tt)
REVERT: R  170 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6641 (tm-30)
  outliers start: 45
  outliers final: 27
  residues processed: 217
  average time/residue: 1.3773
  time to fit residues: 314.8630
Evaluate side-chains
  231 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 193
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  371 ASP
Chi-restraints excluded: chain A residue  379 ARG
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   57 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   59 SER
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   72 LEU
Chi-restraints excluded: chain R residue   77 PHE
Chi-restraints excluded: chain R residue  130 ARG
Chi-restraints excluded: chain R residue  170 GLU
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  275 THR
Chi-restraints excluded: chain R residue  290 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 95 optimal weight:    0.0770
   chunk 54 optimal weight:    0.9980
   chunk 62 optimal weight:    0.4980
   chunk 5 optimal weight:    0.0970
   chunk 99 optimal weight:    0.9990
   chunk 97 optimal weight:    0.6980
   chunk 85 optimal weight:    0.7980
   chunk 88 optimal weight:    6.9990
   chunk 73 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.3736

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 GLN
B  44 GLN
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
N  31 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.126502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.111503 restraints weight = 11613.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 1.71
r_work: 0.3315 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8239  Z= 0.133
  Angle     :  0.536   6.660  11206  Z= 0.283
  Chirality :  0.041   0.189   1266
  Planarity :  0.004   0.051   1444
  Dihedral  :  4.550  42.340   1141
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 25.00 %
    Favored  : 69.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.27), residues: 1037
  helix:  2.14 (0.25), residues: 422
  sheet: -0.65 (0.34), residues: 216
  loop : -0.44 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.026   0.001   PHE R 159 
 TYR   0.023   0.001   TYR R 268 
 ARG   0.006   0.000   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03729 (  439)
  hydrogen bonds       : angle       4.44218 ( 1254)
  SS BOND              : bond        0.00031 (    1)
  SS BOND              : angle       0.36837 (    2)
  covalent geometry    : bond        0.00307 ( 8238)
  covalent geometry    : angle       0.53578 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 195
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7433 (mp-120)
REVERT: A  223 ASP cc_start: 0.8128 (t0) cc_final: 0.7794 (t70)
REVERT: A  245 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8117 (mp)
REVERT: A  312 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7098 (mm-30)
REVERT: A  337 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7369 (ttm170)
REVERT: A  358 ASP cc_start: 0.7983 (t70) cc_final: 0.7682 (t0)
REVERT: B   10 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7050 (tm-30)
REVERT: B   15 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7671 (mptp)
REVERT: B   59 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.6887 (m-80)
REVERT: B   75 GLN cc_start: 0.8413 (mm-40) cc_final: 0.7838 (tp40)
REVERT: B  215 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6563 (mp0)
REVERT: B  251 ARG cc_start: 0.8578 (mtt90) cc_final: 0.8319 (mtt180)
REVERT: B  258 ASP cc_start: 0.7509 (t0) cc_final: 0.7172 (t0)
REVERT: B  285 LEU cc_start: 0.8462 (tp) cc_final: 0.8257 (tp)
REVERT: B  336 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8289 (mt)
REVERT: R  170 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6522 (tm-30)
REVERT: R  191 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7928 (tp)
REVERT: R  232 ILE cc_start: 0.8397 (tt) cc_final: 0.8193 (tt)
  outliers start: 43
  outliers final: 19
  residues processed: 219
  average time/residue: 1.2483
  time to fit residues: 288.6325
Evaluate side-chains
  216 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 187
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  337 ARG
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   77 PHE
Chi-restraints excluded: chain R residue  130 ARG
Chi-restraints excluded: chain R residue  170 GLU
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  275 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 64 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0770
   chunk 78 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0970
   chunk 89 optimal weight:    0.3980
   chunk 73 optimal weight:    0.0070
   chunk 3 optimal weight:    0.3980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.1954

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A 284 GLN
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 239 ASN
B 295 ASN
N  31 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.128381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.113789 restraints weight = 11354.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 1.67
r_work: 0.3349 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8239  Z= 0.115
  Angle     :  0.535   9.319  11206  Z= 0.279
  Chirality :  0.041   0.191   1266
  Planarity :  0.004   0.050   1444
  Dihedral  :  4.405  40.419   1141
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 25.48 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.27), residues: 1037
  helix:  2.21 (0.25), residues: 427
  sheet: -0.51 (0.34), residues: 214
  loop : -0.45 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.015   0.001   PHE R 159 
 TYR   0.024   0.001   TYR R 268 
 ARG   0.006   0.000   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03552 (  439)
  hydrogen bonds       : angle       4.35458 ( 1254)
  SS BOND              : bond        0.00029 (    1)
  SS BOND              : angle       0.28603 (    2)
  covalent geometry    : bond        0.00262 ( 8238)
  covalent geometry    : angle       0.53545 (11204)

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

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

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2074 Ramachandran restraints generated.
    1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 204
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7453 (mp-120)
REVERT: A   32 LYS cc_start: 0.8553 (ttmt) cc_final: 0.8330 (ttmm)
REVERT: A  223 ASP cc_start: 0.8026 (t0) cc_final: 0.7678 (t70)
REVERT: A  245 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8099 (mp)
REVERT: A  283 LYS cc_start: 0.7868 (mttt) cc_final: 0.7633 (mttt)
REVERT: A  312 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7101 (mm-30)
REVERT: A  358 ASP cc_start: 0.7946 (t70) cc_final: 0.7687 (t0)
REVERT: B   10 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7077 (tm-30)
REVERT: B   15 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7656 (mptp)
REVERT: B   59 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.6885 (m-80)
REVERT: B   75 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7839 (tp40)
REVERT: B  212 ASP cc_start: 0.7999 (t70) cc_final: 0.6587 (t70)
REVERT: B  215 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6057 (mp0)
REVERT: B  251 ARG cc_start: 0.8520 (mtt90) cc_final: 0.8281 (mtt180)
REVERT: B  259 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7923 (tt0)
REVERT: B  336 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8271 (mt)
REVERT: R  170 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6411 (tm-30)
REVERT: R  174 MET cc_start: 0.6769 (mmt) cc_final: 0.6555 (mmt)
REVERT: R  191 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7887 (tp)
  outliers start: 38
  outliers final: 18
  residues processed: 226
  average time/residue: 1.2686
  time to fit residues: 303.1865
Evaluate side-chains
  231 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 203
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 GLU
Chi-restraints excluded: chain A residue   31 GLN
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  314 ARG
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   37 LEU
Chi-restraints excluded: chain R residue   51 GLU
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   77 PHE
Chi-restraints excluded: chain R residue  130 ARG
Chi-restraints excluded: chain R residue  170 GLU
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  275 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 77 optimal weight:    0.2980
   chunk 92 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 93 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 GLN
** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 380 GLN
B  13 GLN
B 125 ASN
B 155 ASN
B 176 GLN
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 239 ASN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
R 290 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.125931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.111061 restraints weight = 11487.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.69
r_work: 0.3302 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   8239  Z= 0.183
  Angle     :  0.591   9.435  11206  Z= 0.305
  Chirality :  0.044   0.165   1266
  Planarity :  0.004   0.053   1444
  Dihedral  :  4.270  35.690   1139
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 25.60 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.27), residues: 1037
  helix:  2.19 (0.25), residues: 421
  sheet: -0.62 (0.34), residues: 218
  loop : -0.39 (0.33), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 234 
 HIS   0.013   0.001   HIS A 220 
 PHE   0.025   0.002   PHE R 159 
 TYR   0.021   0.002   TYR R 268 
 ARG   0.007   0.001   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03945 (  439)
  hydrogen bonds       : angle       4.52717 ( 1254)
  SS BOND              : bond        0.00014 (    1)
  SS BOND              : angle       0.42134 (    2)
  covalent geometry    : bond        0.00433 ( 8238)
  covalent geometry    : angle       0.59068 (11204)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7441.80 seconds
wall clock time: 128 minutes 36.41 seconds (7716.41 seconds total)