Starting phenix.real_space_refine
on Tue Mar  3 22:03:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vdh_31918/03_2026/7vdh_31918.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vdh_31918/03_2026/7vdh_31918.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vdh_31918/03_2026/7vdh_31918.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vdh_31918/03_2026/7vdh_31918.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vdh_31918/03_2026/7vdh_31918.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vdh_31918/03_2026/7vdh_31918.map"
  }
  resolution = 2.9
  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=   0.006
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      64      5.16       5
     C    5592      2.51       5
     N    1457      2.21       5
     O    1597      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8710
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2131
          Classifications: {'peptide': 267}
          Link IDs: {'PTRANS': 8, 'TRANS': 258}
    Chain: "A"
      Number of atoms: 1751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1751
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2590
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "G"
      Number of atoms: 415
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 415
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "S"
      Number of atoms: 1757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1757
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 12
    Chain: "R"
      Number of atoms: 66
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 66
          Unusual residues: {'6IB': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.15, per 1000 atoms: 0.25
  Number of scatterers: 8710
  At special positions: 0
  Unit cell: (119.928, 112.564, 102.044, 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      64     16.00
     O    1597      8.00
     N    1457      7.00
     C    5592      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  26 " - pdb=" SG  CYS R 258 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 168 " - pdb=" SG  CYS R 180 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.08
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.05

  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: 0.69
  Conformation dependent library (CDL) restraints added in 242.2 milliseconds
  

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2062

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 13 sheets defined
      37.6% alpha, 23.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'R' and resid 27 through 29
      No H-bonds generated for 'chain 'R' and resid 27 through 29'
    Processing helix  chain 'R' and resid 30 through 57
    Processing helix  chain 'R' and resid 62 through 94
      removed outlier: 3.834A  pdb=" N   VAL R  66 " --> pdb=" O   ASN R  62 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   TYR R  67 " --> pdb=" O   ALA R  63 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   TYR R  89 " --> pdb=" O   ASN R  85 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 103 through 133
      removed outlier: 4.224A  pdb=" N   THR R 107 " --> pdb=" O   SER R 103 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 133 through 139
    Processing helix  chain 'R' and resid 144 through 167
    Processing helix  chain 'R' and resid 176 through 213
      removed outlier: 4.135A  pdb=" N   THR R 182 " --> pdb=" O   GLY R 178 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 235
    Processing helix  chain 'R' and resid 236 through 245
      removed outlier: 3.938A  pdb=" N   GLY R 240 " --> pdb=" O   GLY R 236 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 245 through 250
    Processing helix  chain 'R' and resid 256 through 280
      Proline residue:  R 262  - end of helix
      Proline residue:  R 276  - end of helix
    Processing helix  chain 'R' and resid 280 through 285
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.777A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.874A  pdb=" N   LYS A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.162A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 4.173A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.880A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 4.093A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.810A  pdb=" N   ASP A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL A 342 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 24
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.758A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.706A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.076A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.679A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.513A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.849A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.624A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.685A  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 151
      removed outlier: 3.660A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.765A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.558A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.401A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.258A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.252A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.252A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136
      removed outlier: 6.541A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)

    444 hydrogen bonds defined for protein.
    1269 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.53

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2688
        1.34 -     1.47: 2451
        1.47 -     1.60: 3676
        1.60 -     1.74: 1
        1.74 -     1.87: 88
  Bond restraints: 8904
  Sorted by residual:
  bond pdb=" C17 CLR R 401 "
       pdb=" C20 CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.535  1.672 -0.137 2.00e-02 2.50e+03 4.70e+01
  bond pdb=" C   ALA S  40 "
       pdb=" N   PRO S  41 "
    ideal  model  delta    sigma   weight residual
    1.335  1.392 -0.058 1.28e-02 6.10e+03 2.03e+01
  bond pdb=" CG1 ILE B 232 "
       pdb=" CD1 ILE B 232 "
    ideal  model  delta    sigma   weight residual
    1.513  1.367  0.146 3.90e-02 6.57e+02 1.41e+01
  bond pdb=" N   THR B 143 "
       pdb=" CA  THR B 143 "
    ideal  model  delta    sigma   weight residual
    1.457  1.500 -0.042 1.29e-02 6.01e+03 1.07e+01
  bond pdb=" C31 6IB R 402 "
       pdb=" N5  6IB R 402 "
    ideal  model  delta    sigma   weight residual
    1.447  1.503 -0.056 2.00e-02 2.50e+03 7.87e+00
  ... (remaining 8899 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.30: 11647
        3.30 -     6.60: 353
        6.60 -     9.90: 52
        9.90 -    13.20: 13
       13.20 -    16.50: 5
  Bond angle restraints: 12070
  Sorted by residual:
  angle pdb=" C   ARG S 179 "
        pdb=" N   MET S 180 "
        pdb=" CA  MET S 180 "
      ideal   model   delta    sigma   weight residual
     121.54  138.04  -16.50 1.91e+00 2.74e-01 7.46e+01
  angle pdb=" CA  CYS B 149 "
        pdb=" CB  CYS B 149 "
        pdb=" SG  CYS B 149 "
      ideal   model   delta    sigma   weight residual
     114.40  129.91  -15.51 2.30e+00 1.89e-01 4.55e+01
  angle pdb=" CA  GLY B 144 "
        pdb=" C   GLY B 144 "
        pdb=" N   TYR B 145 "
      ideal   model   delta    sigma   weight residual
     114.58  119.87   -5.29 8.60e-01 1.35e+00 3.78e+01
  angle pdb=" CA  ARG A 208 "
        pdb=" CB  ARG A 208 "
        pdb=" CG  ARG A 208 "
      ideal   model   delta    sigma   weight residual
     114.10  125.10  -11.00 2.00e+00 2.50e-01 3.02e+01
  angle pdb=" C   GLY S 197 "
        pdb=" N   THR S 198 "
        pdb=" CA  THR S 198 "
      ideal   model   delta    sigma   weight residual
     124.31  133.10   -8.79 1.67e+00 3.59e-01 2.77e+01
  ... (remaining 12065 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 4814
       17.93 -    35.86: 386
       35.86 -    53.79: 58
       53.79 -    71.72: 21
       71.72 -    89.65: 7
  Dihedral angle restraints: 5286
    sinusoidal: 2088
      harmonic: 3198
  Sorted by residual:
  dihedral pdb=" CA  ASP B 290 "
           pdb=" C   ASP B 290 "
           pdb=" N   ASP B 291 "
           pdb=" CA  ASP B 291 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.89   30.11     0      5.00e+00 4.00e-02 3.63e+01
  dihedral pdb=" CA  PHE R 172 "
           pdb=" C   PHE R 172 "
           pdb=" N   SER R 173 "
           pdb=" CA  SER R 173 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.15   23.85     0      5.00e+00 4.00e-02 2.28e+01
  dihedral pdb=" CA  GLU S 210 "
           pdb=" C   GLU S 210 "
           pdb=" N   ASP S 211 "
           pdb=" CA  ASP S 211 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.81   23.19     0      5.00e+00 4.00e-02 2.15e+01
  ... (remaining 5283 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.131: 1268
       0.131 -    0.261: 91
       0.261 -    0.392: 8
       0.392 -    0.523: 0
       0.523 -    0.653: 3
  Chirality restraints: 1370
  Sorted by residual:
  chirality pdb=" CG  LEU A 310 "
            pdb=" CB  LEU A 310 "
            pdb=" CD1 LEU A 310 "
            pdb=" CD2 LEU A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.94   -0.65 2.00e-01 2.50e+01 1.07e+01
  chirality pdb=" CG  LEU S 162 "
            pdb=" CB  LEU S 162 "
            pdb=" CD1 LEU S 162 "
            pdb=" CD2 LEU S 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.01   -0.58 2.00e-01 2.50e+01 8.44e+00
  chirality pdb=" CG  LEU S 117 "
            pdb=" CB  LEU S 117 "
            pdb=" CD1 LEU S 117 "
            pdb=" CD2 LEU S 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.01   -0.58 2.00e-01 2.50e+01 8.36e+00
  ... (remaining 1367 not shown)

  Planarity restraints: 1506
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 119 "    0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" CG  ASN B 119 "   -0.059 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 119 "    0.023 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 119 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 105 "    0.007 2.00e-02 2.50e+03   2.00e-02 7.96e+00
        pdb=" CG  TYR B 105 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 105 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 105 "    0.019 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 105 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 105 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 105 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 105 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "   -0.046 5.00e-02 4.00e+02   6.95e-02 7.73e+00
        pdb=" N   PRO B 194 "    0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 1503 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1576
        2.77 -     3.30: 7442
        3.30 -     3.83: 15232
        3.83 -     4.37: 17626
        4.37 -     4.90: 30920
  Nonbonded interactions: 72796
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 163 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OH  TYR R 113 "
            pdb=" O   GLY R 236 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" O   THR R 107 "
            pdb=" OG  SER R 161 "
     model   vdw
     2.313 3.040
  ... (remaining 72791 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.150
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
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      :  0.011   0.146   8908  Z= 0.489
  Angle     :  1.392  16.498  12078  Z= 0.737
  Chirality :  0.078   0.653   1370
  Planarity :  0.008   0.069   1506
  Dihedral  : 13.914  89.652   3212
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 are not related in a simple way.
  whole: -2.38 (0.22), residues: 1093
  helix: -2.07 (0.20), residues: 365
  sheet: -0.54 (0.29), residues: 295
  loop : -1.68 (0.26), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.041   0.002   ARG A  21 
 TYR   0.045   0.004   TYR B  59 
 PHE   0.032   0.004   PHE R 104 
 TRP   0.024   0.003   TRP B  82 
 HIS   0.017   0.002   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.01138 ( 8904)
  covalent geometry    : angle       1.38671 (12070)
  SS BOND              : bond        0.02553 (    4)
  SS BOND              : angle       4.81527 (    8)
  hydrogen bonds       : bond        0.13147 (  440)
  hydrogen bonds       : angle       7.13501 ( 1269)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.329 
Fit side-chains
REVERT: R   58 ARG cc_start: 0.6054 (ttm-80) cc_final: 0.4767 (ttt180)
REVERT: A  273 LEU cc_start: 0.8839 (mm) cc_final: 0.8545 (mm)
REVERT: A  331 ASN cc_start: 0.8399 (m110) cc_final: 0.8179 (m110)
REVERT: A  333 GLN cc_start: 0.8664 (tp40) cc_final: 0.8149 (mm-40)
REVERT: A  337 ASP cc_start: 0.8492 (m-30) cc_final: 0.8114 (m-30)
REVERT: B   12 GLU cc_start: 0.7968 (pp20) cc_final: 0.7759 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 198
  average time/residue: 0.6585
  time to fit residues: 137.0906
Evaluate side-chains
  151 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0870
   chunk 51 optimal weight:    0.3980
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.8964

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
B  91 HIS
B 119 ASN
B 259 GLN
S   3 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.141851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.103270 restraints weight = 12198.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.33
r_work: 0.3183 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3041 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8908  Z= 0.141
  Angle     :  0.673   8.724  12078  Z= 0.340
  Chirality :  0.044   0.238   1370
  Planarity :  0.004   0.041   1506
  Dihedral  :  7.321  74.163   1283
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 10.08 %
    Favored  : 87.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -0.81 (0.24), residues: 1093
  helix:  0.14 (0.25), residues: 372
  sheet: -0.16 (0.31), residues: 275
  loop : -1.28 (0.27), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  21 
 TYR   0.015   0.001   TYR S 178 
 PHE   0.013   0.001   PHE A 189 
 TRP   0.022   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8904)
  covalent geometry    : angle       0.67135 (12070)
  SS BOND              : bond        0.00801 (    4)
  SS BOND              : angle       1.71051 (    8)
  hydrogen bonds       : bond        0.04233 (  440)
  hydrogen bonds       : angle       5.05834 ( 1269)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 174
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: R   58 ARG cc_start: 0.6051 (ttm-80) cc_final: 0.4811 (ttt180)
REVERT: R  234 LEU cc_start: 0.8595 (mt) cc_final: 0.8359 (mm)
REVERT: A  287 TYR cc_start: 0.9046 (m-80) cc_final: 0.8762 (m-80)
REVERT: A  308 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7055 (mp0)
REVERT: B   12 GLU cc_start: 0.8089 (pp20) cc_final: 0.7823 (pp20)
REVERT: G   32 LYS cc_start: 0.8024 (mptt) cc_final: 0.7665 (tptt)
  outliers start: 21
  outliers final: 4
  residues processed: 178
  average time/residue: 0.5414
  time to fit residues: 102.7315
Evaluate side-chains
  157 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 152
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  109 MET
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain S residue   84 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 40 optimal weight:    7.9990
   chunk 13 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 15 optimal weight:   20.0000
   chunk 70 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 60 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 1 optimal weight:    8.9990
   chunk 77 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
A 333 GLN
B 110 ASN
S  82 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.136380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.096732 restraints weight = 12172.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.28
r_work: 0.3082 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057   8908  Z= 0.286
  Angle     :  0.728  10.961  12078  Z= 0.368
  Chirality :  0.047   0.173   1370
  Planarity :  0.004   0.037   1506
  Dihedral  :  6.936  71.367   1283
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 13.16 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -0.38 (0.25), residues: 1093
  helix:  0.82 (0.27), residues: 378
  sheet: -0.32 (0.32), residues: 256
  loop : -1.04 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  24 
 TYR   0.014   0.002   TYR A 296 
 PHE   0.015   0.002   PHE A 189 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00662 ( 8904)
  covalent geometry    : angle       0.72543 (12070)
  SS BOND              : bond        0.01472 (    4)
  SS BOND              : angle       2.41035 (    8)
  hydrogen bonds       : bond        0.04501 (  440)
  hydrogen bonds       : angle       4.84600 ( 1269)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 157
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: R  234 LEU cc_start: 0.8743 (mt) cc_final: 0.8479 (mm)
REVERT: A  276 GLU cc_start: 0.8016 (pp20) cc_final: 0.7752 (pp20)
REVERT: B   12 GLU cc_start: 0.8082 (pp20) cc_final: 0.7692 (pp20)
REVERT: B   23 LYS cc_start: 0.9119 (ttpp) cc_final: 0.8828 (ttpp)
REVERT: B  101 MET cc_start: 0.9250 (mtp) cc_final: 0.8977 (mtp)
REVERT: B  153 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8070 (p0)
REVERT: G   32 LYS cc_start: 0.8063 (mptt) cc_final: 0.7704 (tptt)
  outliers start: 33
  outliers final: 15
  residues processed: 168
  average time/residue: 0.5702
  time to fit residues: 101.6369
Evaluate side-chains
  165 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 149
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  109 MET
Chi-restraints excluded: chain R residue  151 VAL
Chi-restraints excluded: chain R residue  250 TRP
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  309 ASP
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  174 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 92 optimal weight:    6.9990
   chunk 46 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 7 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 99 optimal weight:    7.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
R  82 GLN
A 304 GLN
A 333 GLN
B  44 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.140113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.101339 restraints weight = 12270.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 2.29
r_work: 0.3149 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8908  Z= 0.134
  Angle     :  0.626   8.750  12078  Z= 0.312
  Chirality :  0.043   0.161   1370
  Planarity :  0.003   0.034   1506
  Dihedral  :  6.311  69.209   1283
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 15.29 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole:  0.03 (0.25), residues: 1093
  helix:  1.30 (0.27), residues: 377
  sheet: -0.21 (0.31), residues: 265
  loop : -0.87 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  24 
 TYR   0.012   0.001   TYR S 178 
 PHE   0.012   0.001   PHE A 189 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8904)
  covalent geometry    : angle       0.62509 (12070)
  SS BOND              : bond        0.00715 (    4)
  SS BOND              : angle       1.32055 (    8)
  hydrogen bonds       : bond        0.03746 (  440)
  hydrogen bonds       : angle       4.57989 ( 1269)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 163
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   32 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6053 (tp)
REVERT: R   58 ARG cc_start: 0.6366 (ttm-80) cc_final: 0.5088 (ttt180)
REVERT: R  234 LEU cc_start: 0.8674 (mt) cc_final: 0.8393 (mm)
REVERT: A  193 ASP cc_start: 0.7562 (t0) cc_final: 0.7334 (t0)
REVERT: A  276 GLU cc_start: 0.8051 (pp20) cc_final: 0.7745 (pp20)
REVERT: B   12 GLU cc_start: 0.8094 (pp20) cc_final: 0.7703 (pp20)
REVERT: B   23 LYS cc_start: 0.9099 (ttpp) cc_final: 0.8773 (ttpp)
REVERT: B   46 ARG cc_start: 0.8716 (mtm-85) cc_final: 0.8290 (mtp-110)
REVERT: B  101 MET cc_start: 0.9173 (mtp) cc_final: 0.8895 (mtp)
REVERT: B  153 ASP cc_start: 0.8505 (m-30) cc_final: 0.8175 (p0)
REVERT: S   46 GLU cc_start: 0.8810 (tt0) cc_final: 0.8557 (pt0)
  outliers start: 32
  outliers final: 9
  residues processed: 175
  average time/residue: 0.5238
  time to fit residues: 97.7607
Evaluate side-chains
  165 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 155
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   32 ILE
Chi-restraints excluded: chain R residue  109 MET
Chi-restraints excluded: chain R residue  159 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  174 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 29 optimal weight:    7.9990
   chunk 38 optimal weight:    0.4980
   chunk 27 optimal weight:    3.9990
   chunk 83 optimal weight:    9.9990
   chunk 12 optimal weight:    5.9990
   chunk 100 optimal weight:    7.9990
   chunk 43 optimal weight:    3.9990
   chunk 97 optimal weight:    8.9990
   overall best weight:    2.2988

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 304 GLN
A 333 GLN
B  75 GLN
S  82 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.138134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.099004 restraints weight = 12203.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.28
r_work: 0.3119 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8908  Z= 0.194
  Angle     :  0.663  10.148  12078  Z= 0.330
  Chirality :  0.044   0.165   1370
  Planarity :  0.004   0.039   1506
  Dihedral  :  6.316  69.041   1283
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 15.39 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole:  0.12 (0.26), residues: 1093
  helix:  1.45 (0.27), residues: 376
  sheet: -0.31 (0.31), residues: 274
  loop : -0.79 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  24 
 TYR   0.011   0.002   TYR S 163 
 PHE   0.027   0.001   PHE R  35 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS G  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 8904)
  covalent geometry    : angle       0.66109 (12070)
  SS BOND              : bond        0.01411 (    4)
  SS BOND              : angle       1.91788 (    8)
  hydrogen bonds       : bond        0.03960 (  440)
  hydrogen bonds       : angle       4.55622 ( 1269)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 156
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: R   32 ILE cc_start: 0.6794 (OUTLIER) cc_final: 0.6320 (tp)
REVERT: R  234 LEU cc_start: 0.8688 (mt) cc_final: 0.8443 (mm)
REVERT: A  192 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8822 (mttt)
REVERT: A  193 ASP cc_start: 0.7702 (t0) cc_final: 0.7369 (t0)
REVERT: A  276 GLU cc_start: 0.8130 (pp20) cc_final: 0.7782 (pp20)
REVERT: A  333 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8452 (tm-30)
REVERT: B   12 GLU cc_start: 0.8107 (pp20) cc_final: 0.7705 (pp20)
REVERT: B   23 LYS cc_start: 0.9105 (ttpp) cc_final: 0.8818 (ttpp)
REVERT: B   46 ARG cc_start: 0.8745 (mtm-85) cc_final: 0.8289 (mtp-110)
REVERT: B  101 MET cc_start: 0.9218 (mtp) cc_final: 0.8940 (mtp)
REVERT: B  146 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8800 (mp)
REVERT: B  153 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8100 (p0)
REVERT: S   46 GLU cc_start: 0.8813 (tt0) cc_final: 0.8526 (pt0)
  outliers start: 41
  outliers final: 16
  residues processed: 174
  average time/residue: 0.5414
  time to fit residues: 100.4677
Evaluate side-chains
  167 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   32 ILE
Chi-restraints excluded: chain R residue   83 ILE
Chi-restraints excluded: chain R residue  159 LEU
Chi-restraints excluded: chain R residue  162 ILE
Chi-restraints excluded: chain A residue  192 LYS
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  174 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 95 optimal weight:    0.3980
   chunk 65 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 56 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 98 optimal weight:   20.0000
   chunk 73 optimal weight:    0.7980
   chunk 30 optimal weight:    6.9990
   chunk 79 optimal weight:    6.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
** A 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 HIS
S  82 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.139624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.100950 restraints weight = 12284.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 2.28
r_work: 0.3156 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.2592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8908  Z= 0.139
  Angle     :  0.649  12.527  12078  Z= 0.319
  Chirality :  0.043   0.165   1370
  Planarity :  0.004   0.045   1506
  Dihedral  :  6.153  67.908   1283
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 17.62 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole:  0.26 (0.26), residues: 1093
  helix:  1.57 (0.27), residues: 378
  sheet: -0.19 (0.32), residues: 265
  loop : -0.75 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A  24 
 TYR   0.010   0.001   TYR S 178 
 PHE   0.019   0.001   PHE R  35 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.008   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8904)
  covalent geometry    : angle       0.64813 (12070)
  SS BOND              : bond        0.00800 (    4)
  SS BOND              : angle       1.54958 (    8)
  hydrogen bonds       : bond        0.03680 (  440)
  hydrogen bonds       : angle       4.51285 ( 1269)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 157
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: R   32 ILE cc_start: 0.6877 (OUTLIER) cc_final: 0.6216 (tp)
REVERT: R   58 ARG cc_start: 0.6180 (ttm-80) cc_final: 0.5047 (ttt180)
REVERT: R  234 LEU cc_start: 0.8668 (mt) cc_final: 0.8396 (mm)
REVERT: A  192 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8784 (mttt)
REVERT: A  193 ASP cc_start: 0.7707 (t0) cc_final: 0.7330 (t0)
REVERT: A  276 GLU cc_start: 0.8180 (pp20) cc_final: 0.7831 (pp20)
REVERT: B   12 GLU cc_start: 0.8142 (pp20) cc_final: 0.7743 (pp20)
REVERT: B   23 LYS cc_start: 0.9090 (ttpp) cc_final: 0.8815 (ttpp)
REVERT: B   46 ARG cc_start: 0.8716 (mtm-85) cc_final: 0.8298 (mtp-110)
REVERT: B  101 MET cc_start: 0.9148 (mtp) cc_final: 0.8878 (mtp)
REVERT: B  153 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8253 (p0)
REVERT: S   46 GLU cc_start: 0.8774 (tt0) cc_final: 0.8507 (pt0)
REVERT: S   93 MET cc_start: 0.8575 (ttm) cc_final: 0.8363 (tpp)
  outliers start: 36
  outliers final: 14
  residues processed: 169
  average time/residue: 0.5497
  time to fit residues: 98.8369
Evaluate side-chains
  170 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 153
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   32 ILE
Chi-restraints excluded: chain R residue   83 ILE
Chi-restraints excluded: chain R residue  109 MET
Chi-restraints excluded: chain R residue  159 LEU
Chi-restraints excluded: chain A residue  192 LYS
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  174 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 23 optimal weight:   20.0000
   chunk 104 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 52 optimal weight:    0.8980
   chunk 77 optimal weight:    9.9990
   chunk 82 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 60 optimal weight:    0.0270
   chunk 16 optimal weight:    8.9990
   overall best weight:    2.9844

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 304 GLN
A 333 GLN
B  75 GLN
S  82 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.137033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.098190 restraints weight = 12334.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 2.26
r_work: 0.3106 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8908  Z= 0.234
  Angle     :  0.718  11.420  12078  Z= 0.354
  Chirality :  0.046   0.169   1370
  Planarity :  0.004   0.049   1506
  Dihedral  :  6.356  68.370   1283
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 18.05 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole:  0.21 (0.26), residues: 1093
  helix:  1.57 (0.27), residues: 378
  sheet: -0.32 (0.31), residues: 267
  loop : -0.75 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A  24 
 TYR   0.012   0.002   TYR S 163 
 PHE   0.023   0.002   PHE R 239 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00546 ( 8904)
  covalent geometry    : angle       0.71619 (12070)
  SS BOND              : bond        0.01218 (    4)
  SS BOND              : angle       2.07934 (    8)
  hydrogen bonds       : bond        0.04066 (  440)
  hydrogen bonds       : angle       4.56691 ( 1269)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 154
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: R   32 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6381 (tp)
REVERT: R  234 LEU cc_start: 0.8702 (mt) cc_final: 0.8464 (mm)
REVERT: R  277 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8803 (tp)
REVERT: A  192 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8774 (mttt)
REVERT: A  193 ASP cc_start: 0.7859 (t0) cc_final: 0.7489 (t0)
REVERT: A  276 GLU cc_start: 0.8244 (pp20) cc_final: 0.7910 (pp20)
REVERT: B   12 GLU cc_start: 0.8140 (pp20) cc_final: 0.7721 (pp20)
REVERT: B   23 LYS cc_start: 0.9127 (ttpp) cc_final: 0.8863 (ttpp)
REVERT: B   46 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.8261 (mtp-110)
REVERT: B  101 MET cc_start: 0.9193 (mtp) cc_final: 0.8956 (mtp)
REVERT: B  146 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8725 (tp)
REVERT: B  153 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8341 (p0)
REVERT: B  234 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.8250 (m-80)
REVERT: G   20 LYS cc_start: 0.8976 (ttmm) cc_final: 0.8768 (mtpp)
REVERT: S   46 GLU cc_start: 0.8831 (tt0) cc_final: 0.8531 (pt0)
  outliers start: 41
  outliers final: 20
  residues processed: 171
  average time/residue: 0.5528
  time to fit residues: 100.4152
Evaluate side-chains
  175 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 149
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   32 ILE
Chi-restraints excluded: chain R residue   83 ILE
Chi-restraints excluded: chain R residue  109 MET
Chi-restraints excluded: chain R residue  159 LEU
Chi-restraints excluded: chain R residue  162 ILE
Chi-restraints excluded: chain R residue  209 ILE
Chi-restraints excluded: chain R residue  250 TRP
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain A residue  192 LYS
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  174 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0070
   chunk 1 optimal weight:    6.9990
   chunk 3 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   chunk 87 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 95 optimal weight:    0.2980
   chunk 17 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    1.6402

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
A 333 GLN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.138603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.099846 restraints weight = 12267.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 2.28
r_work: 0.3132 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8908  Z= 0.160
  Angle     :  0.674  11.826  12078  Z= 0.330
  Chirality :  0.043   0.166   1370
  Planarity :  0.004   0.054   1506
  Dihedral  :  6.186  68.156   1283
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 20.06 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole:  0.33 (0.26), residues: 1093
  helix:  1.68 (0.27), residues: 378
  sheet: -0.24 (0.31), residues: 261
  loop : -0.69 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A  24 
 TYR   0.009   0.001   TYR S 178 
 PHE   0.018   0.001   PHE R  35 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 8904)
  covalent geometry    : angle       0.67347 (12070)
  SS BOND              : bond        0.00860 (    4)
  SS BOND              : angle       1.55775 (    8)
  hydrogen bonds       : bond        0.03757 (  440)
  hydrogen bonds       : angle       4.49205 ( 1269)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 156
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: R   32 ILE cc_start: 0.6831 (OUTLIER) cc_final: 0.6281 (tp)
REVERT: R   58 ARG cc_start: 0.6004 (ttm-80) cc_final: 0.4944 (ttt180)
REVERT: R  234 LEU cc_start: 0.8679 (mt) cc_final: 0.8414 (mm)
REVERT: R  270 LEU cc_start: 0.9037 (tp) cc_final: 0.8836 (tt)
REVERT: A  193 ASP cc_start: 0.7877 (t0) cc_final: 0.7493 (t0)
REVERT: A  276 GLU cc_start: 0.8205 (pp20) cc_final: 0.7888 (pp20)
REVERT: B   12 GLU cc_start: 0.8141 (pp20) cc_final: 0.7718 (pp20)
REVERT: B   23 LYS cc_start: 0.9102 (ttpp) cc_final: 0.8829 (ttpp)
REVERT: B   46 ARG cc_start: 0.8718 (mtm-85) cc_final: 0.8261 (mtp-110)
REVERT: B  101 MET cc_start: 0.9187 (mtp) cc_final: 0.8896 (mtp)
REVERT: B  146 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8639 (tp)
REVERT: B  153 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8259 (p0)
REVERT: B  234 PHE cc_start: 0.9352 (OUTLIER) cc_final: 0.8226 (m-80)
REVERT: G   20 LYS cc_start: 0.8991 (ttmm) cc_final: 0.8775 (mtpp)
REVERT: S   13 GLN cc_start: 0.8867 (mm110) cc_final: 0.8666 (mm-40)
REVERT: S   46 GLU cc_start: 0.8828 (tt0) cc_final: 0.8554 (pt0)
REVERT: S   89 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8206 (pm20)
  outliers start: 34
  outliers final: 16
  residues processed: 171
  average time/residue: 0.5390
  time to fit residues: 98.0198
Evaluate side-chains
  173 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 152
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   32 ILE
Chi-restraints excluded: chain R residue   83 ILE
Chi-restraints excluded: chain R residue  109 MET
Chi-restraints excluded: chain R residue  162 ILE
Chi-restraints excluded: chain R residue  209 ILE
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain S residue  174 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 65 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 304 GLN
B  44 GLN
B  75 GLN
B 340 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.139498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.100670 restraints weight = 12294.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.29
r_work: 0.3140 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8908  Z= 0.157
  Angle     :  0.686  11.813  12078  Z= 0.336
  Chirality :  0.044   0.167   1370
  Planarity :  0.004   0.057   1506
  Dihedral  :  6.108  67.971   1283
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 20.91 %
    Favored  : 75.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole:  0.42 (0.26), residues: 1093
  helix:  1.75 (0.27), residues: 378
  sheet: -0.14 (0.32), residues: 260
  loop : -0.68 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A  24 
 TYR   0.010   0.001   TYR S 178 
 PHE   0.018   0.001   PHE R  35 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 8904)
  covalent geometry    : angle       0.68492 (12070)
  SS BOND              : bond        0.00870 (    4)
  SS BOND              : angle       1.59408 (    8)
  hydrogen bonds       : bond        0.03683 (  440)
  hydrogen bonds       : angle       4.45571 ( 1269)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 158
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: R   32 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6300 (tp)
REVERT: R   45 LEU cc_start: 0.8323 (mt) cc_final: 0.8033 (mt)
REVERT: R   58 ARG cc_start: 0.5997 (ttm-80) cc_final: 0.4987 (ttt180)
REVERT: R  234 LEU cc_start: 0.8663 (mt) cc_final: 0.8401 (mm)
REVERT: A  193 ASP cc_start: 0.7919 (t0) cc_final: 0.7529 (t0)
REVERT: A  276 GLU cc_start: 0.8209 (pp20) cc_final: 0.7889 (pp20)
REVERT: B   12 GLU cc_start: 0.8121 (pp20) cc_final: 0.7721 (pp20)
REVERT: B   23 LYS cc_start: 0.9094 (ttpp) cc_final: 0.8821 (ttpp)
REVERT: B   46 ARG cc_start: 0.8706 (mtm-85) cc_final: 0.8263 (mtp-110)
REVERT: B  101 MET cc_start: 0.9188 (mtp) cc_final: 0.8897 (mtp)
REVERT: B  146 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8602 (tp)
REVERT: B  234 PHE cc_start: 0.9350 (OUTLIER) cc_final: 0.8217 (m-80)
REVERT: G   20 LYS cc_start: 0.8999 (ttmm) cc_final: 0.8780 (mtpp)
REVERT: S   13 GLN cc_start: 0.8862 (mm110) cc_final: 0.8655 (mm-40)
REVERT: S   46 GLU cc_start: 0.8804 (tt0) cc_final: 0.8532 (pt0)
REVERT: S   89 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8154 (pm20)
REVERT: S  151 LYS cc_start: 0.8905 (tttm) cc_final: 0.8682 (tttt)
  outliers start: 30
  outliers final: 16
  residues processed: 175
  average time/residue: 0.5446
  time to fit residues: 101.4005
Evaluate side-chains
  171 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   32 ILE
Chi-restraints excluded: chain R residue   83 ILE
Chi-restraints excluded: chain R residue  109 MET
Chi-restraints excluded: chain R residue  162 ILE
Chi-restraints excluded: chain R residue  209 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain S residue  174 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 77 optimal weight:    9.9990
   chunk 104 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 73 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
A 333 GLN
B  44 GLN
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.138625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.099559 restraints weight = 12393.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 2.31
r_work: 0.3131 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.2774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8908  Z= 0.178
  Angle     :  0.704  12.812  12078  Z= 0.344
  Chirality :  0.044   0.191   1370
  Planarity :  0.004   0.061   1506
  Dihedral  :  6.186  67.489   1283
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 21.34 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole:  0.42 (0.26), residues: 1093
  helix:  1.77 (0.27), residues: 379
  sheet: -0.15 (0.32), residues: 260
  loop : -0.68 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A  24 
 TYR   0.014   0.001   TYR B  59 
 PHE   0.018   0.001   PHE R  35 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 8904)
  covalent geometry    : angle       0.70243 (12070)
  SS BOND              : bond        0.00948 (    4)
  SS BOND              : angle       1.84554 (    8)
  hydrogen bonds       : bond        0.03785 (  440)
  hydrogen bonds       : angle       4.49247 ( 1269)

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

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

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2186 Ramachandran restraints generated.
    1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 156
  time to evaluate  : 0.267 
Fit side-chains
REVERT: R   32 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6253 (tp)
REVERT: R   45 LEU cc_start: 0.8349 (mt) cc_final: 0.8072 (mt)
REVERT: R   58 ARG cc_start: 0.5986 (ttm-80) cc_final: 0.4985 (ttt180)
REVERT: R  234 LEU cc_start: 0.8661 (mt) cc_final: 0.8446 (mm)
REVERT: R  277 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8691 (tp)
REVERT: A  193 ASP cc_start: 0.7903 (t0) cc_final: 0.7528 (t0)
REVERT: A  276 GLU cc_start: 0.8208 (pp20) cc_final: 0.7885 (pp20)
REVERT: B   12 GLU cc_start: 0.8125 (pp20) cc_final: 0.7716 (pp20)
REVERT: B   23 LYS cc_start: 0.9075 (ttpp) cc_final: 0.8808 (ttpp)
REVERT: B   46 ARG cc_start: 0.8724 (mtm-85) cc_final: 0.8271 (mtp-110)
REVERT: B  101 MET cc_start: 0.9206 (mtp) cc_final: 0.8917 (mtp)
REVERT: B  146 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8652 (tp)
REVERT: B  234 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.8219 (m-80)
REVERT: G   20 LYS cc_start: 0.8996 (ttmm) cc_final: 0.8769 (mtpp)
REVERT: S   46 GLU cc_start: 0.8815 (tt0) cc_final: 0.8528 (pt0)
REVERT: S   89 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8175 (pm20)
  outliers start: 28
  outliers final: 16
  residues processed: 167
  average time/residue: 0.5723
  time to fit residues: 101.3598
Evaluate side-chains
  171 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   32 ILE
Chi-restraints excluded: chain R residue   83 ILE
Chi-restraints excluded: chain R residue  162 ILE
Chi-restraints excluded: chain R residue  209 ILE
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   89 GLU
Chi-restraints excluded: chain S residue  174 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 73 optimal weight:    0.3980
   chunk 101 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 96 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0770
   chunk 51 optimal weight:    3.9990
   chunk 104 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    1.0742

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

Flipped N/Q/H residues before XYZ refinement:
A 244 HIS
A 269 ASN
A 304 GLN
A 333 GLN
B  44 GLN
** S  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.140164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.101826 restraints weight = 12187.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 2.27
r_work: 0.3169 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8908  Z= 0.139
  Angle     :  0.685  12.022  12078  Z= 0.335
  Chirality :  0.044   0.194   1370
  Planarity :  0.004   0.060   1506
  Dihedral  :  6.061  67.627   1283
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 21.55 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole:  0.55 (0.26), residues: 1093
  helix:  1.85 (0.27), residues: 379
  sheet: -0.06 (0.31), residues: 277
  loop : -0.62 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A  24 
 TYR   0.012   0.001   TYR S 178 
 PHE   0.019   0.001   PHE R  35 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.000   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8904)
  covalent geometry    : angle       0.68399 (12070)
  SS BOND              : bond        0.00716 (    4)
  SS BOND              : angle       1.46065 (    8)
  hydrogen bonds       : bond        0.03604 (  440)
  hydrogen bonds       : angle       4.46435 ( 1269)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3540.27 seconds
wall clock time: 60 minutes 59.41 seconds (3659.41 seconds total)