Starting phenix.real_space_refine
on Wed Sep 17 10:20:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lgm_63068/09_2025/9lgm_63068.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lgm_63068/09_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_63068/09_2025/9lgm_63068.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lgm_63068/09_2025/9lgm_63068.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lgm_63068/09_2025/9lgm_63068.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lgm_63068/09_2025/9lgm_63068.cif"
  }
  resolution = 2.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.019
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: {'GLU:plan': 2, 'GLN:plan1': 1, '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: {'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 8}
          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: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 3}
          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: {'ARG:plan': 6, 'PHE:plan': 3, 'TRP:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 65
  Time building chain proxies: 2.00, per 1000 atoms: 0.25
  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: 0.42
  Conformation dependent library (CDL) restraints added in 291.0 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.17
  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: 0.94

  Time building geometry restraints manager: 0.57 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:             1.340
  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:             0.020
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.610
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.710
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (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
 ARG   0.014   0.001   ARG A  38 
 TYR   0.009   0.001   TYR A 329 
 PHE   0.027   0.002   PHE R 159 
 TRP   0.017   0.002   TRP A 234 
 HIS   0.004   0.001   HIS A 220 

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

*********************** 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  : 0.303 
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: 0.6432
  time to fit residues: 125.3155
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  : 0.215 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.5980
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0970
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.0030
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.3788

-------------------------------------------------------------------------------
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 257 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**
B 295 ASN
R  58 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.126447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.111067 restraints weight = 11510.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.76
r_work: 0.3307 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.1109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8239  Z= 0.139
  Angle     :  0.541   6.705  11206  Z= 0.287
  Chirality :  0.041   0.149   1266
  Planarity :  0.004   0.051   1444
  Dihedral  :  5.124  52.843   1149
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 20.95 %
    Favored  : 73.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.27), residues: 1037
  helix:  2.15 (0.25), residues: 420
  sheet: -0.54 (0.33), residues: 223
  loop : -0.50 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 209 
 TYR   0.013   0.001   TYR A 329 
 PHE   0.016   0.001   PHE R 159 
 TRP   0.017   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8238)
  covalent geometry    : angle       0.54103 (11204)
  SS BOND              : bond        0.00054 (    1)
  SS BOND              : angle       0.52692 (    2)
  hydrogen bonds       : bond        0.04463 (  439)
  hydrogen bonds       : angle       4.78710 ( 1254)

*********************** 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
  246 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 201
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7266 (mp-120)
REVERT: A   34 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8226 (tttm)
REVERT: A  283 LYS cc_start: 0.8110 (mttt) cc_final: 0.7827 (mtpt)
REVERT: A  312 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7215 (mm-30)
REVERT: A  370 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7513 (ttp80)
REVERT: B   59 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.6827 (m-80)
REVERT: B  215 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6704 (mp0)
REVERT: N   39 GLN cc_start: 0.8588 (tt0) cc_final: 0.8310 (tp40)
REVERT: R   49 ARG cc_start: 0.7790 (mmp-170) cc_final: 0.7405 (mmp-170)
REVERT: R  174 MET cc_start: 0.6959 (tpt) cc_final: 0.6648 (mmm)
REVERT: R  277 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7889 (mt)
  outliers start: 45
  outliers final: 23
  residues processed: 225
  average time/residue: 0.6259
  time to fit residues: 148.4301
Evaluate side-chains
  224 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 195
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
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  214 VAL
Chi-restraints excluded: chain A residue  309 THR
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  370 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   70 LEU
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  245 SER
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 N residue   59 SER
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  178 VAL
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  204 ILE
Chi-restraints excluded: chain R residue  243 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 89 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 26 optimal weight:    0.1980
   chunk 69 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 94 optimal weight:    0.0970
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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
** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.125866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.110851 restraints weight = 11234.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 1.66
r_work: 0.3305 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.1368

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= 0.157
  Angle     :  0.533   6.714  11206  Z= 0.282
  Chirality :  0.042   0.165   1266
  Planarity :  0.004   0.052   1444
  Dihedral  :  4.722  49.657   1141
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  6.55 %
    Allowed  : 21.07 %
    Favored  : 72.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.27), residues: 1037
  helix:  2.22 (0.25), residues: 415
  sheet: -0.56 (0.33), residues: 231
  loop : -0.37 (0.33), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG R 209 
 TYR   0.014   0.001   TYR A 329 
 PHE   0.017   0.002   PHE R 159 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.009   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 8238)
  covalent geometry    : angle       0.53313 (11204)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       0.46571 (    2)
  hydrogen bonds       : bond        0.04178 (  439)
  hydrogen bonds       : angle       4.62707 ( 1254)

*********************** 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
  258 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 203
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A   31 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7323 (mp-120)
REVERT: A   50 ASN cc_start: 0.7507 (OUTLIER) cc_final: 0.7138 (p0)
REVERT: A  223 ASP cc_start: 0.7999 (t0) cc_final: 0.7752 (t70)
REVERT: A  312 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7178 (mm-30)
REVERT: A  358 ASP cc_start: 0.8199 (t70) cc_final: 0.7893 (t0)
REVERT: A  370 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7551 (ttp80)
REVERT: B   10 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6988 (tm-30)
REVERT: B   15 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7644 (mptp)
REVERT: B   59 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7012 (m-80)
REVERT: B  215 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6673 (mp0)
REVERT: B  336 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8187 (mt)
REVERT: N   39 GLN cc_start: 0.8582 (tt0) cc_final: 0.8335 (tp40)
REVERT: R  174 MET cc_start: 0.6896 (tpt) cc_final: 0.6635 (mmm)
  outliers start: 55
  outliers final: 26
  residues processed: 235
  average time/residue: 0.6251
  time to fit residues: 155.0069
Evaluate side-chains
  232 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 198
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
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  210 THR
Chi-restraints excluded: chain A residue  266 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 A residue  370 ARG
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  176 GLN
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  245 SER
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  117 TYR
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  204 ILE
Chi-restraints excluded: chain R residue  243 LEU
Chi-restraints excluded: chain R residue  275 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0040
   chunk 51 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0670
   chunk 47 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.5330

-------------------------------------------------------------------------------
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
** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
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 = 0.3633 r_free = 0.3633 target = 0.125730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.110271 restraints weight = 11544.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.77
r_work: 0.3289 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8239  Z= 0.154
  Angle     :  0.528   6.709  11206  Z= 0.280
  Chirality :  0.042   0.132   1266
  Planarity :  0.004   0.052   1444
  Dihedral  :  4.682  46.501   1141
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  6.90 %
    Allowed  : 21.07 %
    Favored  : 72.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.27), residues: 1037
  helix:  2.24 (0.25), residues: 420
  sheet: -0.57 (0.34), residues: 218
  loop : -0.38 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 209 
 TYR   0.016   0.001   TYR R 268 
 PHE   0.022   0.002   PHE R 159 
 TRP   0.014   0.001   TRP A 234 
 HIS   0.010   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 8238)
  covalent geometry    : angle       0.52831 (11204)
  SS BOND              : bond        0.00093 (    1)
  SS BOND              : angle       0.35284 (    2)
  hydrogen bonds       : bond        0.03965 (  439)
  hydrogen bonds       : angle       4.52916 ( 1254)

*********************** 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
  258 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 200
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7329 (mp-120)
REVERT: A   50 ASN cc_start: 0.7403 (OUTLIER) cc_final: 0.7134 (p0)
REVERT: A  223 ASP cc_start: 0.8028 (t0) cc_final: 0.7773 (t70)
REVERT: A  312 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7186 (mm-30)
REVERT: A  320 GLU cc_start: 0.8119 (tt0) cc_final: 0.7914 (tt0)
REVERT: A  358 ASP cc_start: 0.8242 (t70) cc_final: 0.7890 (t0)
REVERT: B   10 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7002 (tm-30)
REVERT: B   15 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7654 (mptp)
REVERT: B   59 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.7034 (m-80)
REVERT: B   61 MET cc_start: 0.8074 (tmm) cc_final: 0.7751 (ppp)
REVERT: B  212 ASP cc_start: 0.8109 (t70) cc_final: 0.7080 (t70)
REVERT: B  215 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6693 (mp0)
REVERT: B  251 ARG cc_start: 0.8697 (mtt90) cc_final: 0.8475 (mtt180)
REVERT: B  336 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8294 (mt)
REVERT: N   39 GLN cc_start: 0.8578 (tt0) cc_final: 0.8299 (tp40)
REVERT: N  108 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7334 (m-80)
REVERT: R   49 ARG cc_start: 0.7787 (mmp-170) cc_final: 0.7565 (mmp-170)
REVERT: R  174 MET cc_start: 0.6905 (tpt) cc_final: 0.6680 (mmm)
  outliers start: 58
  outliers final: 31
  residues processed: 228
  average time/residue: 0.6154
  time to fit residues: 148.1861
Evaluate side-chains
  241 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 202
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
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   50 ASN
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  299 GLU
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  161 SER
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  245 SER
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  191 LEU
Chi-restraints excluded: chain R residue  204 ILE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 99 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 94 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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
** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3622 r_free = 0.3622 target = 0.124883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.109499 restraints weight = 11448.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 1.76
r_work: 0.3280 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8239  Z= 0.187
  Angle     :  0.548   6.720  11206  Z= 0.289
  Chirality :  0.043   0.142   1266
  Planarity :  0.004   0.054   1444
  Dihedral  :  4.725  45.765   1141
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  5.95 %
    Allowed  : 22.62 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.27), residues: 1037
  helix:  2.19 (0.25), residues: 420
  sheet: -0.61 (0.34), residues: 218
  loop : -0.38 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG R 209 
 TYR   0.030   0.002   TYR R 268 
 PHE   0.019   0.002   PHE R 159 
 TRP   0.015   0.002   TRP A 234 
 HIS   0.008   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 8238)
  covalent geometry    : angle       0.54838 (11204)
  SS BOND              : bond        0.00133 (    1)
  SS BOND              : angle       0.30951 (    2)
  hydrogen bonds       : bond        0.04076 (  439)
  hydrogen bonds       : angle       4.57435 ( 1254)

*********************** 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
  251 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 201
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7311 (mp-120)
REVERT: A   50 ASN cc_start: 0.7271 (OUTLIER) cc_final: 0.6950 (p0)
REVERT: A  223 ASP cc_start: 0.8056 (t0) cc_final: 0.7814 (t70)
REVERT: A  312 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7161 (mm-30)
REVERT: A  334 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7736 (mm-30)
REVERT: B   10 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6990 (tm-30)
REVERT: B   15 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7681 (mptp)
REVERT: B   59 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7148 (m-80)
REVERT: B  212 ASP cc_start: 0.8171 (t70) cc_final: 0.7125 (t70)
REVERT: B  215 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6807 (mp0)
REVERT: B  336 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8290 (mt)
REVERT: N  108 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7307 (m-80)
REVERT: R  170 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6562 (tm-30)
  outliers start: 50
  outliers final: 30
  residues processed: 229
  average time/residue: 0.6179
  time to fit residues: 149.3164
Evaluate side-chains
  242 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 203
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
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  336 LEU
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   90 VAL
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  204 ILE
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 59 optimal weight:    0.8980
   chunk 46 optimal weight:    0.5980
   chunk 81 optimal weight:    0.7980
   chunk 90 optimal weight:    0.7980
   chunk 91 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0030
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.5590

-------------------------------------------------------------------------------
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 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
N  31 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.125467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.109983 restraints weight = 11408.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.77
r_work: 0.3289 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8239  Z= 0.158
  Angle     :  0.529   6.703  11206  Z= 0.279
  Chirality :  0.042   0.138   1266
  Planarity :  0.004   0.052   1444
  Dihedral  :  4.631  45.017   1141
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  6.79 %
    Allowed  : 22.50 %
    Favored  : 70.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.27), residues: 1037
  helix:  2.25 (0.25), residues: 420
  sheet: -0.62 (0.34), residues: 218
  loop : -0.37 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 209 
 TYR   0.024   0.002   TYR R 268 
 PHE   0.026   0.002   PHE R 159 
 TRP   0.015   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 8238)
  covalent geometry    : angle       0.52926 (11204)
  SS BOND              : bond        0.00055 (    1)
  SS BOND              : angle       0.37737 (    2)
  hydrogen bonds       : bond        0.03877 (  439)
  hydrogen bonds       : angle       4.49386 ( 1254)

*********************** 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
  253 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 196
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7415 (mp-120)
REVERT: A   50 ASN cc_start: 0.7033 (OUTLIER) cc_final: 0.6645 (p0)
REVERT: A   57 VAL cc_start: 0.6547 (OUTLIER) cc_final: 0.6342 (p)
REVERT: A  223 ASP cc_start: 0.8044 (t0) cc_final: 0.7818 (t70)
REVERT: A  229 ASP cc_start: 0.7751 (p0) cc_final: 0.7550 (p0)
REVERT: A  245 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8152 (mp)
REVERT: A  312 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7143 (mm-30)
REVERT: A  358 ASP cc_start: 0.8034 (t70) cc_final: 0.7735 (t0)
REVERT: B   10 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.6989 (tm-30)
REVERT: B   15 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7662 (mptp)
REVERT: B   59 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7122 (m-80)
REVERT: B  215 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6632 (mp0)
REVERT: B  336 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8288 (mt)
REVERT: N   39 GLN cc_start: 0.8603 (tt0) cc_final: 0.8338 (tp40)
REVERT: N  108 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7275 (m-80)
REVERT: R  170 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6659 (tm-30)
REVERT: R  174 MET cc_start: 0.6816 (tpt) cc_final: 0.6170 (mmm)
REVERT: R  209 ARG cc_start: 0.8372 (ttp80) cc_final: 0.7868 (ttp80)
  outliers start: 57
  outliers final: 30
  residues processed: 227
  average time/residue: 0.6330
  time to fit residues: 151.6022
Evaluate side-chains
  235 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 194
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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   57 VAL
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  299 GLU
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 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   59 TYR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  146 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  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  204 ILE
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 66 optimal weight:    0.4980
   chunk 36 optimal weight:    0.0020
   chunk 91 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 49 optimal weight:    0.2980
   chunk 79 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.3988

-------------------------------------------------------------------------------
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 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
R 290 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.126501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.111162 restraints weight = 11520.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 1.77
r_work: 0.3304 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8239  Z= 0.134
  Angle     :  0.523   9.392  11206  Z= 0.274
  Chirality :  0.041   0.132   1266
  Planarity :  0.004   0.051   1444
  Dihedral  :  4.536  44.082   1141
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 22.98 %
    Favored  : 70.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.27), residues: 1037
  helix:  2.33 (0.25), residues: 420
  sheet: -0.57 (0.33), residues: 217
  loop : -0.38 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 209 
 TYR   0.022   0.001   TYR R 268 
 PHE   0.019   0.001   PHE R 159 
 TRP   0.015   0.001   TRP A 234 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8238)
  covalent geometry    : angle       0.52255 (11204)
  SS BOND              : bond        0.00045 (    1)
  SS BOND              : angle       0.25898 (    2)
  hydrogen bonds       : bond        0.03739 (  439)
  hydrogen bonds       : angle       4.41320 ( 1254)

*********************** 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
  248 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 197
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7392 (mp-120)
REVERT: A   50 ASN cc_start: 0.6978 (OUTLIER) cc_final: 0.6696 (p0)
REVERT: A  223 ASP cc_start: 0.8045 (t0) cc_final: 0.7801 (t70)
REVERT: A  245 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8112 (mp)
REVERT: A  283 LYS cc_start: 0.8108 (mttt) cc_final: 0.7881 (mtpt)
REVERT: A  312 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7149 (mm-30)
REVERT: A  320 GLU cc_start: 0.8126 (tt0) cc_final: 0.7871 (tt0)
REVERT: A  328 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8168 (mtmm)
REVERT: A  334 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7685 (mm-30)
REVERT: A  358 ASP cc_start: 0.8037 (t70) cc_final: 0.7758 (t0)
REVERT: B   10 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7010 (tm-30)
REVERT: B   15 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7651 (mptp)
REVERT: B   59 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.6764 (m-80)
REVERT: B   75 GLN cc_start: 0.8411 (mm-40) cc_final: 0.7873 (tp40)
REVERT: B  212 ASP cc_start: 0.8054 (t70) cc_final: 0.7043 (t70)
REVERT: B  215 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6633 (mp0)
REVERT: B  285 LEU cc_start: 0.8469 (tp) cc_final: 0.8267 (tp)
REVERT: B  336 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8288 (mt)
REVERT: N   39 GLN cc_start: 0.8606 (tt0) cc_final: 0.8315 (tp40)
REVERT: R  170 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6475 (tm-30)
REVERT: R  191 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7974 (tp)
  outliers start: 51
  outliers final: 30
  residues processed: 223
  average time/residue: 0.6262
  time to fit residues: 147.4620
Evaluate side-chains
  235 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 194
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
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  210 THR
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  328 LYS
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 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   90 VAL
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  313 ASN
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   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  204 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0770
   chunk 38 optimal weight:    0.5980
   chunk 8 optimal weight:    0.2980
   chunk 83 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 57 optimal weight:    0.1980
   chunk 91 optimal weight:    0.0970
   overall best weight:    0.2536

-------------------------------------------------------------------------------
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  88 ASN
B 119 ASN
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 295 ASN
N  31 ASN
R 290 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.127908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.112692 restraints weight = 11482.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 1.75
r_work: 0.3328 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.2019

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     :  0.517   8.720  11206  Z= 0.270
  Chirality :  0.040   0.126   1266
  Planarity :  0.003   0.049   1444
  Dihedral  :  4.457  42.791   1141
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 23.81 %
    Favored  : 70.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.27), residues: 1037
  helix:  2.41 (0.25), residues: 414
  sheet: -0.38 (0.35), residues: 210
  loop : -0.38 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 307 
 TYR   0.020   0.001   TYR R 268 
 PHE   0.027   0.001   PHE R 159 
 TRP   0.013   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 8238)
  covalent geometry    : angle       0.51650 (11204)
  SS BOND              : bond        0.00013 (    1)
  SS BOND              : angle       0.75859 (    2)
  hydrogen bonds       : bond        0.03592 (  439)
  hydrogen bonds       : angle       4.33423 ( 1254)

*********************** 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
  252 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 204
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7379 (mp-120)
REVERT: A   50 ASN cc_start: 0.6908 (OUTLIER) cc_final: 0.6443 (p0)
REVERT: A  245 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8070 (mp)
REVERT: A  312 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7147 (mm-30)
REVERT: A  328 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8119 (mtmm)
REVERT: A  334 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7604 (mm-30)
REVERT: A  358 ASP cc_start: 0.7949 (t70) cc_final: 0.7700 (t0)
REVERT: B   10 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7024 (tm-30)
REVERT: B   15 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7665 (mptp)
REVERT: B   59 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.6725 (m-80)
REVERT: B   68 ARG cc_start: 0.8046 (ttt-90) cc_final: 0.7815 (ttt180)
REVERT: B   75 GLN cc_start: 0.8351 (mm-40) cc_final: 0.7842 (tp40)
REVERT: B  212 ASP cc_start: 0.8033 (t70) cc_final: 0.6851 (t70)
REVERT: B  215 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6185 (mp0)
REVERT: B  251 ARG cc_start: 0.8537 (mtt90) cc_final: 0.8336 (mtt180)
REVERT: B  285 LEU cc_start: 0.8407 (tp) cc_final: 0.8198 (tp)
REVERT: B  336 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8313 (mt)
REVERT: N   39 GLN cc_start: 0.8598 (tt0) cc_final: 0.8323 (tp40)
REVERT: R  170 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6451 (tm-30)
REVERT: R  174 MET cc_start: 0.6748 (tpt) cc_final: 0.6147 (mmm)
REVERT: R  191 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7937 (tp)
REVERT: R  232 ILE cc_start: 0.8369 (tt) cc_final: 0.8159 (tt)
  outliers start: 48
  outliers final: 26
  residues processed: 230
  average time/residue: 0.6066
  time to fit residues: 147.3877
Evaluate side-chains
  241 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 204
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
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  214 VAL
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  328 LYS
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 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   55 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   90 VAL
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   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   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  290 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 74 optimal weight:    0.5980
   chunk 39 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0870
   chunk 99 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0670
   overall best weight:    0.4096

-------------------------------------------------------------------------------
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 125 ASN
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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.126888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.111845 restraints weight = 11380.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 1.67
r_work: 0.3320 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   8239  Z= 0.135
  Angle     :  0.539  11.297  11206  Z= 0.278
  Chirality :  0.041   0.137   1266
  Planarity :  0.003   0.051   1444
  Dihedral  :  4.474  41.671   1141
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 24.64 %
    Favored  : 70.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.27), residues: 1037
  helix:  2.34 (0.25), residues: 420
  sheet: -0.39 (0.35), residues: 210
  loop : -0.44 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 307 
 TYR   0.018   0.001   TYR R 268 
 PHE   0.016   0.001   PHE R 159 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.006   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8238)
  covalent geometry    : angle       0.53883 (11204)
  SS BOND              : bond        0.00035 (    1)
  SS BOND              : angle       0.36350 (    2)
  hydrogen bonds       : bond        0.03698 (  439)
  hydrogen bonds       : angle       4.37150 ( 1254)

*********************** 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
  249 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 205
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7392 (mp-120)
REVERT: A   33 ASP cc_start: 0.7754 (t0) cc_final: 0.7422 (t0)
REVERT: A   50 ASN cc_start: 0.6942 (OUTLIER) cc_final: 0.6457 (p0)
REVERT: A  312 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7115 (mm-30)
REVERT: A  320 GLU cc_start: 0.8115 (tt0) cc_final: 0.7876 (tt0)
REVERT: A  328 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8178 (mtmm)
REVERT: A  334 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7480 (tp30)
REVERT: A  358 ASP cc_start: 0.7943 (t70) cc_final: 0.7682 (t0)
REVERT: B   10 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7018 (tm-30)
REVERT: B   15 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7672 (mptp)
REVERT: B   59 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.6752 (m-80)
REVERT: B   75 GLN cc_start: 0.8381 (mm-40) cc_final: 0.7862 (tp40)
REVERT: B   88 ASN cc_start: 0.8485 (m-40) cc_final: 0.8284 (m-40)
REVERT: B  215 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6678 (mp0)
REVERT: B  285 LEU cc_start: 0.8424 (tp) cc_final: 0.8212 (tp)
REVERT: B  336 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8281 (mt)
REVERT: N   39 GLN cc_start: 0.8597 (tt0) cc_final: 0.8340 (tp40)
REVERT: R  170 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6433 (tm-30)
REVERT: R  174 MET cc_start: 0.6710 (tpt) cc_final: 0.6153 (mmm)
REVERT: R  191 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7937 (tp)
REVERT: R  232 ILE cc_start: 0.8365 (tt) cc_final: 0.8161 (tt)
  outliers start: 44
  outliers final: 24
  residues processed: 228
  average time/residue: 0.5977
  time to fit residues: 144.3085
Evaluate side-chains
  235 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 201
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
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  214 VAL
Chi-restraints excluded: chain A residue  328 LYS
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 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   90 VAL
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  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   57 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 90 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 73 optimal weight:    0.0870
   chunk 100 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9990
   chunk 83 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.4958

-------------------------------------------------------------------------------
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 119 ASN
B 125 ASN
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 239 ASN
B 259 GLN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.126620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.111684 restraints weight = 11456.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 1.66
r_work: 0.3321 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.2006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   8239  Z= 0.151
  Angle     :  0.554   9.842  11206  Z= 0.286
  Chirality :  0.042   0.177   1266
  Planarity :  0.004   0.052   1444
  Dihedral  :  4.212  36.213   1139
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 24.88 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.27), residues: 1037
  helix:  2.30 (0.25), residues: 420
  sheet: -0.40 (0.35), residues: 210
  loop : -0.44 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 307 
 TYR   0.018   0.002   TYR R 268 
 PHE   0.027   0.001   PHE R 159 
 TRP   0.014   0.001   TRP A 234 
 HIS   0.006   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 8238)
  covalent geometry    : angle       0.55399 (11204)
  SS BOND              : bond        0.00025 (    1)
  SS BOND              : angle       0.50014 (    2)
  hydrogen bonds       : bond        0.03782 (  439)
  hydrogen bonds       : angle       4.42636 ( 1254)

********************** 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
  243 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 200
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7377 (mp-120)
REVERT: A   33 ASP cc_start: 0.7783 (t0) cc_final: 0.7457 (t0)
REVERT: A   50 ASN cc_start: 0.6637 (OUTLIER) cc_final: 0.6100 (p0)
REVERT: A  245 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8106 (mp)
REVERT: A  312 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7099 (mm-30)
REVERT: A  334 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7644 (mm-30)
REVERT: A  384 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7272 (mp)
REVERT: B   10 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7025 (tm-30)
REVERT: B   15 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7660 (mptp)
REVERT: B   59 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.6764 (m-80)
REVERT: B   75 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7866 (tp40)
REVERT: B  212 ASP cc_start: 0.7992 (t70) cc_final: 0.6885 (t70)
REVERT: B  215 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6611 (mp0)
REVERT: B  251 ARG cc_start: 0.8571 (mtt90) cc_final: 0.8306 (mtt180)
REVERT: B  285 LEU cc_start: 0.8422 (tp) cc_final: 0.8203 (tp)
REVERT: B  336 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8302 (mt)
REVERT: N   39 GLN cc_start: 0.8599 (tt0) cc_final: 0.8326 (tp40)
REVERT: R  170 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6515 (tm-30)
REVERT: R  174 MET cc_start: 0.6785 (tpt) cc_final: 0.6231 (mmm)
REVERT: R  191 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7956 (tp)
REVERT: R  232 ILE cc_start: 0.8374 (tt) cc_final: 0.8168 (tt)
  outliers start: 43
  outliers final: 23
  residues processed: 223
  average time/residue: 0.6172
  time to fit residues: 145.4214
Evaluate side-chains
  229 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 195
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
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  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 A residue  371 ASP
Chi-restraints excluded: chain A residue  384 LEU
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   90 VAL
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  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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0970
   chunk 49 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0570
   chunk 3 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0980
   chunk 67 optimal weight:    0.5980
   chunk 56 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0770
   chunk 94 optimal weight:    0.0980
   overall best weight:    0.0854

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
B 239 ASN
B 295 ASN
N  31 ASN
R  85 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.131127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.116423 restraints weight = 11429.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 1.69
r_work: 0.3391 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.059   8239  Z= 0.103
  Angle     :  0.529  10.311  11206  Z= 0.272
  Chirality :  0.040   0.127   1266
  Planarity :  0.003   0.048   1444
  Dihedral  :  3.988  39.108   1139
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 26.31 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.27), residues: 1037
  helix:  2.39 (0.25), residues: 420
  sheet: -0.07 (0.35), residues: 203
  loop : -0.51 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 307 
 TYR   0.018   0.001   TYR A 329 
 PHE   0.014   0.001   PHE R 159 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 8238)
  covalent geometry    : angle       0.52890 (11204)
  SS BOND              : bond        0.00022 (    1)
  SS BOND              : angle       0.39301 (    2)
  hydrogen bonds       : bond        0.03401 (  439)
  hydrogen bonds       : angle       4.28109 ( 1254)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3567.13 seconds
wall clock time: 61 minutes 30.49 seconds (3690.49 seconds total)