Starting phenix.real_space_refine
on Wed Jul 30 12:18:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6oik_20079/07_2025/6oik_20079.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6oik_20079/07_2025/6oik_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6oik_20079/07_2025/6oik_20079.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6oik_20079/07_2025/6oik_20079.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6oik_20079/07_2025/6oik_20079.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6oik_20079/07_2025/6oik_20079.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'ASP:plan': 2, 'HIS:plan': 1}
          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: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3}
          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: {'GLU:plan': 1, 'ARG:plan': 2}
          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, 'ARG:plan': 2, 'ASP:plan': 1}
          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: 7.19, per 1000 atoms: 0.85
  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: 2.66
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.23
  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: 2.78

  Time building geometry restraints manager: 3.12 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: 4896
       28.80 -    57.60: 169
       57.60 -    86.41: 10
       86.41 -   115.21: 2
      115.21 -   144.01: 3
  Dihedral angle restraints: 5080
    sinusoidal: 1821
      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 5077 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:             1.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     26.990
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  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:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
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  : 14.958 144.009   2968
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 8.48
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.026   0.003   TRP B 211 
 HIS   0.005   0.002   HIS B  91 
 PHE   0.028   0.003   PHE R  25 
 TYR   0.034   0.003   TYR R 104 
 ARG   0.003   0.001   ARG H  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12080 (  422)
  hydrogen bonds       : angle       7.02980 ( 1209)
  SS BOND              : bond        0.16757 (    4)
  SS BOND              : angle      11.58109 (    8)
  covalent geometry    : bond        0.00942 ( 8683)
  covalent geometry    : angle       1.06015 (11823)

*********************** 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  : 1.043 
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: 0.6686 (tttm)
REVERT: A  217 GLU cc_start: 0.7473 (pt0) cc_final: 0.7027 (pt0)
REVERT: A  246 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7820 (tp30)
  outliers start: 9
  outliers final: 5
  residues processed: 211
  average time/residue: 0.2553
  time to fit residues: 71.3335
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  : 1.024 
-------------------------------------------------------------------------------
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 92 optimal weight:    2.9990
   chunk 82 optimal weight:   10.0000
   chunk 45 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 44 optimal weight:    9.9990
   chunk 85 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0570
   chunk 63 optimal weight:    0.9980
   chunk 98 optimal weight:    4.9990
   overall best weight:    1.5502

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

Flipped N/Q/H residues before XYZ refinement:
R  41 ASN
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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.120981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.092327 restraints weight = 15638.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.095516 restraints weight = 8528.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.097536 restraints weight = 5870.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.1758

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= 0.171
  Angle     :  0.657   7.663  11831  Z= 0.353
  Chirality :  0.045   0.162   1366
  Planarity :  0.006   0.096   1488
  Dihedral  :  7.762 140.820   1234
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 17.65 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.23), residues: 1107
  helix: -0.62 (0.26), residues: 376
  sheet: -1.58 (0.28), residues: 285
  loop : -2.21 (0.26), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 211 
 HIS   0.007   0.001   HIS A 322 
 PHE   0.029   0.001   PHE R 447 
 TYR   0.016   0.001   TYR B 105 
 ARG   0.006   0.000   ARG B 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04091 (  422)
  hydrogen bonds       : angle       5.50316 ( 1209)
  SS BOND              : bond        0.00369 (    4)
  SS BOND              : angle       1.08779 (    8)
  covalent geometry    : bond        0.00380 ( 8683)
  covalent geometry    : angle       0.65620 (11823)

*********************** 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
  207 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 170
  time to evaluate  : 1.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  134 LYS cc_start: 0.7224 (mmtt) cc_final: 0.6560 (tttm)
REVERT: R  150 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7483 (tt)
REVERT: A  244 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7788 (mpp)
REVERT: A  246 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7857 (tp30)
REVERT: A  325 CYS cc_start: 0.5643 (p) cc_final: 0.5310 (p)
REVERT: B   32 GLN cc_start: 0.8585 (mt0) cc_final: 0.8298 (mt0)
REVERT: H  223 ASP cc_start: 0.8217 (m-30) cc_final: 0.7463 (m-30)
  outliers start: 37
  outliers final: 22
  residues processed: 192
  average time/residue: 0.2229
  time to fit residues: 57.9216
Evaluate side-chains
  180 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 156
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
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  143 MET
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  392 ILE
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  185 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  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  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 98 optimal weight:    0.9990
   chunk 79 optimal weight:    7.9990
   chunk 81 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 13 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9980
   chunk 105 optimal weight:    9.9990
   chunk 53 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** R 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 453 HIS
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.122462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.093725 restraints weight = 15710.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.096902 restraints weight = 8455.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.098993 restraints weight = 5843.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2145

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= 0.131
  Angle     :  0.605   8.314  11831  Z= 0.322
  Chirality :  0.045   0.191   1366
  Planarity :  0.004   0.051   1488
  Dihedral  :  6.616 140.723   1232
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 19.03 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.24), residues: 1107
  helix:  0.11 (0.27), residues: 379
  sheet: -1.27 (0.28), residues: 285
  loop : -1.79 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 322 
 PHE   0.021   0.001   PHE R 447 
 TYR   0.013   0.001   TYR H 190 
 ARG   0.005   0.000   ARG B 304 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03637 (  422)
  hydrogen bonds       : angle       5.06400 ( 1209)
  SS BOND              : bond        0.00172 (    4)
  SS BOND              : angle       1.38848 (    8)
  covalent geometry    : bond        0.00293 ( 8683)
  covalent geometry    : angle       0.60402 (11823)

*********************** 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
  220 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 178
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   69 ASP cc_start: 0.8137 (m-30) cc_final: 0.7807 (t0)
REVERT: R  120 ASP cc_start: 0.8678 (t0) cc_final: 0.8420 (t0)
REVERT: R  134 LYS cc_start: 0.7312 (mmtt) cc_final: 0.6654 (tttm)
REVERT: R  150 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7504 (tt)
REVERT: R  435 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8271 (mt)
REVERT: R  439 CYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7784 (p)
REVERT: A  205 GLN cc_start: 0.8424 (tp40) cc_final: 0.8178 (tp40)
REVERT: A  244 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7619 (mpp)
REVERT: A  246 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7870 (tp30)
REVERT: A  254 ILE cc_start: 0.9482 (tp) cc_final: 0.9219 (tp)
REVERT: A  333 GLN cc_start: 0.8321 (tp40) cc_final: 0.8079 (tp40)
REVERT: B   70 LEU cc_start: 0.8913 (tp) cc_final: 0.8671 (tp)
REVERT: H   38 ARG cc_start: 0.8436 (ptt-90) cc_final: 0.8055 (ptp90)
REVERT: H  223 ASP cc_start: 0.8114 (m-30) cc_final: 0.7602 (m-30)
  outliers start: 42
  outliers final: 20
  residues processed: 205
  average time/residue: 0.1966
  time to fit residues: 56.0502
Evaluate side-chains
  176 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   57 VAL
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  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  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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 103 optimal weight:    0.0170
   chunk 67 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0570
   chunk 8 optimal weight:    0.9990
   chunk 43 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 11 optimal weight:   10.0000
   chunk 102 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0870
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.3714

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

Flipped N/Q/H residues before XYZ refinement:
R 410 ASN
R 453 HIS
A 307 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.121003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.090918 restraints weight = 15574.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.094193 restraints weight = 8194.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.096334 restraints weight = 5577.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   8687  Z= 0.113
  Angle     :  0.583   7.482  11831  Z= 0.309
  Chirality :  0.044   0.194   1366
  Planarity :  0.004   0.046   1488
  Dihedral  :  6.434 140.733   1232
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 22.49 %
    Favored  : 73.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.25), residues: 1107
  helix:  0.54 (0.28), residues: 377
  sheet: -0.88 (0.28), residues: 287
  loop : -1.56 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 453 
 PHE   0.017   0.001   PHE H  68 
 TYR   0.020   0.001   TYR R 177 
 ARG   0.008   0.000   ARG R 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03405 (  422)
  hydrogen bonds       : angle       4.84160 ( 1209)
  SS BOND              : bond        0.00191 (    4)
  SS BOND              : angle       1.13318 (    8)
  covalent geometry    : bond        0.00244 ( 8683)
  covalent geometry    : angle       0.58291 (11823)

*********************** 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
  221 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 183
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   89 TRP cc_start: 0.7503 (t-100) cc_final: 0.6822 (t-100)
REVERT: R  120 ASP cc_start: 0.8628 (t0) cc_final: 0.8372 (t0)
REVERT: R  134 LYS cc_start: 0.7146 (mmtt) cc_final: 0.6593 (tttm)
REVERT: R  150 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7485 (tt)
REVERT: R  436 ASN cc_start: 0.7924 (m-40) cc_final: 0.7523 (m-40)
REVERT: A  246 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7824 (tp30)
REVERT: A  254 ILE cc_start: 0.9458 (tp) cc_final: 0.9175 (tp)
REVERT: A  325 CYS cc_start: 0.5512 (p) cc_final: 0.5211 (p)
REVERT: A  333 GLN cc_start: 0.8391 (tp40) cc_final: 0.8125 (tp40)
REVERT: B   70 LEU cc_start: 0.8908 (tp) cc_final: 0.8611 (tp)
REVERT: B  111 TYR cc_start: 0.9045 (m-80) cc_final: 0.8824 (m-80)
REVERT: B  209 LYS cc_start: 0.8758 (mttm) cc_final: 0.8517 (mttt)
REVERT: H   38 ARG cc_start: 0.8392 (ptt-90) cc_final: 0.8057 (ptp90)
REVERT: H  223 ASP cc_start: 0.7952 (m-30) cc_final: 0.7669 (m-30)
  outliers start: 38
  outliers final: 21
  residues processed: 209
  average time/residue: 0.2072
  time to fit residues: 59.5491
Evaluate side-chains
  185 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 163
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   57 VAL
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  453 HIS
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  158 VAL
Chi-restraints excluded: chain B residue  189 SER
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 G residue   15 LEU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   74 ASP
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 37 optimal weight:    9.9990
   chunk 14 optimal weight:    0.0070
   chunk 30 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 103 optimal weight:    4.9990
   chunk 90 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    2.9404

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

Flipped N/Q/H residues before XYZ refinement:
** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 453 HIS
** B  75 GLN ** 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 = 0.3665 r_free = 0.3665 target = 0.116900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.087995 restraints weight = 16093.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.090914 restraints weight = 8856.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.092870 restraints weight = 6174.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   8687  Z= 0.246
  Angle     :  0.665   8.130  11831  Z= 0.351
  Chirality :  0.047   0.191   1366
  Planarity :  0.005   0.053   1488
  Dihedral  :  6.523 140.706   1230
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  6.11 %
    Allowed  : 21.57 %
    Favored  : 72.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.25), residues: 1107
  helix:  0.57 (0.28), residues: 378
  sheet: -0.81 (0.29), residues: 277
  loop : -1.57 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.006   0.001   HIS R 453 
 PHE   0.014   0.002   PHE R  25 
 TYR   0.017   0.002   TYR H 190 
 ARG   0.005   0.001   ARG H  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03823 (  422)
  hydrogen bonds       : angle       4.95403 ( 1209)
  SS BOND              : bond        0.00313 (    4)
  SS BOND              : angle       1.38226 (    8)
  covalent geometry    : bond        0.00560 ( 8683)
  covalent geometry    : angle       0.66463 (11823)

*********************** 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
  216 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 163
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 TYR cc_start: 0.8592 (t80) cc_final: 0.8329 (t80)
REVERT: R  120 ASP cc_start: 0.8702 (t0) cc_final: 0.8444 (t0)
REVERT: R  134 LYS cc_start: 0.7221 (mmtt) cc_final: 0.6607 (tttm)
REVERT: R  150 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7471 (tt)
REVERT: R  436 ASN cc_start: 0.8096 (m-40) cc_final: 0.7699 (m-40)
REVERT: R  439 CYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7778 (p)
REVERT: A  246 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7901 (tp30)
REVERT: A  325 CYS cc_start: 0.5530 (p) cc_final: 0.5291 (p)
REVERT: A  333 GLN cc_start: 0.8447 (tp40) cc_final: 0.8170 (tp40)
REVERT: H   38 ARG cc_start: 0.8444 (ptt-90) cc_final: 0.8068 (ptp90)
REVERT: H  223 ASP cc_start: 0.8165 (m-30) cc_final: 0.7892 (m-30)
  outliers start: 53
  outliers final: 38
  residues processed: 199
  average time/residue: 0.2053
  time to fit residues: 57.8459
Evaluate side-chains
  188 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 148
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
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  103 ASP
Chi-restraints excluded: chain R residue  117 ILE
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  199 VAL
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  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  189 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 G residue   15 LEU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   74 ASP
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue  141 THR
Chi-restraints excluded: chain H residue  144 THR
Chi-restraints excluded: chain H residue  189 ILE
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 19 optimal weight:    0.3980
   chunk 96 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 103 optimal weight:    5.9990
   chunk 3 optimal weight:    0.0270
   chunk 40 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 102 optimal weight:    0.8980
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
R 179 GLN
A 307 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.119804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.089669 restraints weight = 15623.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.093006 restraints weight = 8099.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.095099 restraints weight = 5447.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2840

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= 0.118
  Angle     :  0.602   8.894  11831  Z= 0.315
  Chirality :  0.044   0.196   1366
  Planarity :  0.004   0.047   1488
  Dihedral  :  6.428 140.861   1230
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 23.53 %
    Favored  : 71.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.26), residues: 1107
  helix:  0.69 (0.28), residues: 378
  sheet: -0.60 (0.29), residues: 282
  loop : -1.40 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R 453 
 PHE   0.015   0.001   PHE R  25 
 TYR   0.019   0.001   TYR R 177 
 ARG   0.004   0.000   ARG H 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03422 (  422)
  hydrogen bonds       : angle       4.83033 ( 1209)
  SS BOND              : bond        0.00318 (    4)
  SS BOND              : angle       1.22426 (    8)
  covalent geometry    : bond        0.00260 ( 8683)
  covalent geometry    : angle       0.60148 (11823)

*********************** 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
  217 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 174
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 TYR cc_start: 0.8551 (t80) cc_final: 0.8268 (t80)
REVERT: R  120 ASP cc_start: 0.8555 (t0) cc_final: 0.8326 (t0)
REVERT: R  134 LYS cc_start: 0.7138 (mmtt) cc_final: 0.6549 (tttm)
REVERT: R  150 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7519 (tt)
REVERT: R  436 ASN cc_start: 0.7935 (m-40) cc_final: 0.7521 (m-40)
REVERT: A  244 MET cc_start: 0.8262 (tpp) cc_final: 0.7504 (mpp)
REVERT: A  246 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7905 (tp30)
REVERT: A  254 ILE cc_start: 0.9496 (tp) cc_final: 0.9238 (tp)
REVERT: A  333 GLN cc_start: 0.8463 (tp40) cc_final: 0.7849 (tm-30)
REVERT: B  209 LYS cc_start: 0.8777 (mttm) cc_final: 0.8505 (mttt)
REVERT: H   38 ARG cc_start: 0.8381 (ptt-90) cc_final: 0.7995 (ptp90)
  outliers start: 43
  outliers final: 28
  residues processed: 203
  average time/residue: 0.1769
  time to fit residues: 50.7265
Evaluate side-chains
  187 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 158
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   25 PHE
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  103 ASP
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 A residue  299 ASP
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  158 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  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   84 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 94 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 48 optimal weight:   10.0000
   chunk 66 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 97 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    3.1786

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

Flipped N/Q/H residues before XYZ refinement:
R 453 HIS
** B  75 GLN ** 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 = 0.3654 r_free = 0.3654 target = 0.116105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.089285 restraints weight = 16212.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.090967 restraints weight = 8490.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.092413 restraints weight = 6782.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   8687  Z= 0.267
  Angle     :  0.714   8.158  11831  Z= 0.375
  Chirality :  0.048   0.249   1366
  Planarity :  0.005   0.070   1488
  Dihedral  :  6.642 140.166   1230
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 24.57 %
    Favored  : 69.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.26), residues: 1107
  helix:  0.60 (0.27), residues: 378
  sheet: -0.68 (0.29), residues: 276
  loop : -1.39 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 400 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.016   0.002   PHE A 275 
 TYR   0.019   0.002   TYR H 190 
 ARG   0.008   0.001   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04033 (  422)
  hydrogen bonds       : angle       4.99143 ( 1209)
  SS BOND              : bond        0.00356 (    4)
  SS BOND              : angle       1.54726 (    8)
  covalent geometry    : bond        0.00608 ( 8683)
  covalent geometry    : angle       0.71262 (11823)

*********************** 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
  197 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 148
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 TYR cc_start: 0.8577 (t80) cc_final: 0.8293 (t80)
REVERT: R  134 LYS cc_start: 0.7266 (mmtt) cc_final: 0.6621 (tttm)
REVERT: R  436 ASN cc_start: 0.8159 (m-40) cc_final: 0.7816 (m-40)
REVERT: A  244 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7419 (mpp)
REVERT: A  246 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7970 (tp30)
REVERT: A  333 GLN cc_start: 0.8377 (tp40) cc_final: 0.7820 (tm-30)
REVERT: H   38 ARG cc_start: 0.8494 (ptt-90) cc_final: 0.8120 (ptp90)
  outliers start: 49
  outliers final: 39
  residues processed: 185
  average time/residue: 0.1955
  time to fit residues: 50.4300
Evaluate side-chains
  174 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 134
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
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  103 ASP
Chi-restraints excluded: chain R residue  117 ILE
Chi-restraints excluded: chain R residue  390 LEU
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  219 VAL
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 A residue  324 THR
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  189 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 G residue   15 LEU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   74 ASP
Chi-restraints excluded: chain H residue   84 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  230 MET
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 83 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 15 optimal weight:    0.1980
   chunk 10 optimal weight:    0.7980
   chunk 105 optimal weight:    8.9990
   chunk 61 optimal weight:    0.3980
   chunk 24 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
R 453 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.120348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.092818 restraints weight = 16161.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.095290 restraints weight = 9181.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.096023 restraints weight = 6214.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.3079

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= 0.125
  Angle     :  0.635   9.370  11831  Z= 0.333
  Chirality :  0.045   0.218   1366
  Planarity :  0.004   0.051   1488
  Dihedral  :  6.320 140.648   1230
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 26.41 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.26), residues: 1107
  helix:  0.81 (0.28), residues: 376
  sheet: -0.52 (0.29), residues: 282
  loop : -1.29 (0.31), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B  82 
 HIS   0.010   0.001   HIS R 453 
 PHE   0.016   0.001   PHE R  25 
 TYR   0.018   0.001   TYR R 177 
 ARG   0.006   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03473 (  422)
  hydrogen bonds       : angle       4.80948 ( 1209)
  SS BOND              : bond        0.00225 (    4)
  SS BOND              : angle       1.21564 (    8)
  covalent geometry    : bond        0.00281 ( 8683)
  covalent geometry    : angle       0.63490 (11823)

*********************** 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
  202 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 163
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 TYR cc_start: 0.8517 (t80) cc_final: 0.8205 (t80)
REVERT: R  120 ASP cc_start: 0.8568 (t0) cc_final: 0.8338 (t0)
REVERT: R  134 LYS cc_start: 0.7160 (mmtt) cc_final: 0.6577 (tttm)
REVERT: R  150 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7433 (tt)
REVERT: R  436 ASN cc_start: 0.7988 (m-40) cc_final: 0.7610 (m-40)
REVERT: A  244 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7482 (mpp)
REVERT: A  246 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7891 (tp30)
REVERT: A  325 CYS cc_start: 0.5470 (p) cc_final: 0.5163 (p)
REVERT: A  333 GLN cc_start: 0.8340 (tp40) cc_final: 0.7749 (tm-30)
REVERT: H   38 ARG cc_start: 0.8329 (ptt-90) cc_final: 0.8077 (ptp90)
  outliers start: 39
  outliers final: 31
  residues processed: 192
  average time/residue: 0.1891
  time to fit residues: 50.8083
Evaluate side-chains
  179 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 146
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
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  426 TYR
Chi-restraints excluded: chain R residue  434 THR
Chi-restraints excluded: chain R residue  435 ILE
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain A residue  304 ILE
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  158 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  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   69 THR
Chi-restraints excluded: chain H residue   74 ASP
Chi-restraints excluded: chain H residue   84 THR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 0 optimal weight:   20.0000
   chunk 31 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 100 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** B  17 GLN ** 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 = 0.3712 r_free = 0.3712 target = 0.120231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.094271 restraints weight = 16077.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.095064 restraints weight = 11301.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.096691 restraints weight = 8132.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.3135

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= 0.127
  Angle     :  0.636   9.370  11831  Z= 0.333
  Chirality :  0.045   0.218   1366
  Planarity :  0.005   0.081   1488
  Dihedral  :  6.319 140.648   1230
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 27.34 %
    Favored  : 68.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.26), residues: 1107
  helix:  0.81 (0.28), residues: 376
  sheet: -0.52 (0.29), residues: 282
  loop : -1.29 (0.31), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B  82 
 HIS   0.010   0.001   HIS R 453 
 PHE   0.016   0.001   PHE R  25 
 TYR   0.018   0.001   TYR R 177 
 ARG   0.006   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03473 (  422)
  hydrogen bonds       : angle       4.80948 ( 1209)
  SS BOND              : bond        0.00400 (    4)
  SS BOND              : angle       1.68088 (    8)
  covalent geometry    : bond        0.00284 ( 8683)
  covalent geometry    : angle       0.63478 (11823)

*********************** 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
  179 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 146
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 TYR cc_start: 0.8488 (t80) cc_final: 0.8216 (t80)
REVERT: R  120 ASP cc_start: 0.8523 (t0) cc_final: 0.8307 (t0)
REVERT: R  134 LYS cc_start: 0.7189 (mmtt) cc_final: 0.6604 (tttm)
REVERT: R  150 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7436 (tt)
REVERT: R  436 ASN cc_start: 0.7958 (m-40) cc_final: 0.7614 (m-40)
REVERT: A  244 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7485 (mpp)
REVERT: A  246 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7828 (tp30)
REVERT: A  325 CYS cc_start: 0.5506 (p) cc_final: 0.5208 (p)
REVERT: A  333 GLN cc_start: 0.8306 (tp40) cc_final: 0.7719 (tm-30)
REVERT: H   38 ARG cc_start: 0.8293 (ptt-90) cc_final: 0.8065 (ptp90)
  outliers start: 33
  outliers final: 31
  residues processed: 170
  average time/residue: 0.1899
  time to fit residues: 45.1035
Evaluate side-chains
  180 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 147
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
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  426 TYR
Chi-restraints excluded: chain R residue  434 THR
Chi-restraints excluded: chain R residue  435 ILE
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  244 MET
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain A residue  304 ILE
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  158 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  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   69 THR
Chi-restraints excluded: chain H residue   74 ASP
Chi-restraints excluded: chain H residue   84 THR
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 27 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3706 r_free = 0.3706 target = 0.119768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.094135 restraints weight = 15934.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.095397 restraints weight = 10897.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.096879 restraints weight = 7868.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.3139

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= 0.147
  Angle     :  0.654   9.177  11831  Z= 0.341
  Chirality :  0.046   0.230   1366
  Planarity :  0.005   0.070   1488
  Dihedral  :  6.314 140.484   1230
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 26.76 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.26), residues: 1107
  helix:  0.87 (0.28), residues: 376
  sheet: -0.45 (0.29), residues: 281
  loop : -1.31 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R 453 
 PHE   0.017   0.001   PHE R  25 
 TYR   0.021   0.001   TYR B 105 
 ARG   0.009   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03516 (  422)
  hydrogen bonds       : angle       4.78764 ( 1209)
  SS BOND              : bond        0.00223 (    4)
  SS BOND              : angle       1.40451 (    8)
  covalent geometry    : bond        0.00343 ( 8683)
  covalent geometry    : angle       0.65341 (11823)

********************** 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
  182 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 145
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   83 TYR cc_start: 0.8479 (t80) cc_final: 0.8225 (t80)
REVERT: R  120 ASP cc_start: 0.8514 (t0) cc_final: 0.8310 (t0)
REVERT: R  134 LYS cc_start: 0.7244 (mmtt) cc_final: 0.6648 (tttm)
REVERT: R  150 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7433 (tt)
REVERT: R  436 ASN cc_start: 0.7924 (m-40) cc_final: 0.7601 (m-40)
REVERT: A  244 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7464 (mpp)
REVERT: A  246 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7703 (tp30)
REVERT: A  325 CYS cc_start: 0.5670 (p) cc_final: 0.5370 (p)
REVERT: A  333 GLN cc_start: 0.8223 (tp40) cc_final: 0.7655 (tm-30)
  outliers start: 37
  outliers final: 34
  residues processed: 172
  average time/residue: 0.1986
  time to fit residues: 47.8946
Evaluate side-chains
  178 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 142
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
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   57 VAL
Chi-restraints excluded: chain R residue   96 CYS
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 A residue  244 MET
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain A residue  304 ILE
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  157 ILE
Chi-restraints excluded: chain B residue  158 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  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   69 THR
Chi-restraints excluded: chain H residue   74 ASP
Chi-restraints excluded: chain H residue   84 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  230 MET
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 85 optimal weight:    0.0470
   chunk 83 optimal weight:   10.0000
   chunk 72 optimal weight:    4.9990
   chunk 100 optimal weight:    7.9990
   chunk 95 optimal weight:    4.9990
   chunk 96 optimal weight:    0.7980
   chunk 25 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    1.5684

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3704 r_free = 0.3704 target = 0.119510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.093132 restraints weight = 16096.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.094839 restraints weight = 8037.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.095538 restraints weight = 6408.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.3139

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= 0.147
  Angle     :  0.655   9.177  11831  Z= 0.341
  Chirality :  0.046   0.230   1366
  Planarity :  0.005   0.070   1488
  Dihedral  :  6.314 140.484   1230
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 26.87 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.26), residues: 1107
  helix:  0.87 (0.28), residues: 376
  sheet: -0.45 (0.29), residues: 281
  loop : -1.31 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R 453 
 PHE   0.017   0.001   PHE R  25 
 TYR   0.021   0.001   TYR B 105 
 ARG   0.009   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03516 (  422)
  hydrogen bonds       : angle       4.78764 ( 1209)
  SS BOND              : bond        0.00230 (    4)
  SS BOND              : angle       1.62200 (    8)
  covalent geometry    : bond        0.00343 ( 8683)
  covalent geometry    : angle       0.65341 (11823)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3205.67 seconds
wall clock time: 56 minutes 17.16 seconds (3377.16 seconds total)