Starting phenix.real_space_refine
on Fri Sep 11 23:47:09 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6oik_20079/09_2026/6oik_20079.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6oik_20079/09_2026/6oik_20079.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/6oik_20079/09_2026/6oik_20079.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6oik_20079/09_2026/6oik_20079.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6oik_20079/09_2026/6oik_20079.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6oik_20079/09_2026/6oik_20079.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6oik_20079/09_2026/6oik_20079.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6oik_20079/09_2026/6oik_20079.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4681 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     Cl      1      4.86       5
     C    5427      2.51       5
     N    1436      2.21       5
     O    1572      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8496
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2087
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2087
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 11, 'TRANS': 266}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 127
          Unresolved non-hydrogen angles: 158
          Unresolved non-hydrogen dihedrals: 100
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 44
    Chain: "A"
      Number of atoms: 1678
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1678
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 4, 'TRANS': 212}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 23
    Chain: "B"
      Number of atoms: 2538
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2538
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 77
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 50
    Chain: "G"
      Number of atoms: 403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 403
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "H"
      Number of atoms: 1747
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1747
          Classifications: {'peptide': 236}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 52
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 37
    Chain: "R"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 43
          Unusual residues: {'2CU': 1, 'IXO': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.96, per 1000 atoms: 0.23
  Number of scatterers: 8496
  At special positions: 0
  Unit cell: (107.06, 115.54, 109.18, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      60     16.00
     O    1572      8.00
     N    1436      7.00
     C    5427      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 176 " distance=2.37
    Simple disulfide: pdb=" SG  CYS R 413 " - pdb=" SG  CYS R 416 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " distance=2.04

  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: 0.82
  Conformation dependent library (CDL) restraints added in 251.0 milliseconds
  

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2100

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 13 sheets defined
      35.4% alpha, 22.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'R' and resid 20 through 50
    Processing helix  chain 'R' and resid 56 through 87
      removed outlier: 4.020A  pdb=" N   ILE R  71 " --> pdb=" O   CYS R  67 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   ILE R  72 " --> pdb=" O   ALA R  68 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   PHE R  75 " --> pdb=" O   ILE R  71 " (cutoff:3.500A)
      removed outlier: 5.625A  pdb=" N   MET R  77 " --> pdb=" O   GLY R  73 " (cutoff:3.500A)
      removed outlier: 5.812A  pdb=" N   ASN R  78 " --> pdb=" O   VAL R  74 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU R  79 " --> pdb=" O   PHE R  75 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   TYR R  80 " --> pdb=" O   SER R  76 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 94 through 127
    Processing helix  chain 'R' and resid 136 through 161
      Proline residue:  R 157  - end of helix
    Processing helix  chain 'R' and resid 161 through 167
    Processing helix  chain 'R' and resid 184 through 195
      removed outlier: 3.882A  pdb=" N   ALA R 193 " --> pdb=" O   GLY R 189 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   PHE R 195 " --> pdb=" O   ALA R 191 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 195 through 213
    Processing helix  chain 'R' and resid 380 through 410
      removed outlier: 4.657A  pdb=" N   VAL R 385 " --> pdb=" O   ARG R 381 " (cutoff:3.500A)
      Proline residue:  R 402  - end of helix
    Processing helix  chain 'R' and resid 419 through 431
    Processing helix  chain 'R' and resid 431 through 436
    Processing helix  chain 'R' and resid 436 through 441
    Processing helix  chain 'R' and resid 444 through 454
    Processing helix  chain 'A' and resid 9 through 32
    Processing helix  chain 'A' and resid 45 through 51
    Processing helix  chain 'A' and resid 208 through 212
      removed outlier: 3.635A  pdb=" N   LYS A 211 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 255
    Processing helix  chain 'A' and resid 271 through 282
    Processing helix  chain 'A' and resid 296 through 310
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'G' and resid 8 through 23
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.660A  pdb=" N   SER H  31 " --> pdb=" O   ALA H  28 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 53 through 56
      removed outlier: 3.632A  pdb=" N   GLY H  56 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 53 through 56'
    Processing helix  chain 'H' and resid 220 through 224
      removed outlier: 4.051A  pdb=" N   VAL H 224 " --> pdb=" O   ALA H 221 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191
      removed outlier: 6.150A  pdb=" N   VAL A  34 " --> pdb=" O   ARG A 198 " (cutoff:3.500A)
      removed outlier: 7.515A  pdb=" N   PHE A 200 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ALA A 221 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 5.537A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 6.814A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.767A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.916A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.814A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.000A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.571A  pdb=" N   SER B 191 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.594A  pdb=" N   CYS B 233 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.954A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.803A  pdb=" N   THR H 118 " --> pdb=" O   GLY H  10 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   VAL H  12 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 5.931A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.198A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.803A  pdb=" N   THR H 118 " --> pdb=" O   GLY H  10 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   VAL H  12 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 149
      removed outlier: 3.665A  pdb=" N   GLU H 246 " --> pdb=" O   VAL H 147 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   LEU H 174 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   TYR H 190 " --> pdb=" O   LEU H 174 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   TRP H 176 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 155 through 160

    427 hydrogen bonds defined for protein.
    1209 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: 1.38

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1367
        1.31 -     1.44: 2433
        1.44 -     1.56: 4794
        1.56 -     1.69: 1
        1.69 -     1.81: 88
  Bond restraints: 8683
  Sorted by residual:
  bond pdb=" C10 IXO R 501 "
       pdb=" N11 IXO R 501 "
    ideal  model  delta    sigma   weight residual
    1.270  1.473 -0.203 2.00e-02 2.50e+03 1.03e+02
  bond pdb=" C10 IXO R 501 "
       pdb=" C14 IXO R 501 "
    ideal  model  delta    sigma   weight residual
    1.492  1.331  0.161 2.00e-02 2.50e+03 6.52e+01
  bond pdb=" C13 IXO R 501 "
       pdb=" O12 IXO R 501 "
    ideal  model  delta    sigma   weight residual
    1.439  1.543 -0.104 2.00e-02 2.50e+03 2.71e+01
  bond pdb=" C05 IXO R 501 "
       pdb=" C06 IXO R 501 "
    ideal  model  delta    sigma   weight residual
    1.450  1.534 -0.084 2.00e-02 2.50e+03 1.78e+01
  bond pdb=" C   TRP B  99 "
       pdb=" N   VAL B 100 "
    ideal  model  delta    sigma   weight residual
    1.331  1.283  0.047 1.32e-02 5.74e+03 1.29e+01
  ... (remaining 8678 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.60: 11439
        2.60 -     5.20: 339
        5.20 -     7.80: 35
        7.80 -    10.40: 7
       10.40 -    13.00: 3
  Bond angle restraints: 11823
  Sorted by residual:
  angle pdb=" C   VAL H  12 "
        pdb=" N   GLN H  13 "
        pdb=" CA  GLN H  13 "
      ideal   model   delta    sigma   weight residual
     120.39  133.39  -13.00 1.39e+00 5.18e-01 8.74e+01
  angle pdb=" N   VAL R  94 "
        pdb=" CA  VAL R  94 "
        pdb=" C   VAL R  94 "
      ideal   model   delta    sigma   weight residual
     111.90  106.72    5.18 8.10e-01 1.52e+00 4.09e+01
  angle pdb=" C   ARG H 191 "
        pdb=" N   MET H 192 "
        pdb=" CA  MET H 192 "
      ideal   model   delta    sigma   weight residual
     121.54  130.41   -8.87 1.91e+00 2.74e-01 2.16e+01
  angle pdb=" N   ILE R 159 "
        pdb=" CA  ILE R 159 "
        pdb=" C   ILE R 159 "
      ideal   model   delta    sigma   weight residual
     113.53  109.43    4.10 9.80e-01 1.04e+00 1.75e+01
  angle pdb=" C   THR B  86 "
        pdb=" N   THR B  87 "
        pdb=" CA  THR B  87 "
      ideal   model   delta    sigma   weight residual
     121.54  129.50   -7.96 1.91e+00 2.74e-01 1.74e+01
  ... (remaining 11818 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.80: 4894
       28.80 -    57.60: 167
       57.60 -    86.41: 10
       86.41 -   115.21: 2
      115.21 -   144.01: 2
  Dihedral angle restraints: 5075
    sinusoidal: 1816
      harmonic: 3259
  Sorted by residual:
  dihedral pdb=" CB  CYS R 413 "
           pdb=" SG  CYS R 413 "
           pdb=" SG  CYS R 416 "
           pdb=" CB  CYS R 416 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  151.61  -58.61     1      1.00e+01 1.00e-02 4.60e+01
  dihedral pdb=" CA  ILE B  81 "
           pdb=" C   ILE B  81 "
           pdb=" N   TRP B  82 "
           pdb=" CA  TRP B  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.03  -25.97     0      5.00e+00 4.00e-02 2.70e+01
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.64   25.36     0      5.00e+00 4.00e-02 2.57e+01
  ... (remaining 5072 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1068
       0.073 -    0.147: 265
       0.147 -    0.220: 28
       0.220 -    0.294: 2
       0.294 -    0.367: 3
  Chirality restraints: 1366
  Sorted by residual:
  chirality pdb=" CB  THR H 172 "
            pdb=" CA  THR H 172 "
            pdb=" OG1 THR H 172 "
            pdb=" CG2 THR H 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.18    0.37 2.00e-01 2.50e+01 3.37e+00
  chirality pdb=" CA  ASP H  74 "
            pdb=" N   ASP H  74 "
            pdb=" C   ASP H  74 "
            pdb=" CB  ASP H  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.46e+00
  chirality pdb=" CB  VAL A 202 "
            pdb=" CA  VAL A 202 "
            pdb=" CG1 VAL A 202 "
            pdb=" CG2 VAL A 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.28e+00
  ... (remaining 1363 not shown)

  Planarity restraints: 1488
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C12 2CU R 502 "    0.001 2.00e-02 2.50e+03   2.14e-02 1.60e+01
        pdb=" C13 2CU R 502 "    0.006 2.00e-02 2.50e+03
        pdb=" C15 2CU R 502 "    0.002 2.00e-02 2.50e+03
        pdb=" C16 2CU R 502 "    0.007 2.00e-02 2.50e+03
        pdb=" C17 2CU R 502 "   -0.009 2.00e-02 2.50e+03
        pdb=" C18 2CU R 502 "   -0.015 2.00e-02 2.50e+03
        pdb=" C20 2CU R 502 "    0.009 2.00e-02 2.50e+03
        pdb=" C22 2CU R 502 "   -0.013 2.00e-02 2.50e+03
        pdb=" C24 2CU R 502 "    0.057 2.00e-02 2.50e+03
        pdb=" N19 2CU R 502 "   -0.037 2.00e-02 2.50e+03
        pdb=" N23 2CU R 502 "   -0.008 2.00e-02 2.50e+03
        pdb=" O11 2CU R 502 "    0.006 2.00e-02 2.50e+03
        pdb=" S21 2CU R 502 "   -0.025 2.00e-02 2.50e+03
        pdb="CL1  2CU R 502 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C04 2CU R 502 "   -0.017 2.00e-02 2.50e+03   2.41e-02 8.68e+00
        pdb=" C06 2CU R 502 "    0.035 2.00e-02 2.50e+03
        pdb=" C08 2CU R 502 "   -0.007 2.00e-02 2.50e+03
        pdb=" C10 2CU R 502 "    0.031 2.00e-02 2.50e+03
        pdb=" N05 2CU R 502 "   -0.023 2.00e-02 2.50e+03
        pdb=" O09 2CU R 502 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "    0.044 5.00e-02 4.00e+02   6.59e-02 6.95e+00
        pdb=" N   PRO G  49 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1485 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 82
        2.57 -     3.15: 6605
        3.15 -     3.73: 13561
        3.73 -     4.32: 18224
        4.32 -     4.90: 30663
  Nonbonded interactions: 69135
  Sorted by model distance:
  nonbonded pdb=" OH  TYR R 104 "
            pdb=" OH  TYR R 426 "
     model   vdw
     1.986 3.040
  nonbonded pdb=" OH  TYR A 291 "
            pdb=" OD2 ASP A 299 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG1 THR B 321 "
            pdb=" OD1 ASP B 323 "
     model   vdw
     2.257 3.040
  ... (remaining 69130 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     9.050
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
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      :  0.010   0.335   8687  Z= 0.477
  Angle     :  1.102  31.956  11831  Z= 0.631
  Chirality :  0.063   0.367   1366
  Planarity :  0.007   0.066   1488
  Dihedral  : 14.766 144.009   2963
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 13.26 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -3.68 (0.21), residues: 1107
  helix: -2.35 (0.21), residues: 373
  sheet: -1.87 (0.28), residues: 275
  loop : -2.73 (0.24), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG H  18 
 TYR   0.034   0.003   TYR R 104 
 PHE   0.028   0.003   PHE R  25 
 TRP   0.026   0.003   TRP B 211 
 HIS   0.005   0.002   HIS B  91 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00942 /  0.44 ( 8683)
  covalent geometry    : angle       1.06015 /  0.61 (11823)
  SS BOND              : bond        0.16757 /  8.82 (    4)
  SS BOND              : angle      11.58109 /  5.34 (    8)
  hydrogen bonds       : bond        0.12080 /  7.87 (  422)
  hydrogen bonds       : angle       7.02980 /  5.09 ( 1209)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 204
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  120 ASP cc_start: 0.8752 (t70) cc_final: 0.8405 (t0)
REVERT: R  134 LYS cc_start: 0.7363 (mmtt) cc_final: 0.6687 (tttm)
REVERT: A  217 GLU cc_start: 0.7473 (pt0) cc_final: 0.7030 (pt0)
REVERT: A  246 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7819 (tp30)
  outliers start: 9
  outliers final: 5
  residues processed: 211
  average time/residue: 0.1010
  time to fit residues: 28.3666
Evaluate side-chains
  142 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 137
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  316 ASN
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain H residue  216 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    8.9990
   chunk 106 optimal weight:    3.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** R  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  59 ASN
** R 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 453 HIS
A  22 ASN
A 214 HIS
A 347 ASN
B  88 ASN
B 259 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.120069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.091364 restraints weight = 15697.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.094503 restraints weight = 8563.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.096534 restraints weight = 5909.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.097786 restraints weight = 4690.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.098328 restraints weight = 4062.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8687  Z= 0.193
  Angle     :  0.672   7.828  11831  Z= 0.360
  Chirality :  0.045   0.161   1366
  Planarity :  0.006   0.083   1488
  Dihedral  :  7.451 140.879   1229
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 17.99 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -2.31 (0.23), residues: 1107
  helix: -0.59 (0.26), residues: 376
  sheet: -1.59 (0.28), residues: 285
  loop : -2.20 (0.27), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 304 
 TYR   0.016   0.002   TYR B 105 
 PHE   0.029   0.001   PHE R 447 
 TRP   0.025   0.002   TRP B 211 
 HIS   0.007   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00434 /  0.19 ( 8683)
  covalent geometry    : angle       0.67136 /  0.36 (11823)
  SS BOND              : bond        0.00368 /  0.18 (    4)
  SS BOND              : angle       1.20704 /  0.64 (    8)
  hydrogen bonds       : bond        0.04174 /  2.71 (  422)
  hydrogen bonds       : angle       5.47863 /  3.93 ( 1209)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 167
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  120 ASP cc_start: 0.8675 (t70) cc_final: 0.8471 (t0)
REVERT: R  134 LYS cc_start: 0.7271 (mmtt) cc_final: 0.6621 (tttm)
REVERT: R  150 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7479 (tt)
REVERT: A  205 GLN cc_start: 0.8683 (tp40) cc_final: 0.8446 (tp40)
REVERT: A  244 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7852 (mpp)
REVERT: A  246 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7874 (tp30)
REVERT: A  325 CYS cc_start: 0.5664 (p) cc_final: 0.5335 (p)
REVERT: B   32 GLN cc_start: 0.8570 (mt0) cc_final: 0.8291 (mt0)
REVERT: H  223 ASP cc_start: 0.8221 (m-30) cc_final: 0.7511 (m-30)
  outliers start: 39
  outliers final: 23
  residues processed: 193
  average time/residue: 0.0897
  time to fit residues: 23.8821
Evaluate side-chains
  174 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 149
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  117 ILE
Chi-restraints excluded: chain R residue  143 MET
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  426 TYR
Chi-restraints excluded: chain R residue  435 ILE
Chi-restraints excluded: chain R residue  453 HIS
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  157 ILE
Chi-restraints excluded: chain H residue  216 ILE
Chi-restraints excluded: chain H residue  238 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9980
   chunk 108 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 104 optimal weight:   10.0000
   chunk 58 optimal weight:    4.9990
   chunk 81 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** R  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 453 HIS
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.120002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.091161 restraints weight = 15668.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.094232 restraints weight = 8624.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.096272 restraints weight = 5987.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.097525 restraints weight = 4752.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.098228 restraints weight = 4120.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8687  Z= 0.189
  Angle     :  0.636   7.791  11831  Z= 0.341
  Chirality :  0.046   0.193   1366
  Planarity :  0.005   0.054   1488
  Dihedral  :  6.790 140.721   1227
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 19.03 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -1.61 (0.25), residues: 1107
  helix:  0.09 (0.27), residues: 379
  sheet: -1.34 (0.28), residues: 291
  loop : -1.80 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 304 
 TYR   0.015   0.001   TYR H 190 
 PHE   0.023   0.001   PHE R 447 
 TRP   0.025   0.002   TRP B  82 
 HIS   0.007   0.001   HIS R 453 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00431 /  0.19 ( 8683)
  covalent geometry    : angle       0.63541 /  0.34 (11823)
  SS BOND              : bond        0.00241 /  0.10 (    4)
  SS BOND              : angle       1.30339 /  0.71 (    8)
  hydrogen bonds       : bond        0.03896 /  2.53 (  422)
  hydrogen bonds       : angle       5.15464 /  3.67 ( 1209)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 156
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   69 ASP cc_start: 0.8045 (m-30) cc_final: 0.7799 (t0)
REVERT: R  134 LYS cc_start: 0.7292 (mmtt) cc_final: 0.6616 (tttm)
REVERT: R  150 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7464 (tt)
REVERT: R  435 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8201 (mt)
REVERT: R  439 CYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7792 (p)
REVERT: A  205 GLN cc_start: 0.8629 (tp40) cc_final: 0.8417 (tp40)
REVERT: A  244 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7620 (mpp)
REVERT: H  223 ASP cc_start: 0.8163 (m-30) cc_final: 0.7746 (m-30)
  outliers start: 46
  outliers final: 26
  residues processed: 188
  average time/residue: 0.0850
  time to fit residues: 22.5670
Evaluate side-chains
  171 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 141
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue  117 ILE
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  390 LEU
Chi-restraints excluded: chain R residue  426 TYR
Chi-restraints excluded: chain R residue  435 ILE
Chi-restraints excluded: chain R residue  439 CYS
Chi-restraints excluded: chain R residue  453 HIS
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   74 ASP
Chi-restraints excluded: chain H residue  144 THR
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  216 ILE
Chi-restraints excluded: chain H residue  230 MET
Chi-restraints excluded: chain H residue  237 LEU
Chi-restraints excluded: chain H residue  238 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 74 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 104 optimal weight:   10.0000
   chunk 105 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    1.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R  41 ASN
** R 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 453 HIS
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.121428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.093728 restraints weight = 15918.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.095586 restraints weight = 8588.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.096789 restraints weight = 6672.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.096955 restraints weight = 5728.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.097450 restraints weight = 5521.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8687  Z= 0.149
  Angle     :  0.607   8.129  11831  Z= 0.323
  Chirality :  0.045   0.195   1366
  Planarity :  0.004   0.051   1488
  Dihedral  :  6.495 140.645   1227
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 21.45 %
    Favored  : 73.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -1.17 (0.25), residues: 1107
  helix:  0.45 (0.28), residues: 379
  sheet: -0.93 (0.28), residues: 283
  loop : -1.67 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG R 169 
 TYR   0.018   0.001   TYR R 177 
 PHE   0.030   0.001   PHE H  68 
 TRP   0.025   0.001   TRP B  82 
 HIS   0.008   0.001   HIS R 453 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.15 ( 8683)
  covalent geometry    : angle       0.60651 /  0.32 (11823)
  SS BOND              : bond        0.00225 /  0.10 (    4)
  SS BOND              : angle       1.28305 /  0.70 (    8)
  hydrogen bonds       : bond        0.03621 /  2.36 (  422)
  hydrogen bonds       : angle       4.95547 /  3.53 ( 1209)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 171
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  120 ASP cc_start: 0.8669 (t0) cc_final: 0.8440 (t0)
REVERT: R  134 LYS cc_start: 0.7249 (mmtt) cc_final: 0.6601 (tttm)
REVERT: R  150 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7472 (tt)
REVERT: R  400 TRP cc_start: 0.8112 (m100) cc_final: 0.7862 (m100)
REVERT: R  435 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8165 (mt)
REVERT: R  439 CYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7700 (p)
REVERT: A  205 GLN cc_start: 0.8596 (tp40) cc_final: 0.8378 (tp40)
REVERT: A  213 ILE cc_start: 0.8898 (pt) cc_final: 0.8694 (pt)
REVERT: A  244 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7562 (mpp)
REVERT: A  246 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7941 (tp30)
REVERT: A  325 CYS cc_start: 0.5591 (p) cc_final: 0.5302 (p)
REVERT: H  223 ASP cc_start: 0.8220 (m-30) cc_final: 0.7965 (m-30)
  outliers start: 45
  outliers final: 25
  residues processed: 203
  average time/residue: 0.0802
  time to fit residues: 22.9947
Evaluate side-chains
  173 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 144
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  117 ILE
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  426 TYR
Chi-restraints excluded: chain R residue  434 THR
Chi-restraints excluded: chain R residue  435 ILE
Chi-restraints excluded: chain R residue  439 CYS
Chi-restraints excluded: chain R residue  453 HIS
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   74 ASP
Chi-restraints excluded: chain H residue  144 THR
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  216 ILE
Chi-restraints excluded: chain H residue  238 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 51 optimal weight:    8.9990
   chunk 34 optimal weight:    7.9990
   chunk 67 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 106 optimal weight:    0.2980
   chunk 98 optimal weight:    0.0370
   chunk 42 optimal weight:   10.0000
   chunk 101 optimal weight:    7.9990
   chunk 19 optimal weight:    0.4980
   overall best weight:    1.1662

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 453 HIS
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.121949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.094232 restraints weight = 15824.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.096344 restraints weight = 8641.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.097726 restraints weight = 6422.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.097871 restraints weight = 5705.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.098245 restraints weight = 5322.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8687  Z= 0.138
  Angle     :  0.607   7.988  11831  Z= 0.318
  Chirality :  0.044   0.200   1366
  Planarity :  0.004   0.050   1488
  Dihedral  :  6.342 140.830   1227
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 23.99 %
    Favored  : 71.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.89 (0.25), residues: 1107
  helix:  0.67 (0.28), residues: 379
  sheet: -0.74 (0.29), residues: 280
  loop : -1.53 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 169 
 TYR   0.016   0.001   TYR R 177 
 PHE   0.019   0.001   PHE H  68 
 TRP   0.023   0.001   TRP B  82 
 HIS   0.007   0.001   HIS R 453 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 ( 8683)
  covalent geometry    : angle       0.60591 /  0.32 (11823)
  SS BOND              : bond        0.00235 /  0.11 (    4)
  SS BOND              : angle       1.26164 /  0.70 (    8)
  hydrogen bonds       : bond        0.03447 /  2.24 (  422)
  hydrogen bonds       : angle       4.79604 /  3.41 ( 1209)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 169
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 TYR cc_start: 0.8537 (t80) cc_final: 0.8294 (t80)
REVERT: R  103 ASP cc_start: 0.8103 (t70) cc_final: 0.7546 (m-30)
REVERT: R  120 ASP cc_start: 0.8652 (t0) cc_final: 0.8446 (t0)
REVERT: R  134 LYS cc_start: 0.7288 (mmtt) cc_final: 0.6617 (tttm)
REVERT: A  205 GLN cc_start: 0.8617 (tp40) cc_final: 0.8398 (tp40)
REVERT: A  246 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7911 (tp30)
REVERT: A  333 GLN cc_start: 0.8312 (tp40) cc_final: 0.8032 (tp40)
REVERT: G   36 ASP cc_start: 0.8363 (p0) cc_final: 0.8160 (p0)
REVERT: H  202 ARG cc_start: 0.7542 (ptt-90) cc_final: 0.7188 (ptt-90)
REVERT: H  223 ASP cc_start: 0.8144 (m-30) cc_final: 0.7492 (m-30)
  outliers start: 43
  outliers final: 28
  residues processed: 202
  average time/residue: 0.0801
  time to fit residues: 22.8255
Evaluate side-chains
  182 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 154
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  117 ILE
Chi-restraints excluded: chain R residue  426 TYR
Chi-restraints excluded: chain R residue  434 THR
Chi-restraints excluded: chain R residue  453 HIS
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   74 ASP
Chi-restraints excluded: chain H residue  144 THR
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  216 ILE
Chi-restraints excluded: chain H residue  237 LEU
Chi-restraints excluded: chain H residue  238 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 107 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 73 optimal weight:    0.5980
   chunk 104 optimal weight:    0.9980
   chunk 94 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9990
   chunk 46 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R 179 GLN
R 410 ASN
R 453 HIS
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.122872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.096365 restraints weight = 15610.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.098393 restraints weight = 8655.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.099487 restraints weight = 6354.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.099830 restraints weight = 5822.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.099978 restraints weight = 5298.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8687  Z= 0.126
  Angle     :  0.611   8.793  11831  Z= 0.319
  Chirality :  0.045   0.223   1366
  Planarity :  0.004   0.049   1488
  Dihedral  :  6.241 140.581   1227
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 24.57 %
    Favored  : 70.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.69 (0.26), residues: 1107
  helix:  0.80 (0.28), residues: 379
  sheet: -0.53 (0.29), residues: 278
  loop : -1.46 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 169 
 TYR   0.017   0.001   TYR R 177 
 PHE   0.026   0.001   PHE R 447 
 TRP   0.035   0.001   TRP R 422 
 HIS   0.008   0.001   HIS R 453 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.13 ( 8683)
  covalent geometry    : angle       0.61007 /  0.32 (11823)
  SS BOND              : bond        0.00250 /  0.11 (    4)
  SS BOND              : angle       1.21775 /  0.66 (    8)
  hydrogen bonds       : bond        0.03412 /  2.22 (  422)
  hydrogen bonds       : angle       4.70840 /  3.35 ( 1209)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 180
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  103 ASP cc_start: 0.8020 (t70) cc_final: 0.7500 (m-30)
REVERT: R  134 LYS cc_start: 0.7297 (mmtt) cc_final: 0.6620 (tttm)
REVERT: R  150 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7430 (tt)
REVERT: R  436 ASN cc_start: 0.7962 (m-40) cc_final: 0.7530 (m-40)
REVERT: R  451 PHE cc_start: 0.5813 (t80) cc_final: 0.5415 (t80)
REVERT: A  205 GLN cc_start: 0.8595 (tp40) cc_final: 0.8331 (tp40)
REVERT: A  246 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7774 (tp30)
REVERT: A  254 ILE cc_start: 0.9470 (tp) cc_final: 0.9244 (tp)
REVERT: A  325 CYS cc_start: 0.5706 (p) cc_final: 0.5352 (p)
REVERT: A  333 GLN cc_start: 0.8360 (tp40) cc_final: 0.8098 (tp40)
REVERT: B  111 TYR cc_start: 0.9045 (m-80) cc_final: 0.8798 (m-80)
REVERT: G   36 ASP cc_start: 0.8204 (p0) cc_final: 0.7929 (p0)
REVERT: H  192 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7968 (ptt)
  outliers start: 45
  outliers final: 29
  residues processed: 213
  average time/residue: 0.0828
  time to fit residues: 24.8807
Evaluate side-chains
  187 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 156
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  434 THR
Chi-restraints excluded: chain R residue  435 ILE
Chi-restraints excluded: chain R residue  443 CYS
Chi-restraints excluded: chain R residue  453 HIS
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   74 ASP
Chi-restraints excluded: chain H residue  141 THR
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  216 ILE
Chi-restraints excluded: chain H residue  237 LEU
Chi-restraints excluded: chain H residue  238 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.0870
   chunk 37 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 84 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 17 optimal weight:    6.9990
   chunk 95 optimal weight:    3.9990
   chunk 48 optimal weight:   20.0000
   chunk 38 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.5764

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R 453 HIS
A 307 GLN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.121572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.094169 restraints weight = 15892.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.096110 restraints weight = 8597.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.097753 restraints weight = 6693.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.097957 restraints weight = 5461.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.098153 restraints weight = 5192.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.3049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8687  Z= 0.161
  Angle     :  0.640   8.131  11831  Z= 0.337
  Chirality :  0.046   0.218   1366
  Planarity :  0.004   0.061   1488
  Dihedral  :  6.331 140.591   1227
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 25.03 %
    Favored  : 69.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.65 (0.26), residues: 1107
  helix:  0.77 (0.28), residues: 379
  sheet: -0.45 (0.30), residues: 273
  loop : -1.41 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  27 
 TYR   0.014   0.001   TYR R 177 
 PHE   0.038   0.001   PHE H  68 
 TRP   0.049   0.002   TRP R 422 
 HIS   0.006   0.001   HIS R 453 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.16 ( 8683)
  covalent geometry    : angle       0.63963 /  0.34 (11823)
  SS BOND              : bond        0.00234 /  0.11 (    4)
  SS BOND              : angle       1.33847 /  0.71 (    8)
  hydrogen bonds       : bond        0.03517 /  2.28 (  422)
  hydrogen bonds       : angle       4.72994 /  3.37 ( 1209)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 161
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 TYR cc_start: 0.8585 (t80) cc_final: 0.8351 (t80)
REVERT: R  103 ASP cc_start: 0.8020 (t70) cc_final: 0.7516 (m-30)
REVERT: R  134 LYS cc_start: 0.7289 (mmtt) cc_final: 0.6664 (tttm)
REVERT: R  150 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7427 (tt)
REVERT: R  436 ASN cc_start: 0.7996 (m-40) cc_final: 0.7663 (m-40)
REVERT: R  451 PHE cc_start: 0.5557 (t80) cc_final: 0.5132 (t80)
REVERT: A  201 ASP cc_start: 0.8455 (t0) cc_final: 0.8244 (t0)
REVERT: A  205 GLN cc_start: 0.8584 (tp40) cc_final: 0.8320 (tp40)
REVERT: A  244 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7444 (mpp)
REVERT: A  246 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7882 (tp30)
REVERT: A  325 CYS cc_start: 0.5667 (p) cc_final: 0.5308 (p)
REVERT: A  333 GLN cc_start: 0.8348 (tp40) cc_final: 0.8088 (tp40)
REVERT: B  111 TYR cc_start: 0.9051 (m-80) cc_final: 0.8817 (m-80)
REVERT: G   36 ASP cc_start: 0.8168 (p0) cc_final: 0.7878 (p0)
REVERT: H  220 GLU cc_start: 0.7757 (mp0) cc_final: 0.7532 (mp0)
  outliers start: 51
  outliers final: 36
  residues processed: 199
  average time/residue: 0.0841
  time to fit residues: 23.8596
Evaluate side-chains
  193 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 155
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  117 ILE
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  434 THR
Chi-restraints excluded: chain R residue  435 ILE
Chi-restraints excluded: chain R residue  443 CYS
Chi-restraints excluded: chain R residue  453 HIS
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   74 ASP
Chi-restraints excluded: chain H residue  141 THR
Chi-restraints excluded: chain H residue  144 THR
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  216 ILE
Chi-restraints excluded: chain H residue  226 VAL
Chi-restraints excluded: chain H residue  237 LEU
Chi-restraints excluded: chain H residue  238 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 30 optimal weight:    0.0070
   chunk 20 optimal weight:    2.9990
   chunk 100 optimal weight:   10.0000
   chunk 106 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 88 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 102 optimal weight:    0.9990
   overall best weight:    0.8002

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 113 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.119343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.088822 restraints weight = 15828.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.092164 restraints weight = 8354.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.094339 restraints weight = 5668.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.095544 restraints weight = 4443.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.096544 restraints weight = 3840.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8687  Z= 0.128
  Angle     :  0.631   8.000  11831  Z= 0.331
  Chirality :  0.045   0.223   1366
  Planarity :  0.004   0.063   1488
  Dihedral  :  6.241 140.579   1227
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 26.76 %
    Favored  : 68.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.51 (0.26), residues: 1107
  helix:  0.89 (0.28), residues: 380
  sheet: -0.41 (0.30), residues: 276
  loop : -1.30 (0.31), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H 202 
 TYR   0.016   0.001   TYR R 177 
 PHE   0.018   0.001   PHE R 447 
 TRP   0.032   0.002   TRP R 422 
 HIS   0.006   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 8683)
  covalent geometry    : angle       0.63062 /  0.33 (11823)
  SS BOND              : bond        0.00182 /  0.09 (    4)
  SS BOND              : angle       1.30529 /  0.66 (    8)
  hydrogen bonds       : bond        0.03405 /  2.22 (  422)
  hydrogen bonds       : angle       4.66026 /  3.32 ( 1209)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 169
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 TYR cc_start: 0.8525 (t80) cc_final: 0.8253 (t80)
REVERT: R  103 ASP cc_start: 0.7981 (t70) cc_final: 0.7486 (m-30)
REVERT: R  134 LYS cc_start: 0.7274 (mmtt) cc_final: 0.6668 (tttm)
REVERT: R  150 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7453 (tt)
REVERT: R  436 ASN cc_start: 0.7968 (m-40) cc_final: 0.7554 (m-40)
REVERT: R  451 PHE cc_start: 0.5715 (t80) cc_final: 0.5267 (t80)
REVERT: A  201 ASP cc_start: 0.8429 (t0) cc_final: 0.8189 (t0)
REVERT: A  205 GLN cc_start: 0.8680 (tp40) cc_final: 0.8345 (tp40)
REVERT: A  246 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7908 (tp30)
REVERT: A  254 ILE cc_start: 0.9500 (tp) cc_final: 0.9198 (tp)
REVERT: A  325 CYS cc_start: 0.5635 (p) cc_final: 0.5418 (p)
REVERT: A  333 GLN cc_start: 0.8455 (tp40) cc_final: 0.8181 (tp40)
REVERT: B   70 LEU cc_start: 0.8972 (tp) cc_final: 0.8703 (tp)
REVERT: B  111 TYR cc_start: 0.9085 (m-80) cc_final: 0.8838 (m-80)
REVERT: G   36 ASP cc_start: 0.8175 (p0) cc_final: 0.7899 (p0)
  outliers start: 43
  outliers final: 39
  residues processed: 200
  average time/residue: 0.0848
  time to fit residues: 23.9404
Evaluate side-chains
  193 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 153
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   25 PHE
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  417 ILE
Chi-restraints excluded: chain R residue  434 THR
Chi-restraints excluded: chain R residue  435 ILE
Chi-restraints excluded: chain R residue  443 CYS
Chi-restraints excluded: chain R residue  453 HIS
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   74 ASP
Chi-restraints excluded: chain H residue  141 THR
Chi-restraints excluded: chain H residue  144 THR
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  216 ILE
Chi-restraints excluded: chain H residue  226 VAL
Chi-restraints excluded: chain H residue  237 LEU
Chi-restraints excluded: chain H residue  238 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 101 optimal weight:    0.0040
   chunk 40 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 105 optimal weight:    6.9990
   chunk 107 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   chunk 9 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0770
   overall best weight:    1.3954

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.118304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.088045 restraints weight = 15821.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.091229 restraints weight = 8349.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.093404 restraints weight = 5716.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.094780 restraints weight = 4473.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.095576 restraints weight = 3815.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.3305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8687  Z= 0.154
  Angle     :  0.651   8.723  11831  Z= 0.342
  Chirality :  0.046   0.225   1366
  Planarity :  0.004   0.056   1488
  Dihedral  :  6.288 140.583   1227
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 27.57 %
    Favored  : 67.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.47 (0.26), residues: 1107
  helix:  0.96 (0.28), residues: 379
  sheet: -0.42 (0.30), residues: 276
  loop : -1.30 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G  27 
 TYR   0.017   0.001   TYR B 105 
 PHE   0.018   0.001   PHE R 447 
 TRP   0.019   0.001   TRP R 422 
 HIS   0.006   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00357 /  0.15 ( 8683)
  covalent geometry    : angle       0.65064 /  0.34 (11823)
  SS BOND              : bond        0.00220 /  0.10 (    4)
  SS BOND              : angle       1.35937 /  0.69 (    8)
  hydrogen bonds       : bond        0.03471 /  2.25 (  422)
  hydrogen bonds       : angle       4.66273 /  3.33 ( 1209)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 161
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   45 MET cc_start: 0.8060 (mmm) cc_final: 0.7785 (mmt)
REVERT: R   83 TYR cc_start: 0.8537 (t80) cc_final: 0.8204 (t80)
REVERT: R  103 ASP cc_start: 0.8025 (t70) cc_final: 0.7493 (m-30)
REVERT: R  134 LYS cc_start: 0.7294 (mmtt) cc_final: 0.6682 (tttm)
REVERT: R  150 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7492 (tt)
REVERT: R  163 GLN cc_start: 0.8465 (pm20) cc_final: 0.8225 (pm20)
REVERT: R  169 ARG cc_start: 0.5275 (mmt90) cc_final: 0.4345 (mmm-85)
REVERT: R  436 ASN cc_start: 0.8018 (m-40) cc_final: 0.7609 (m-40)
REVERT: R  451 PHE cc_start: 0.5602 (t80) cc_final: 0.5117 (t80)
REVERT: A  205 GLN cc_start: 0.8592 (tp40) cc_final: 0.8267 (tp40)
REVERT: A  244 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7397 (mpp)
REVERT: A  246 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7940 (tp30)
REVERT: A  325 CYS cc_start: 0.5671 (p) cc_final: 0.5273 (p)
REVERT: A  333 GLN cc_start: 0.8488 (tp40) cc_final: 0.8201 (tp40)
REVERT: B  111 TYR cc_start: 0.9112 (m-80) cc_final: 0.8877 (m-80)
REVERT: G   36 ASP cc_start: 0.8183 (p0) cc_final: 0.7884 (p0)
REVERT: H  222 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7090 (tm-30)
  outliers start: 42
  outliers final: 38
  residues processed: 191
  average time/residue: 0.0881
  time to fit residues: 23.6192
Evaluate side-chains
  192 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 152
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  434 THR
Chi-restraints excluded: chain R residue  435 ILE
Chi-restraints excluded: chain R residue  453 HIS
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   74 ASP
Chi-restraints excluded: chain H residue  141 THR
Chi-restraints excluded: chain H residue  144 THR
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  216 ILE
Chi-restraints excluded: chain H residue  237 LEU
Chi-restraints excluded: chain H residue  238 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 93 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0670
   chunk 69 optimal weight:    0.0370
   overall best weight:    0.4996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
R 179 GLN
A 307 GLN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 186 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.120836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.090608 restraints weight = 15680.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.093972 restraints weight = 8214.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.096154 restraints weight = 5541.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.097571 restraints weight = 4317.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.098320 restraints weight = 3686.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.3527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8687  Z= 0.122
  Angle     :  0.644   8.667  11831  Z= 0.337
  Chirality :  0.045   0.225   1366
  Planarity :  0.004   0.048   1488
  Dihedral  :  6.142 140.494   1227
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 27.45 %
    Favored  : 67.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.35 (0.26), residues: 1107
  helix:  1.01 (0.28), residues: 386
  sheet: -0.21 (0.31), residues: 276
  loop : -1.31 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 209 
 TYR   0.019   0.001   TYR R 177 
 PHE   0.018   0.001   PHE R  25 
 TRP   0.022   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.12 ( 8683)
  covalent geometry    : angle       0.64333 /  0.34 (11823)
  SS BOND              : bond        0.00223 /  0.10 (    4)
  SS BOND              : angle       1.23707 /  0.63 (    8)
  hydrogen bonds       : bond        0.03269 /  2.12 (  422)
  hydrogen bonds       : angle       4.52127 /  3.23 ( 1209)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 166
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   45 MET cc_start: 0.8015 (mmm) cc_final: 0.7774 (mmt)
REVERT: R   83 TYR cc_start: 0.8442 (t80) cc_final: 0.8125 (t80)
REVERT: R  103 ASP cc_start: 0.7947 (t70) cc_final: 0.7446 (m-30)
REVERT: R  134 LYS cc_start: 0.7240 (mmtt) cc_final: 0.6654 (tttm)
REVERT: R  150 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7469 (tt)
REVERT: R  436 ASN cc_start: 0.8061 (m-40) cc_final: 0.7706 (m-40)
REVERT: R  451 PHE cc_start: 0.5583 (t80) cc_final: 0.5047 (t80)
REVERT: A  205 GLN cc_start: 0.8666 (tp40) cc_final: 0.8333 (tp40)
REVERT: A  244 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7213 (mpp)
REVERT: A  246 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7876 (tp30)
REVERT: A  254 ILE cc_start: 0.9478 (tp) cc_final: 0.9214 (tp)
REVERT: A  325 CYS cc_start: 0.5579 (p) cc_final: 0.5184 (p)
REVERT: A  333 GLN cc_start: 0.8370 (tp40) cc_final: 0.8106 (tp40)
REVERT: B   17 GLN cc_start: 0.8733 (pt0) cc_final: 0.8430 (mm-40)
REVERT: B   70 LEU cc_start: 0.8992 (tp) cc_final: 0.8663 (tp)
REVERT: B  111 TYR cc_start: 0.9064 (m-80) cc_final: 0.8749 (m-80)
REVERT: G   36 ASP cc_start: 0.8107 (p0) cc_final: 0.7863 (p0)
  outliers start: 41
  outliers final: 36
  residues processed: 197
  average time/residue: 0.0853
  time to fit residues: 23.8237
Evaluate side-chains
  200 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 162
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  399 THR
Chi-restraints excluded: chain R residue  417 ILE
Chi-restraints excluded: chain R residue  453 HIS
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  211 TRP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   74 ASP
Chi-restraints excluded: chain H residue  141 THR
Chi-restraints excluded: chain H residue  144 THR
Chi-restraints excluded: chain H residue  192 MET
Chi-restraints excluded: chain H residue  216 ILE
Chi-restraints excluded: chain H residue  226 VAL
Chi-restraints excluded: chain H residue  237 LEU
Chi-restraints excluded: chain H residue  238 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 57 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 74 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.120378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.090154 restraints weight = 15611.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.093473 restraints weight = 8245.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.095671 restraints weight = 5583.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.096900 restraints weight = 4358.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.097885 restraints weight = 3755.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.3555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8687  Z= 0.132
  Angle     :  0.651  11.068  11831  Z= 0.336
  Chirality :  0.045   0.214   1366
  Planarity :  0.005   0.127   1488
  Dihedral  :  6.168 140.514   1227
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 27.34 %
    Favored  : 67.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.32 (0.26), residues: 1107
  helix:  1.03 (0.28), residues: 385
  sheet: -0.18 (0.31), residues: 276
  loop : -1.29 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG R 169 
 TYR   0.020   0.001   TYR R 177 
 PHE   0.018   0.001   PHE R  25 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 322 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.13 ( 8683)
  covalent geometry    : angle       0.65004 /  0.34 (11823)
  SS BOND              : bond        0.00193 /  0.09 (    4)
  SS BOND              : angle       1.19052 /  0.61 (    8)
  hydrogen bonds       : bond        0.03334 /  2.16 (  422)
  hydrogen bonds       : angle       4.50808 /  3.22 ( 1209)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1613.50 seconds
wall clock time: 28 minutes 38.55 seconds (1718.55 seconds total)