Starting phenix.real_space_refine
on Thu May  1 06:29:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xgm_38328/05_2025/8xgm_38328.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xgm_38328/05_2025/8xgm_38328.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xgm_38328/05_2025/8xgm_38328.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xgm_38328/05_2025/8xgm_38328.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xgm_38328/05_2025/8xgm_38328.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xgm_38328/05_2025/8xgm_38328.cif"
  }
  resolution = 3.29
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.065
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    6615      2.51       5
     N    1756      2.21       5
     O    1882      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 10319
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "S"
      Number of atoms: 1772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1772
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 10, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "A"
      Number of atoms: 2539
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2539
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 10, 'TRANS': 295}
    Chain: "B"
      Number of atoms: 2589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2589
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "C"
      Number of atoms: 1850
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1850
          Classifications: {'peptide': 233}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 2, 'TRANS': 230}
          Chain breaks: 1
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 13
    Chain: "G"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "D"
      Number of atoms: 1117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 1117
          Classifications: {'peptide': 137}
          Link IDs: {'PTRANS': 9, 'TRANS': 127}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.13, per 1000 atoms: 0.59
  Number of scatterers: 10319
  At special positions: 0
  Unit cell: (99.45, 104.55, 169.15, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      66     16.00
     O    1882      8.00
     N    1756      7.00
     C    6615      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 110 " - pdb=" SG  CYS A 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  57 " - pdb=" SG  CYS D  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  78 " - pdb=" SG  CYS D  97 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  81 " - pdb=" SG  CYS D 115 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.44
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2444

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 15 sheets defined
      33.3% alpha, 23.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.892A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 65
      removed outlier: 3.864A  pdb=" N   TRP A  39 " --> pdb=" O   GLY A  35 " (cutoff:3.500A)
      Proline residue:  A  54  - end of helix
      removed outlier: 3.615A  pdb=" N   PHE A  65 " --> pdb=" O   TRP A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 89
      removed outlier: 3.541A  pdb=" N   LEU A  74 " --> pdb=" O   THR A  70 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   PHE A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 99
      removed outlier: 3.930A  pdb=" N   TYR A  93 " --> pdb=" O   PHE A  89 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   MET A  99 " --> pdb=" O   SER A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 141
      removed outlier: 3.839A  pdb=" N   CYS A 110 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 147
      removed outlier: 3.917A  pdb=" N   ARG A 147 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 170
    Processing helix  chain 'A' and resid 171 through 175
    Processing helix  chain 'A' and resid 198 through 215
    Processing helix  chain 'A' and resid 215 through 237
      removed outlier: 3.957A  pdb=" N   ILE A 230 " --> pdb=" O   TYR A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 269
      removed outlier: 3.629A  pdb=" N   VAL A 252 " --> pdb=" O   ILE A 248 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   VAL A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR A 260 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      Proline residue:  A 261  - end of helix
      removed outlier: 4.760A  pdb=" N   PHE A 265 " --> pdb=" O   PRO A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 273
    Processing helix  chain 'A' and resid 279 through 284
    Processing helix  chain 'A' and resid 285 through 305
      Proline residue:  A 301  - end of helix
    Processing helix  chain 'A' and resid 308 through 318
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 33
    Processing helix  chain 'B' and resid 280 through 282
      No H-bonds generated for 'chain 'B' and resid 280 through 282'
    Processing helix  chain 'C' and resid 6 through 30
      removed outlier: 3.534A  pdb=" N   LYS C  29 " --> pdb=" O   GLU C  25 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 53
    Processing helix  chain 'C' and resid 241 through 254
    Processing helix  chain 'C' and resid 270 through 279
      removed outlier: 4.200A  pdb=" N   LYS C 279 " --> pdb=" O   GLU C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 299 through 309
    Processing helix  chain 'C' and resid 329 through 351
      removed outlier: 3.824A  pdb=" N   GLN C 333 " --> pdb=" O   THR C 329 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 23
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.855A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'D' and resid 4 through 19
    Processing helix  chain 'D' and resid 86 through 88
      No H-bonds generated for 'chain 'D' and resid 86 through 88'
    Processing helix  chain 'D' and resid 105 through 120
      removed outlier: 3.613A  pdb=" N   ARG D 117 " --> pdb=" O   THR D 113 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'S' and resid 4 through 7
    Processing sheet with id=AA2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.755A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 4.364A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'S' and resid 140 through 141
      removed outlier: 3.505A  pdb=" N   ALA S 211 " --> pdb=" O   SER S 208 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.826A  pdb=" N   GLU S 246 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 25 through 26
      removed outlier: 3.974A  pdb=" N   GLU A  25 " --> pdb=" O   ARG D  93 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ARG D  93 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLY D  92 " --> pdb=" O   LYS D  83 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   GLY D  43 " --> pdb=" O   PRO D  39 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   PHE D  45 " --> pdb=" O   ASP D  37 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   ASP D  37 " --> pdb=" O   PHE D  45 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   ARG D  47 " --> pdb=" O   ALA D  35 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   ALA D  35 " --> pdb=" O   ARG D  47 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   GLU D  49 " --> pdb=" O   GLU D  33 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   GLN D  53 " --> pdb=" O   GLU D  29 " (cutoff:3.500A)
      removed outlier: 5.493A  pdb=" N   GLU D  29 " --> pdb=" O   GLN D  53 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 176 through 180
    Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.217A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.680A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.916A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.365A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.880A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.234A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 191 through 192
      removed outlier: 3.582A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.873A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.708A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 191
      removed outlier: 6.164A  pdb=" N   VAL C  34 " --> pdb=" O   LYS C 197 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   PHE C 199 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   LEU C  36 " --> pdb=" O   PHE C 199 " (cutoff:3.500A)
      removed outlier: 8.215A  pdb=" N   VAL C 201 " --> pdb=" O   LEU C  36 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   LEU C  38 " --> pdb=" O   VAL C 201 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   LYS C  35 " --> pdb=" O   ALA C 220 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   ILE C 222 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
      removed outlier: 5.949A  pdb=" N   LEU C  37 " --> pdb=" O   ILE C 222 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   CYS C 224 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   LEU C  39 " --> pdb=" O   CYS C 224 " (cutoff:3.500A)
      removed outlier: 8.946A  pdb=" N   ALA C 226 " --> pdb=" O   LEU C  39 " (cutoff:3.500A)

    466 hydrogen bonds defined for protein.
    1332 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: 3.05

  Time building geometry restraints manager: 2.90 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1662
        1.32 -     1.45: 2984
        1.45 -     1.57: 5827
        1.57 -     1.70: 1
        1.70 -     1.83: 92
  Bond restraints: 10566
  Sorted by residual:
  bond pdb=" CA  ARG C  21 "
       pdb=" C   ARG C  21 "
    ideal  model  delta    sigma   weight residual
    1.524  1.450  0.073 1.27e-02 6.20e+03 3.34e+01
  bond pdb=" CA  ALA C 338 "
       pdb=" CB  ALA C 338 "
    ideal  model  delta    sigma   weight residual
    1.528  1.453  0.075 1.59e-02 3.96e+03 2.23e+01
  bond pdb=" N   ALA C 338 "
       pdb=" CA  ALA C 338 "
    ideal  model  delta    sigma   weight residual
    1.459  1.404  0.055 1.23e-02 6.61e+03 1.99e+01
  bond pdb=" C   VAL C 335 "
       pdb=" O   VAL C 335 "
    ideal  model  delta    sigma   weight residual
    1.237  1.191  0.047 1.17e-02 7.31e+03 1.58e+01
  bond pdb=" CA  VAL C 335 "
       pdb=" CB  VAL C 335 "
    ideal  model  delta    sigma   weight residual
    1.540  1.492  0.048 1.25e-02 6.40e+03 1.49e+01
  ... (remaining 10561 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 13994
        2.03 -     4.07: 274
        4.07 -     6.10: 42
        6.10 -     8.13: 13
        8.13 -    10.17: 2
  Bond angle restraints: 14325
  Sorted by residual:
  angle pdb=" N   GLU S 234 "
        pdb=" CA  GLU S 234 "
        pdb=" C   GLU S 234 "
      ideal   model   delta    sigma   weight residual
     109.95  100.61    9.34 1.59e+00 3.96e-01 3.45e+01
  angle pdb=" N   LEU S 233 "
        pdb=" CA  LEU S 233 "
        pdb=" C   LEU S 233 "
      ideal   model   delta    sigma   weight residual
     111.11  104.85    6.26 1.20e+00 6.94e-01 2.72e+01
  angle pdb=" N   LYS D  19 "
        pdb=" CA  LYS D  19 "
        pdb=" C   LYS D  19 "
      ideal   model   delta    sigma   weight residual
     113.02  107.45    5.57 1.20e+00 6.94e-01 2.16e+01
  angle pdb=" N   VAL C 335 "
        pdb=" CA  VAL C 335 "
        pdb=" C   VAL C 335 "
      ideal   model   delta    sigma   weight residual
     110.62  105.97    4.65 1.02e+00 9.61e-01 2.07e+01
  angle pdb=" C   ARG C  21 "
        pdb=" CA  ARG C  21 "
        pdb=" CB  ARG C  21 "
      ideal   model   delta    sigma   weight residual
     110.88  104.41    6.47 1.57e+00 4.06e-01 1.70e+01
  ... (remaining 14320 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.45: 5673
       24.45 -    48.89: 542
       48.89 -    73.34: 60
       73.34 -    97.79: 7
       97.79 -   122.24: 3
  Dihedral angle restraints: 6285
    sinusoidal: 2502
      harmonic: 3783
  Sorted by residual:
  dihedral pdb=" CB  CYS A 110 "
           pdb=" SG  CYS A 110 "
           pdb=" SG  CYS A 187 "
           pdb=" CB  CYS A 187 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -165.92   79.92     1      1.00e+01 1.00e-02 7.92e+01
  dihedral pdb=" C10 CLR A 401 "
           pdb=" C1  CLR A 401 "
           pdb=" C2  CLR A 401 "
           pdb=" C3  CLR A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.83   65.41 -122.24     1      3.00e+01 1.11e-03 1.64e+01
  dihedral pdb=" CA  GLN B  75 "
           pdb=" C   GLN B  75 "
           pdb=" N   ASP B  76 "
           pdb=" CA  ASP B  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.04   19.96     0      5.00e+00 4.00e-02 1.59e+01
  ... (remaining 6282 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 1449
       0.075 -    0.150: 148
       0.150 -    0.225: 6
       0.225 -    0.300: 1
       0.300 -    0.375: 1
  Chirality restraints: 1605
  Sorted by residual:
  chirality pdb=" C13 CLR A 401 "
            pdb=" C12 CLR A 401 "
            pdb=" C14 CLR A 401 "
            pdb=" C17 CLR A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.56   -0.38 2.00e-01 2.50e+01 3.52e+00
  chirality pdb=" C14 CLR A 401 "
            pdb=" C13 CLR A 401 "
            pdb=" C15 CLR A 401 "
            pdb=" C8  CLR A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.56    0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CA  LEU C 348 "
            pdb=" N   LEU C 348 "
            pdb=" C   LEU C 348 "
            pdb=" CB  LEU C 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 1602 not shown)

  Planarity restraints: 1802
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS D  18 "    0.014 2.00e-02 2.50e+03   2.75e-02 7.55e+00
        pdb=" C   HIS D  18 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   HIS D  18 "    0.018 2.00e-02 2.50e+03
        pdb=" N   LYS D  19 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS D  96 "   -0.012 2.00e-02 2.50e+03   2.33e-02 5.45e+00
        pdb=" C   HIS D  96 "    0.040 2.00e-02 2.50e+03
        pdb=" O   HIS D  96 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   CYS D  97 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 281 "    0.038 5.00e-02 4.00e+02   5.80e-02 5.39e+00
        pdb=" N   PRO C 282 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO C 282 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO C 282 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1799 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 222
        2.67 -     3.23: 9663
        3.23 -     3.78: 15563
        3.78 -     4.34: 20512
        4.34 -     4.90: 35126
  Nonbonded interactions: 81086
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.112 3.040
  nonbonded pdb=" NZ  LYS S 244 "
            pdb=" OE2 GLU S 246 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" OE1 GLN A 118 "
            pdb=" OG  SER D 137 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" NZ  LYS D  83 "
            pdb=" O   ALA D 121 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" O   HIS A 141 "
            pdb=" OG  SER A 145 "
     model   vdw
     2.247 3.040
  ... (remaining 81081 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     24.870
  Find NCS groups from input model:        0.150
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.088  10572  Z= 0.249
  Angle     :  0.692  10.168  14337  Z= 0.387
  Chirality :  0.046   0.375   1605
  Planarity :  0.005   0.058   1802
  Dihedral  : 17.553 122.237   3823
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 30.26 %
    Favored  : 69.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.23), residues: 1285
  helix:  1.02 (0.26), residues: 413
  sheet: -0.37 (0.26), residues: 346
  loop : -1.68 (0.26), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP S  36 
 HIS   0.008   0.001   HIS D  18 
 PHE   0.013   0.001   PHE C 189 
 TYR   0.028   0.002   TYR S 235 
 ARG   0.006   0.000   ARG C 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12945 (  459)
  hydrogen bonds       : angle       6.19383 ( 1332)
  SS BOND              : bond        0.00542 (    6)
  SS BOND              : angle       1.10465 (   12)
  covalent geometry    : bond        0.00444 (10566)
  covalent geometry    : angle       0.69192 (14325)

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

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

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 149
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: S   38 ARG cc_start: 0.5373 (ttp-170) cc_final: 0.4563 (ttm-80)
REVERT: S   60 TYR cc_start: 0.4605 (m-80) cc_final: 0.3784 (m-80)
REVERT: S   98 ARG cc_start: 0.7030 (ptm160) cc_final: 0.6823 (ptm-80)
REVERT: S  141 THR cc_start: 0.5403 (m) cc_final: 0.5072 (p)
REVERT: S  230 MET cc_start: 0.7161 (tmm) cc_final: 0.6921 (tmm)
REVERT: C  251 ASP cc_start: 0.8384 (t0) cc_final: 0.8181 (t0)
REVERT: C  252 SER cc_start: 0.8148 (t) cc_final: 0.7734 (p)
  outliers start: 4
  outliers final: 2
  residues processed: 151
  average time/residue: 0.2473
  time to fit residues: 51.6718
Evaluate side-chains
  150 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 148
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  269 ASN
Chi-restraints excluded: chain C residue  348 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 107 optimal weight:    0.0980
   chunk 96 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0040
   chunk 64 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 99 optimal weight:    0.0980
   chunk 38 optimal weight:    0.2980
   chunk 60 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0010
   chunk 115 optimal weight:    6.9990
   overall best weight:    0.0998

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

Flipped N/Q/H residues before XYZ refinement:
S 194 ASN
A 192 GLN
B 220 GLN
B 259 GLN
D  54 GLN
D 133 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.182145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.122694 restraints weight = 13834.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 3.27
r_work: 0.3361 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.1130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10572  Z= 0.106
  Angle     :  0.563   8.681  14337  Z= 0.292
  Chirality :  0.042   0.144   1605
  Planarity :  0.004   0.054   1802
  Dihedral  :  5.120  44.601   1471
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 28.02 %
    Favored  : 68.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.24), residues: 1285
  helix:  1.62 (0.26), residues: 414
  sheet: -0.08 (0.27), residues: 339
  loop : -1.52 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  75 
 HIS   0.006   0.001   HIS D  20 
 PHE   0.014   0.001   PHE A 105 
 TYR   0.020   0.001   TYR S 235 
 ARG   0.006   0.000   ARG C 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03622 (  459)
  hydrogen bonds       : angle       4.62457 ( 1332)
  SS BOND              : bond        0.00307 (    6)
  SS BOND              : angle       0.84436 (   12)
  covalent geometry    : bond        0.00219 (10566)
  covalent geometry    : angle       0.56251 (14325)

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

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

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 171
  time to evaluate  : 1.536 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: S   38 ARG cc_start: 0.5404 (ttp-170) cc_final: 0.4515 (ttm-80)
REVERT: S   98 ARG cc_start: 0.6309 (ptm160) cc_final: 0.6107 (ptm160)
REVERT: S  141 THR cc_start: 0.5636 (m) cc_final: 0.5238 (p)
REVERT: S  233 LEU cc_start: 0.7074 (tm) cc_final: 0.6773 (tm)
REVERT: B   27 ASP cc_start: 0.7440 (t0) cc_final: 0.7221 (t0)
REVERT: B  292 PHE cc_start: 0.8431 (m-80) cc_final: 0.8004 (m-80)
REVERT: C  227 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7893 (pp)
REVERT: C  251 ASP cc_start: 0.8181 (t0) cc_final: 0.7939 (t0)
REVERT: C  252 SER cc_start: 0.8350 (t) cc_final: 0.7811 (p)
REVERT: C  305 CYS cc_start: 0.7763 (t) cc_final: 0.7337 (t)
REVERT: C  309 ASP cc_start: 0.7727 (m-30) cc_final: 0.7416 (m-30)
REVERT: G   32 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7875 (ttpp)
REVERT: G   36 ASP cc_start: 0.7723 (m-30) cc_final: 0.7470 (m-30)
REVERT: D   88 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7224 (t70)
REVERT: D  124 ASP cc_start: 0.7762 (t0) cc_final: 0.7475 (t0)
REVERT: D  133 GLN cc_start: 0.7581 (mt0) cc_final: 0.7363 (mt0)
  outliers start: 37
  outliers final: 16
  residues processed: 196
  average time/residue: 0.2447
  time to fit residues: 69.0063
Evaluate side-chains
  172 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 153
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   32 LYS
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue   88 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0570
   chunk 32 optimal weight:    0.3980
   chunk 79 optimal weight:    7.9990
   chunk 86 optimal weight:    0.0170
   chunk 45 optimal weight:    0.5980
   chunk 72 optimal weight:    0.0010
   chunk 43 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 123 optimal weight:    0.3980
   chunk 95 optimal weight:    3.9990
   overall best weight:    0.1742

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

Flipped N/Q/H residues before XYZ refinement:
A 120 ASN
A 192 GLN
B 220 GLN
C 241 ASN
D 119 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.184404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.126263 restraints weight = 13976.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 3.27
r_work: 0.3379 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10572  Z= 0.102
  Angle     :  0.545   7.810  14337  Z= 0.282
  Chirality :  0.041   0.143   1605
  Planarity :  0.004   0.054   1802
  Dihedral  :  4.462  50.222   1467
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 28.02 %
    Favored  : 68.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.24), residues: 1285
  helix:  1.81 (0.26), residues: 415
  sheet:  0.10 (0.28), residues: 334
  loop : -1.45 (0.26), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  75 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.012   0.001   PHE C 189 
 TYR   0.025   0.001   TYR S 235 
 ARG   0.009   0.000   ARG S 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03420 (  459)
  hydrogen bonds       : angle       4.38469 ( 1332)
  SS BOND              : bond        0.00509 (    6)
  SS BOND              : angle       1.71520 (   12)
  covalent geometry    : bond        0.00213 (10566)
  covalent geometry    : angle       0.54248 (14325)

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

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

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 164
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: S   60 TYR cc_start: 0.4613 (m-80) cc_final: 0.3713 (m-80)
REVERT: S   98 ARG cc_start: 0.6399 (ptm160) cc_final: 0.6163 (ptm160)
REVERT: S  233 LEU cc_start: 0.7138 (tm) cc_final: 0.6927 (tm)
REVERT: A  192 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8281 (tm-30)
REVERT: B   27 ASP cc_start: 0.7160 (t0) cc_final: 0.6876 (t0)
REVERT: B  198 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8155 (mt)
REVERT: B  254 ASP cc_start: 0.8097 (t70) cc_final: 0.7746 (t0)
REVERT: B  292 PHE cc_start: 0.8464 (m-80) cc_final: 0.8076 (m-80)
REVERT: C  251 ASP cc_start: 0.8187 (t0) cc_final: 0.7914 (t0)
REVERT: C  252 SER cc_start: 0.8336 (t) cc_final: 0.7832 (p)
REVERT: C  309 ASP cc_start: 0.7865 (m-30) cc_final: 0.7512 (m-30)
REVERT: G   32 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7919 (ttpp)
REVERT: G   36 ASP cc_start: 0.7712 (m-30) cc_final: 0.7453 (m-30)
REVERT: D   45 PHE cc_start: 0.7001 (t80) cc_final: 0.6785 (t80)
REVERT: D   79 LEU cc_start: 0.6840 (tt) cc_final: 0.6145 (tp)
REVERT: D  133 GLN cc_start: 0.7501 (mt0) cc_final: 0.7231 (mt0)
  outliers start: 37
  outliers final: 23
  residues processed: 188
  average time/residue: 0.2200
  time to fit residues: 58.5260
Evaluate side-chains
  184 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 158
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain A residue   99 MET
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  192 GLN
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  188 MET
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   32 LYS
Chi-restraints excluded: chain D residue   84 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 1 optimal weight:    9.9990
   chunk 109 optimal weight:   20.0000
   chunk 88 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 13 optimal weight:   20.0000
   chunk 45 optimal weight:    0.0000
   chunk 119 optimal weight:   10.0000
   chunk 98 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    2.5992

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.173472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.114533 restraints weight = 13927.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 3.20
r_work: 0.3239 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  10572  Z= 0.265
  Angle     :  0.679   8.655  14337  Z= 0.358
  Chirality :  0.046   0.159   1605
  Planarity :  0.005   0.048   1802
  Dihedral  :  5.155  51.187   1467
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 26.95 %
    Favored  : 67.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.24), residues: 1285
  helix:  1.40 (0.26), residues: 413
  sheet: -0.29 (0.27), residues: 353
  loop : -1.44 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.008   0.002   HIS B 183 
 PHE   0.019   0.002   PHE A 217 
 TYR   0.026   0.002   TYR S 235 
 ARG   0.004   0.000   ARG S  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05452 (  459)
  hydrogen bonds       : angle       4.88870 ( 1332)
  SS BOND              : bond        0.00916 (    6)
  SS BOND              : angle       2.54934 (   12)
  covalent geometry    : bond        0.00628 (10566)
  covalent geometry    : angle       0.67572 (14325)

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

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

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 162
  time to evaluate  : 1.194 
Fit side-chains
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   60 TYR cc_start: 0.6184 (m-80) cc_final: 0.5310 (m-80)
REVERT: S  141 THR cc_start: 0.5800 (m) cc_final: 0.5382 (p)
REVERT: S  171 ASN cc_start: 0.7090 (m-40) cc_final: 0.6686 (m-40)
REVERT: B   27 ASP cc_start: 0.7713 (t0) cc_final: 0.7292 (t0)
REVERT: B  215 GLU cc_start: 0.8311 (mp0) cc_final: 0.8096 (mp0)
REVERT: B  292 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8111 (m-80)
REVERT: C   22 ASN cc_start: 0.7701 (t0) cc_final: 0.7427 (t0)
REVERT: C  306 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7623 (tp40)
REVERT: C  309 ASP cc_start: 0.7661 (m-30) cc_final: 0.7422 (m-30)
  outliers start: 60
  outliers final: 39
  residues processed: 205
  average time/residue: 0.2052
  time to fit residues: 60.8156
Evaluate side-chains
  193 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 152
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue   99 MET
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain C residue  306 GLN
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  118 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 112 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 90 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 106 optimal weight:    2.9990
   chunk 123 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 189 ASN
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
D  11 GLN
D  54 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.175503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.117766 restraints weight = 13979.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 3.11
r_work: 0.3343 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10572  Z= 0.128
  Angle     :  0.579   8.317  14337  Z= 0.304
  Chirality :  0.042   0.168   1605
  Planarity :  0.004   0.049   1802
  Dihedral  :  4.861  51.259   1467
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 28.83 %
    Favored  : 66.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.11 (0.24), residues: 1285
  helix:  1.61 (0.26), residues: 413
  sheet: -0.19 (0.28), residues: 340
  loop : -1.34 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  75 
 HIS   0.006   0.001   HIS S 167 
 PHE   0.014   0.001   PHE C 189 
 TYR   0.024   0.001   TYR S 235 
 ARG   0.004   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04076 (  459)
  hydrogen bonds       : angle       4.52274 ( 1332)
  SS BOND              : bond        0.00469 (    6)
  SS BOND              : angle       1.68838 (   12)
  covalent geometry    : bond        0.00289 (10566)
  covalent geometry    : angle       0.57723 (14325)

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

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

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 163
  time to evaluate  : 1.391 
Fit side-chains
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   60 TYR cc_start: 0.5971 (m-80) cc_final: 0.5134 (m-80)
REVERT: S  141 THR cc_start: 0.5753 (m) cc_final: 0.5384 (p)
REVERT: S  171 ASN cc_start: 0.7134 (m-40) cc_final: 0.6733 (m-40)
REVERT: B   27 ASP cc_start: 0.7663 (t0) cc_final: 0.7436 (t0)
REVERT: B  292 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8038 (m-80)
REVERT: C   21 ARG cc_start: 0.7410 (ttp80) cc_final: 0.6981 (mtm110)
REVERT: C   22 ASN cc_start: 0.7742 (t0) cc_final: 0.7446 (t0)
REVERT: C  227 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8028 (pp)
REVERT: C  309 ASP cc_start: 0.7753 (m-30) cc_final: 0.7383 (m-30)
REVERT: G   32 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.7877 (ttpp)
REVERT: G   36 ASP cc_start: 0.7998 (m-30) cc_final: 0.7610 (m-30)
REVERT: D   45 PHE cc_start: 0.7431 (t80) cc_final: 0.7171 (t80)
REVERT: D   79 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6835 (tp)
  outliers start: 53
  outliers final: 33
  residues processed: 205
  average time/residue: 0.2126
  time to fit residues: 63.1706
Evaluate side-chains
  194 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 157
  time to evaluate  : 1.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   85 SER
Chi-restraints excluded: chain S residue  168 SER
Chi-restraints excluded: chain S residue  237 LEU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   32 LYS
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  103 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 119 optimal weight:    9.9990
   chunk 67 optimal weight:    2.9990
   chunk 6 optimal weight:   10.0000
   chunk 85 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0170
   chunk 69 optimal weight:    5.9990
   overall best weight:    1.5022

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

Flipped N/Q/H residues before XYZ refinement:
A 189 ASN
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  11 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.173529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.115646 restraints weight = 14174.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 3.11
r_work: 0.3311 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10572  Z= 0.169
  Angle     :  0.607   8.960  14337  Z= 0.318
  Chirality :  0.043   0.156   1605
  Planarity :  0.004   0.052   1802
  Dihedral  :  4.929  51.381   1467
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 29.01 %
    Favored  : 65.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.24), residues: 1285
  helix:  1.54 (0.26), residues: 413
  sheet: -0.26 (0.28), residues: 339
  loop : -1.29 (0.26), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP S 111 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.014   0.001   PHE C 189 
 TYR   0.026   0.002   TYR S 235 
 ARG   0.003   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04455 (  459)
  hydrogen bonds       : angle       4.58846 ( 1332)
  SS BOND              : bond        0.00591 (    6)
  SS BOND              : angle       1.82188 (   12)
  covalent geometry    : bond        0.00399 (10566)
  covalent geometry    : angle       0.60464 (14325)

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

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

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 155
  time to evaluate  : 1.241 
Fit side-chains
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   18 ARG cc_start: 0.6092 (mmm-85) cc_final: 0.5791 (mmm-85)
REVERT: S   60 TYR cc_start: 0.6136 (m-80) cc_final: 0.5269 (m-80)
REVERT: S  141 THR cc_start: 0.5685 (m) cc_final: 0.5281 (p)
REVERT: S  171 ASN cc_start: 0.7172 (m-40) cc_final: 0.6836 (m-40)
REVERT: B   27 ASP cc_start: 0.7671 (t0) cc_final: 0.7304 (t0)
REVERT: B  292 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8119 (m-80)
REVERT: C   22 ASN cc_start: 0.7777 (t0) cc_final: 0.7537 (t0)
REVERT: C  227 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8074 (pp)
REVERT: C  309 ASP cc_start: 0.7767 (m-30) cc_final: 0.7403 (m-30)
REVERT: G   32 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7889 (ttpp)
REVERT: G   36 ASP cc_start: 0.7939 (m-30) cc_final: 0.7551 (m-30)
REVERT: D   11 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8609 (pp30)
REVERT: D   79 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6872 (tp)
REVERT: D   81 CYS cc_start: 0.6436 (t) cc_final: 0.6018 (t)
  outliers start: 58
  outliers final: 40
  residues processed: 199
  average time/residue: 0.2514
  time to fit residues: 71.7867
Evaluate side-chains
  199 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 154
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  253 ILE
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   32 LYS
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain D residue    3 THR
Chi-restraints excluded: chain D residue   11 GLN
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  103 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 8 optimal weight:    8.9990
   chunk 70 optimal weight:    0.9990
   chunk 11 optimal weight:   10.0000
   chunk 60 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 125 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 59 optimal weight:    0.6980
   chunk 12 optimal weight:   20.0000
   chunk 100 optimal weight:    2.9990
   chunk 115 optimal weight:    6.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN
D  11 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.171297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.113362 restraints weight = 14349.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 3.11
r_work: 0.3284 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  10572  Z= 0.222
  Angle     :  0.643   8.990  14337  Z= 0.340
  Chirality :  0.045   0.167   1605
  Planarity :  0.004   0.053   1802
  Dihedral  :  5.097  51.618   1467
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 29.63 %
    Favored  : 64.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.24), residues: 1285
  helix:  1.36 (0.26), residues: 413
  sheet: -0.42 (0.28), residues: 335
  loop : -1.35 (0.26), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP S 111 
 HIS   0.006   0.001   HIS D  18 
 PHE   0.042   0.002   PHE D  45 
 TYR   0.026   0.002   TYR S 235 
 ARG   0.003   0.000   ARG G  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04916 (  459)
  hydrogen bonds       : angle       4.75035 ( 1332)
  SS BOND              : bond        0.00702 (    6)
  SS BOND              : angle       1.98924 (   12)
  covalent geometry    : bond        0.00528 (10566)
  covalent geometry    : angle       0.64101 (14325)

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

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

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 157
  time to evaluate  : 1.188 
Fit side-chains
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   18 ARG cc_start: 0.6199 (mmm-85) cc_final: 0.5878 (mmm-85)
REVERT: S   60 TYR cc_start: 0.6287 (m-80) cc_final: 0.5423 (m-80)
REVERT: S  141 THR cc_start: 0.5654 (m) cc_final: 0.5270 (p)
REVERT: S  171 ASN cc_start: 0.7198 (m-40) cc_final: 0.6950 (m-40)
REVERT: B   27 ASP cc_start: 0.7707 (t0) cc_final: 0.7278 (t0)
REVERT: B  292 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8157 (m-80)
REVERT: C   21 ARG cc_start: 0.7325 (ttp80) cc_final: 0.6868 (mtm110)
REVERT: C   22 ASN cc_start: 0.7769 (t0) cc_final: 0.7467 (t0)
REVERT: C  227 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8085 (pp)
REVERT: C  309 ASP cc_start: 0.7755 (m-30) cc_final: 0.7390 (m-30)
REVERT: G   32 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7888 (ttpp)
REVERT: G   36 ASP cc_start: 0.8065 (m-30) cc_final: 0.7707 (m-30)
  outliers start: 65
  outliers final: 51
  residues processed: 207
  average time/residue: 0.2517
  time to fit residues: 74.6358
Evaluate side-chains
  208 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 154
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  145 SER
Chi-restraints excluded: chain S residue  168 SER
Chi-restraints excluded: chain A residue   23 SER
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  307 ILE
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain C residue  253 ILE
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain C residue  314 LYS
Chi-restraints excluded: chain G residue   25 ILE
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   32 LYS
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain D residue    3 THR
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  103 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 121 optimal weight:    9.9990
   chunk 54 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9990
   chunk 19 optimal weight:    0.1980
   chunk 107 optimal weight:    0.5980
   chunk 18 optimal weight:    6.9990
   chunk 94 optimal weight:    0.2980
   chunk 32 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0770
   chunk 111 optimal weight:    3.9990
   overall best weight:    0.4340

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.176801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.119591 restraints weight = 14112.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 3.13
r_work: 0.3363 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10572  Z= 0.110
  Angle     :  0.573   7.968  14337  Z= 0.301
  Chirality :  0.042   0.149   1605
  Planarity :  0.004   0.055   1802
  Dihedral  :  4.810  52.889   1467
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 31.42 %
    Favored  : 64.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.24), residues: 1285
  helix:  1.69 (0.26), residues: 412
  sheet: -0.19 (0.28), residues: 323
  loop : -1.28 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  75 
 HIS   0.015   0.001   HIS D  20 
 PHE   0.033   0.001   PHE D  45 
 TYR   0.025   0.001   TYR S 235 
 ARG   0.005   0.000   ARG C 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03685 (  459)
  hydrogen bonds       : angle       4.39547 ( 1332)
  SS BOND              : bond        0.00391 (    6)
  SS BOND              : angle       1.72597 (   12)
  covalent geometry    : bond        0.00236 (10566)
  covalent geometry    : angle       0.57079 (14325)

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

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

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 157
  time to evaluate  : 1.167 
Fit side-chains
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   18 ARG cc_start: 0.6037 (mmm-85) cc_final: 0.5722 (mmm-85)
REVERT: S   60 TYR cc_start: 0.6083 (m-80) cc_final: 0.5243 (m-80)
REVERT: S  171 ASN cc_start: 0.7161 (m-40) cc_final: 0.6935 (m-40)
REVERT: A   23 SER cc_start: 0.7844 (OUTLIER) cc_final: 0.7053 (t)
REVERT: A   68 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8266 (ttpp)
REVERT: A  282 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.7898 (mtp)
REVERT: B   27 ASP cc_start: 0.7565 (t0) cc_final: 0.7316 (t0)
REVERT: B  197 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6735 (tpt170)
REVERT: C   21 ARG cc_start: 0.7394 (ttp80) cc_final: 0.6907 (mtm110)
REVERT: C   22 ASN cc_start: 0.7761 (t0) cc_final: 0.7455 (t0)
REVERT: C  309 ASP cc_start: 0.7780 (m-30) cc_final: 0.7374 (m-30)
REVERT: G   32 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8316 (ttpp)
  outliers start: 46
  outliers final: 36
  residues processed: 194
  average time/residue: 0.2144
  time to fit residues: 59.3201
Evaluate side-chains
  194 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 153
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain A residue   23 SER
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   68 LYS
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   32 LYS
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  103 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 49 optimal weight:   10.0000
   chunk 50 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 5 optimal weight:   10.0000
   chunk 116 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 114 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0470
   overall best weight:    1.1682

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

Flipped N/Q/H residues before XYZ refinement:
A 189 ASN
** A 192 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 = 0.4101 r_free = 0.4101 target = 0.174299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.116597 restraints weight = 14189.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 3.12
r_work: 0.3323 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10572  Z= 0.145
  Angle     :  0.597   8.798  14337  Z= 0.311
  Chirality :  0.043   0.151   1605
  Planarity :  0.004   0.055   1802
  Dihedral  :  4.801  52.538   1467
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 31.15 %
    Favored  : 64.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.24), residues: 1285
  helix:  1.67 (0.26), residues: 413
  sheet: -0.23 (0.28), residues: 331
  loop : -1.27 (0.26), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP S  47 
 HIS   0.012   0.001   HIS D  20 
 PHE   0.033   0.001   PHE D  45 
 TYR   0.025   0.001   TYR S 235 
 ARG   0.006   0.000   ARG C 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04124 (  459)
  hydrogen bonds       : angle       4.37343 ( 1332)
  SS BOND              : bond        0.00552 (    6)
  SS BOND              : angle       1.83112 (   12)
  covalent geometry    : bond        0.00339 (10566)
  covalent geometry    : angle       0.59513 (14325)

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

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

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 150
  time to evaluate  : 1.889 
Fit side-chains
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   60 TYR cc_start: 0.6128 (m-80) cc_final: 0.5287 (m-80)
REVERT: S  171 ASN cc_start: 0.7168 (m-40) cc_final: 0.6904 (m-40)
REVERT: A  268 TRP cc_start: 0.8272 (t60) cc_final: 0.7936 (t60)
REVERT: A  282 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8015 (mtp)
REVERT: B   27 ASP cc_start: 0.7611 (t0) cc_final: 0.7374 (t0)
REVERT: B  292 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8096 (m-80)
REVERT: C   22 ASN cc_start: 0.7757 (t0) cc_final: 0.7483 (t0)
REVERT: C  309 ASP cc_start: 0.7714 (m-30) cc_final: 0.7299 (m-30)
REVERT: C  341 ASP cc_start: 0.8262 (t0) cc_final: 0.7529 (m-30)
REVERT: G   32 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8258 (ttpp)
  outliers start: 51
  outliers final: 40
  residues processed: 190
  average time/residue: 0.2338
  time to fit residues: 66.2772
Evaluate side-chains
  194 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 151
  time to evaluate  : 1.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  145 SER
Chi-restraints excluded: chain A residue   23 SER
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  198 MET
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   32 LYS
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  103 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 65 optimal weight:    0.0670
   chunk 75 optimal weight:    4.9990
   chunk 103 optimal weight:    8.9990
   chunk 58 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 123 optimal weight:    7.9990
   chunk 63 optimal weight:    0.0970
   chunk 59 optimal weight:    0.7980
   chunk 1 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9980
   chunk 13 optimal weight:   20.0000
   overall best weight:    0.9918

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

Flipped N/Q/H residues before XYZ refinement:
A 189 ASN
** A 192 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 = 0.4110 r_free = 0.4110 target = 0.175158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.117721 restraints weight = 14148.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 3.12
r_work: 0.3335 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10572  Z= 0.131
  Angle     :  0.583   8.233  14337  Z= 0.304
  Chirality :  0.042   0.153   1605
  Planarity :  0.004   0.053   1802
  Dihedral  :  4.751  53.134   1467
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 31.60 %
    Favored  : 64.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.24), residues: 1285
  helix:  1.70 (0.26), residues: 413
  sheet: -0.15 (0.28), residues: 319
  loop : -1.29 (0.26), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  75 
 HIS   0.011   0.001   HIS D  20 
 PHE   0.032   0.001   PHE D  45 
 TYR   0.024   0.001   TYR S 235 
 ARG   0.006   0.000   ARG C 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03911 (  459)
  hydrogen bonds       : angle       4.32341 ( 1332)
  SS BOND              : bond        0.00570 (    6)
  SS BOND              : angle       1.72525 (   12)
  covalent geometry    : bond        0.00302 (10566)
  covalent geometry    : angle       0.58158 (14325)

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

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

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2570 Ramachandran restraints generated.
    1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 149
  time to evaluate  : 1.147 
Fit side-chains
TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   60 TYR cc_start: 0.6169 (m-80) cc_final: 0.5398 (m-80)
REVERT: S   81 LEU cc_start: 0.7959 (tp) cc_final: 0.7749 (tp)
REVERT: S  171 ASN cc_start: 0.7216 (m-40) cc_final: 0.6978 (m-40)
REVERT: A  268 TRP cc_start: 0.8231 (t60) cc_final: 0.7894 (t60)
REVERT: A  282 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8039 (mtp)
REVERT: B   27 ASP cc_start: 0.7611 (t0) cc_final: 0.7371 (t0)
REVERT: B  292 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8127 (m-80)
REVERT: C   21 ARG cc_start: 0.7419 (ttp80) cc_final: 0.7032 (mtp-110)
REVERT: C   22 ASN cc_start: 0.7800 (t0) cc_final: 0.7459 (t0)
REVERT: C  309 ASP cc_start: 0.7719 (m-30) cc_final: 0.7291 (m-30)
REVERT: G   32 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8306 (ttpp)
  outliers start: 45
  outliers final: 41
  residues processed: 185
  average time/residue: 0.2123
  time to fit residues: 57.0254
Evaluate side-chains
  191 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 147
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   45 LEU
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue  145 SER
Chi-restraints excluded: chain A residue   23 SER
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  154 ASP
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  278 ILE
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain G residue   32 LYS
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  103 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 109 optimal weight:   10.0000
   chunk 5 optimal weight:    8.9990
   chunk 91 optimal weight:    0.8980
   chunk 9 optimal weight:   10.0000
   chunk 28 optimal weight:    0.0060
   chunk 44 optimal weight:    0.0870
   chunk 51 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 74 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    2.1978

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

Flipped N/Q/H residues before XYZ refinement:
A 189 ASN
** A 192 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 = 0.4068 r_free = 0.4068 target = 0.171005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.113382 restraints weight = 14130.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 3.08
r_work: 0.3277 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  10572  Z= 0.225
  Angle     :  0.650   8.792  14337  Z= 0.342
  Chirality :  0.045   0.163   1605
  Planarity :  0.004   0.052   1802
  Dihedral  :  5.013  52.236   1467
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 31.60 %
    Favored  : 64.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.24), residues: 1285
  helix:  1.51 (0.26), residues: 413
  sheet: -0.36 (0.28), residues: 331
  loop : -1.33 (0.27), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.010   0.001   HIS D  20 
 PHE   0.031   0.002   PHE D  45 
 TYR   0.026   0.002   TYR S 235 
 ARG   0.006   0.000   ARG C 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04852 (  459)
  hydrogen bonds       : angle       4.59237 ( 1332)
  SS BOND              : bond        0.00735 (    6)
  SS BOND              : angle       2.12731 (   12)
  covalent geometry    : bond        0.00537 (10566)
  covalent geometry    : angle       0.64752 (14325)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6237.75 seconds
wall clock time: 110 minutes 6.39 seconds (6606.39 seconds total)