Starting phenix.real_space_refine
on Sun Jan 19 19:24:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rk5_19260/01_2025/8rk5_19260.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rk5_19260/01_2025/8rk5_19260.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rk5_19260/01_2025/8rk5_19260.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rk5_19260/01_2025/8rk5_19260.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rk5_19260/01_2025/8rk5_19260.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rk5_19260/01_2025/8rk5_19260.cif"
  }
  resolution = 4.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      48      5.16       5
     C    9177      2.51       5
     N    2496      2.21       5
     O    2703      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 72 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 14424
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2470
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2470
          Classifications: {'peptide': 317}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 295}
    Chain: "B"
      Number of atoms: 2338
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2338
          Classifications: {'peptide': 305}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 285}
  Restraints were copied for chains:
    E, F, C, D
  Time building chain proxies: 8.10, per 1000 atoms: 0.56
  Number of scatterers: 14424
  At special positions: 0
  Unit cell: (118.371, 114.203, 145.046, 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      48     16.00
     O    2703      8.00
     N    2496      7.00
     C    9177      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 142 " - pdb=" SG  CYS B 174 " 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=10, symmetry=0
  Number of additional bonds: simple=10, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.88
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3336

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 21 sheets defined
      11.1% alpha, 29.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 25
    Processing helix  chain 'A' and resid 25 through 31
    Processing helix  chain 'A' and resid 94 through 98
      removed outlier: 3.534A  pdb=" N   ILE A  98 " --> pdb=" O   PRO A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 223
      removed outlier: 3.618A  pdb=" N   TYR A 222 " --> pdb=" O   GLU A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 235
    Processing helix  chain 'A' and resid 308 through 310
      No H-bonds generated for 'chain 'A' and resid 308 through 310'
    Processing helix  chain 'B' and resid 10 through 25
      removed outlier: 3.533A  pdb=" N   LEU B  14 " --> pdb=" O   ASN B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 184
    Processing helix  chain 'B' and resid 217 through 223
      removed outlier: 3.560A  pdb=" N   ILE B 221 " --> pdb=" O   ASP B 217 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 25
    Processing helix  chain 'C' and resid 25 through 31
    Processing helix  chain 'C' and resid 94 through 98
      removed outlier: 3.533A  pdb=" N   ILE C  98 " --> pdb=" O   PRO C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 219 through 223
      removed outlier: 3.618A  pdb=" N   TYR C 222 " --> pdb=" O   GLU C 219 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 231 through 235
    Processing helix  chain 'C' and resid 308 through 310
      No H-bonds generated for 'chain 'C' and resid 308 through 310'
    Processing helix  chain 'E' and resid 10 through 25
      removed outlier: 3.533A  pdb=" N   LEU E  14 " --> pdb=" O   ASN E  10 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 180 through 184
    Processing helix  chain 'E' and resid 217 through 223
      removed outlier: 3.560A  pdb=" N   ILE E 221 " --> pdb=" O   ASP E 217 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 10 through 25
    Processing helix  chain 'D' and resid 25 through 31
    Processing helix  chain 'D' and resid 94 through 98
      removed outlier: 3.534A  pdb=" N   ILE D  98 " --> pdb=" O   PRO D  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 219 through 223
      removed outlier: 3.618A  pdb=" N   TYR D 222 " --> pdb=" O   GLU D 219 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 231 through 235
    Processing helix  chain 'D' and resid 308 through 310
      No H-bonds generated for 'chain 'D' and resid 308 through 310'
    Processing helix  chain 'F' and resid 10 through 25
      removed outlier: 3.533A  pdb=" N   LEU F  14 " --> pdb=" O   ASN F  10 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 180 through 184
    Processing helix  chain 'F' and resid 217 through 223
      removed outlier: 3.561A  pdb=" N   ILE F 221 " --> pdb=" O   ASP F 217 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8
      removed outlier: 4.882A  pdb=" N   LEU A 166 " --> pdb=" O   ARG A 201 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 41
      removed outlier: 6.466A  pdb=" N   THR A  56 " --> pdb=" O   VAL A  38 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   ASP A  40 " --> pdb=" O   GLN A  54 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   GLN A  54 " --> pdb=" O   ASP A  40 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN A 116 " --> pdb=" O   TYR A 172 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   TYR A 172 " --> pdb=" O   GLN A 116 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 225 through 227
      removed outlier: 9.889A  pdb=" N   LYS A 256 " --> pdb=" O   GLY A 276 " (cutoff:3.500A)
      removed outlier: 8.856A  pdb=" N   GLY A 276 " --> pdb=" O   LYS A 256 " (cutoff:3.500A)
      removed outlier: 5.332A  pdb=" N   LEU A 258 " --> pdb=" O   PHE A 274 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   GLY A 272 " --> pdb=" O   PHE A 260 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   THR A 262 " --> pdb=" O   TYR A 270 " (cutoff:3.500A)
      removed outlier: 5.642A  pdb=" N   TYR A 270 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   GLY A 276 " --> pdb=" O   ARG A 316 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 247
      removed outlier: 4.585A  pdb=" N   TYR B 250 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
      removed outlier: 5.513A  pdb=" N   TYR B 250 " --> pdb=" O   ALA B 241 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   ALA B 241 " --> pdb=" O   TYR B 250 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   GLY B 252 " --> pdb=" O   ILE B 239 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 8
      removed outlier: 5.719A  pdb=" N   ALA B   8 " --> pdb=" O   THR B  98 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   THR B  98 " --> pdb=" O   ALA B   8 " (cutoff:3.500A)
      removed outlier: 8.503A  pdb=" N   PHE B  97 " --> pdb=" O   ALA B 116 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ALA B 116 " --> pdb=" O   PHE B  97 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   HIS B 110 " --> pdb=" O   ILE B 125 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   ILE B 125 " --> pdb=" O   HIS B 110 " (cutoff:3.500A)
      removed outlier: 5.362A  pdb=" N   HIS B 112 " --> pdb=" O   VAL B 123 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   VAL B 123 " --> pdb=" O   HIS B 112 " (cutoff:3.500A)
      removed outlier: 5.497A  pdb=" N   GLU B 114 " --> pdb=" O   ARG B 121 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   ARG B 121 " --> pdb=" O   GLU B 114 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   GLN B 139 " --> pdb=" O   ARG B 177 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 28 through 32
      removed outlier: 5.031A  pdb=" N   THR B  29 " --> pdb=" O   HIS B  40 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   HIS B  40 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   TYR B  45 " --> pdb=" O   ASN B  60 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 257 through 261
      removed outlier: 4.310A  pdb=" N   THR B 277 " --> pdb=" O   VAL B 305 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 8
      removed outlier: 4.882A  pdb=" N   LEU C 166 " --> pdb=" O   ARG C 201 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 36 through 41
      removed outlier: 6.465A  pdb=" N   THR C  56 " --> pdb=" O   VAL C  38 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   ASP C  40 " --> pdb=" O   GLN C  54 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   GLN C  54 " --> pdb=" O   ASP C  40 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLN C 116 " --> pdb=" O   TYR C 172 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   TYR C 172 " --> pdb=" O   GLN C 116 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 225 through 227
      removed outlier: 9.889A  pdb=" N   LYS C 256 " --> pdb=" O   GLY C 276 " (cutoff:3.500A)
      removed outlier: 8.856A  pdb=" N   GLY C 276 " --> pdb=" O   LYS C 256 " (cutoff:3.500A)
      removed outlier: 5.332A  pdb=" N   LEU C 258 " --> pdb=" O   PHE C 274 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   GLY C 272 " --> pdb=" O   PHE C 260 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   THR C 262 " --> pdb=" O   TYR C 270 " (cutoff:3.500A)
      removed outlier: 5.642A  pdb=" N   TYR C 270 " --> pdb=" O   THR C 262 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   GLY C 276 " --> pdb=" O   ARG C 316 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 246 through 247
      removed outlier: 4.584A  pdb=" N   TYR E 250 " --> pdb=" O   ARG C 247 " (cutoff:3.500A)
      removed outlier: 5.513A  pdb=" N   TYR E 250 " --> pdb=" O   ALA E 241 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ALA E 241 " --> pdb=" O   TYR E 250 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   GLY E 252 " --> pdb=" O   ILE E 239 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 8
      removed outlier: 5.719A  pdb=" N   ALA E   8 " --> pdb=" O   THR E  98 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   THR E  98 " --> pdb=" O   ALA E   8 " (cutoff:3.500A)
      removed outlier: 8.503A  pdb=" N   PHE E  97 " --> pdb=" O   ALA E 116 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ALA E 116 " --> pdb=" O   PHE E  97 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   HIS E 110 " --> pdb=" O   ILE E 125 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   ILE E 125 " --> pdb=" O   HIS E 110 " (cutoff:3.500A)
      removed outlier: 5.363A  pdb=" N   HIS E 112 " --> pdb=" O   VAL E 123 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   VAL E 123 " --> pdb=" O   HIS E 112 " (cutoff:3.500A)
      removed outlier: 5.496A  pdb=" N   GLU E 114 " --> pdb=" O   ARG E 121 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   ARG E 121 " --> pdb=" O   GLU E 114 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   GLN E 139 " --> pdb=" O   ARG E 177 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 28 through 32
      removed outlier: 5.031A  pdb=" N   THR E  29 " --> pdb=" O   HIS E  40 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   HIS E  40 " --> pdb=" O   THR E  29 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   TYR E  45 " --> pdb=" O   ASN E  60 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 257 through 261
      removed outlier: 4.310A  pdb=" N   THR E 277 " --> pdb=" O   VAL E 305 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 8
      removed outlier: 4.882A  pdb=" N   LEU D 166 " --> pdb=" O   ARG D 201 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 36 through 41
      removed outlier: 6.466A  pdb=" N   THR D  56 " --> pdb=" O   VAL D  38 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   ASP D  40 " --> pdb=" O   GLN D  54 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   GLN D  54 " --> pdb=" O   ASP D  40 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLN D 116 " --> pdb=" O   TYR D 172 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   TYR D 172 " --> pdb=" O   GLN D 116 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 225 through 227
      removed outlier: 9.890A  pdb=" N   LYS D 256 " --> pdb=" O   GLY D 276 " (cutoff:3.500A)
      removed outlier: 8.856A  pdb=" N   GLY D 276 " --> pdb=" O   LYS D 256 " (cutoff:3.500A)
      removed outlier: 5.332A  pdb=" N   LEU D 258 " --> pdb=" O   PHE D 274 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   GLY D 272 " --> pdb=" O   PHE D 260 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   THR D 262 " --> pdb=" O   TYR D 270 " (cutoff:3.500A)
      removed outlier: 5.642A  pdb=" N   TYR D 270 " --> pdb=" O   THR D 262 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   GLY D 276 " --> pdb=" O   ARG D 316 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 246 through 247
      removed outlier: 4.585A  pdb=" N   TYR F 250 " --> pdb=" O   ARG D 247 " (cutoff:3.500A)
      removed outlier: 5.513A  pdb=" N   TYR F 250 " --> pdb=" O   ALA F 241 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ALA F 241 " --> pdb=" O   TYR F 250 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   GLY F 252 " --> pdb=" O   ILE F 239 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 3 through 8
      removed outlier: 5.719A  pdb=" N   ALA F   8 " --> pdb=" O   THR F  98 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   THR F  98 " --> pdb=" O   ALA F   8 " (cutoff:3.500A)
      removed outlier: 8.502A  pdb=" N   PHE F  97 " --> pdb=" O   ALA F 116 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ALA F 116 " --> pdb=" O   PHE F  97 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   HIS F 110 " --> pdb=" O   ILE F 125 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   ILE F 125 " --> pdb=" O   HIS F 110 " (cutoff:3.500A)
      removed outlier: 5.363A  pdb=" N   HIS F 112 " --> pdb=" O   VAL F 123 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   VAL F 123 " --> pdb=" O   HIS F 112 " (cutoff:3.500A)
      removed outlier: 5.496A  pdb=" N   GLU F 114 " --> pdb=" O   ARG F 121 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   ARG F 121 " --> pdb=" O   GLU F 114 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   GLN F 139 " --> pdb=" O   ARG F 177 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 28 through 32
      removed outlier: 5.031A  pdb=" N   THR F  29 " --> pdb=" O   HIS F  40 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   HIS F  40 " --> pdb=" O   THR F  29 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   TYR F  45 " --> pdb=" O   ASN F  60 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 257 through 261
      removed outlier: 4.309A  pdb=" N   THR F 277 " --> pdb=" O   VAL F 305 " (cutoff:3.500A)

    459 hydrogen bonds defined for protein.
    1224 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: 4.84

  Time building geometry restraints manager: 4.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4731
        1.34 -     1.46: 2990
        1.46 -     1.57: 7078
        1.57 -     1.69: 0
        1.69 -     1.81: 69
  Bond restraints: 14868
  Sorted by residual:
  bond pdb=" C   ILE D  43 "
       pdb=" N   PRO D  44 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.20e-02 6.94e+03 1.99e+00
  bond pdb=" C   ILE C  43 "
       pdb=" N   PRO C  44 "
    ideal  model  delta    sigma   weight residual
    1.329  1.345 -0.017 1.20e-02 6.94e+03 1.89e+00
  bond pdb=" C   ILE A  43 "
       pdb=" N   PRO A  44 "
    ideal  model  delta    sigma   weight residual
    1.329  1.345 -0.016 1.20e-02 6.94e+03 1.87e+00
  bond pdb=" N   GLU D 288 "
       pdb=" CA  GLU D 288 "
    ideal  model  delta    sigma   weight residual
    1.458  1.475 -0.017 1.37e-02 5.33e+03 1.53e+00
  bond pdb=" CB  TRP F  37 "
       pdb=" CG  TRP F  37 "
    ideal  model  delta    sigma   weight residual
    1.498  1.460  0.038 3.10e-02 1.04e+03 1.48e+00
  ... (remaining 14863 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 19329
        1.40 -     2.80: 822
        2.80 -     4.20: 137
        4.20 -     5.60: 25
        5.60 -     7.00: 9
  Bond angle restraints: 20322
  Sorted by residual:
  angle pdb=" C   ALA D 287 "
        pdb=" N   GLU D 288 "
        pdb=" CA  GLU D 288 "
      ideal   model   delta    sigma   weight residual
     125.02  131.23   -6.21 1.76e+00 3.23e-01 1.25e+01
  angle pdb=" C   ALA C 287 "
        pdb=" N   GLU C 288 "
        pdb=" CA  GLU C 288 "
      ideal   model   delta    sigma   weight residual
     125.02  131.21   -6.19 1.76e+00 3.23e-01 1.24e+01
  angle pdb=" C   ALA A 287 "
        pdb=" N   GLU A 288 "
        pdb=" CA  GLU A 288 "
      ideal   model   delta    sigma   weight residual
     125.02  131.20   -6.18 1.76e+00 3.23e-01 1.23e+01
  angle pdb=" CA  GLU D 288 "
        pdb=" CB  GLU D 288 "
        pdb=" CG  GLU D 288 "
      ideal   model   delta    sigma   weight residual
     114.10  120.17   -6.07 2.00e+00 2.50e-01 9.23e+00
  angle pdb=" CA  GLU C 288 "
        pdb=" CB  GLU C 288 "
        pdb=" CG  GLU C 288 "
      ideal   model   delta    sigma   weight residual
     114.10  120.15   -6.05 2.00e+00 2.50e-01 9.16e+00
  ... (remaining 20317 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 7901
       17.96 -    35.92: 497
       35.92 -    53.88: 86
       53.88 -    71.84: 6
       71.84 -    89.80: 9
  Dihedral angle restraints: 8499
    sinusoidal: 3195
      harmonic: 5304
  Sorted by residual:
  dihedral pdb=" CA  TRP F  37 "
           pdb=" C   TRP F  37 "
           pdb=" N   LEU F  38 "
           pdb=" CA  LEU F  38 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.92   17.08     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  TRP E  37 "
           pdb=" C   TRP E  37 "
           pdb=" N   LEU E  38 "
           pdb=" CA  LEU E  38 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.94   17.06     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  TRP B  37 "
           pdb=" C   TRP B  37 "
           pdb=" N   LEU B  38 "
           pdb=" CA  LEU B  38 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.96   17.04     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 8496 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1098
       0.027 -    0.054: 654
       0.054 -    0.082: 181
       0.082 -    0.109: 117
       0.109 -    0.136: 62
  Chirality restraints: 2112
  Sorted by residual:
  chirality pdb=" CA  ILE D 144 "
            pdb=" N   ILE D 144 "
            pdb=" C   ILE D 144 "
            pdb=" CB  ILE D 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  chirality pdb=" CA  ILE A 144 "
            pdb=" N   ILE A 144 "
            pdb=" C   ILE A 144 "
            pdb=" CB  ILE A 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.33e-01
  chirality pdb=" CA  ILE F 125 "
            pdb=" N   ILE F 125 "
            pdb=" C   ILE F 125 "
            pdb=" CB  ILE F 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 2109 not shown)

  Planarity restraints: 2694
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 204 "   -0.039 5.00e-02 4.00e+02   5.98e-02 5.73e+00
        pdb=" N   PRO B 205 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO B 205 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 205 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY F 204 "    0.039 5.00e-02 4.00e+02   5.98e-02 5.73e+00
        pdb=" N   PRO F 205 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO F 205 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO F 205 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY E 204 "    0.039 5.00e-02 4.00e+02   5.98e-02 5.72e+00
        pdb=" N   PRO E 205 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO E 205 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO E 205 "    0.033 5.00e-02 4.00e+02
  ... (remaining 2691 not shown)

  Histogram of nonbonded interaction distances:
        0.55 -     1.42: 69
        1.42 -     2.29: 238
        2.29 -     3.16: 13064
        3.16 -     4.03: 36671
        4.03 -     4.90: 68628
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 118670
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B 245 "
            pdb=" CA  ALA C  79 "
     model   vdw
     0.555 3.470
  nonbonded pdb=" CD  ARG A 306 "
            pdb=" CB  VAL C 183 "
     model   vdw
     0.573 3.870
  nonbonded pdb=" CA  ALA A  79 "
            pdb=" CD  GLN E 245 "
     model   vdw
     0.605 3.700
  nonbonded pdb=" N   PRO A  99 "
            pdb=" NH1 ARG F 286 "
     model   vdw
     0.652 3.200
  nonbonded pdb=" CA  ALA A  79 "
            pdb=" OE1 GLN E 245 "
     model   vdw
     0.664 3.470
  ... (remaining 118665 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: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  Number of NCS constrained groups: 2
  pdb_interpretation.ncs_group {
  reference = chain 'B'
  selection = chain 'E'
  selection = chain 'F'
}
pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'D'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.640
  Check model and map are aligned:         0.110
  Set scattering table:                    0.120
  Process input model:                     34.090
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  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:   39.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4375
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      :  0.003   0.038  14868  Z= 0.190
  Angle     :  0.674   7.003  20322  Z= 0.391
  Chirality :  0.044   0.136   2112
  Planarity :  0.006   0.060   2694
  Dihedral  : 12.152  89.798   5160
  Min Nonbonded Distance : 0.555

Molprobity Statistics.
  All-atom Clashscore : 21.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.18), residues: 1854
  helix:  0.02 (0.38), residues: 153
  sheet:  0.08 (0.20), residues: 597
  loop : -1.23 (0.18), residues: 1104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 189 
 HIS   0.003   0.001   HIS A 298 
 PHE   0.018   0.001   PHE A 128 
 TYR   0.019   0.002   TYR E  82 
 ARG   0.011   0.001   ARG A 179 

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

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

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3708 Ramachandran restraints generated.
    1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   70 ASN cc_start: 0.7275 (p0) cc_final: 0.7062 (t0)
REVERT: B  286 ARG cc_start: 0.3551 (ttt-90) cc_final: 0.3028 (tpt170)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.1361
  time to fit residues: 10.1077
Evaluate side-chains
  40 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.275 
Evaluate side-chains
  66 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 TRP cc_start: 0.6618 (m100) cc_final: 0.6279 (m100)
REVERT: A  200 LEU cc_start: 0.8144 (tp) cc_final: 0.7925 (tp)
REVERT: A  260 PHE cc_start: 0.7328 (m-80) cc_final: 0.6391 (m-80)
REVERT: A  269 ARG cc_start: 0.6735 (ptp90) cc_final: 0.6003 (ttm170)
REVERT: A  288 GLU cc_start: 0.4162 (pp20) cc_final: 0.3907 (pp20)
REVERT: A  318 ASP cc_start: 0.7451 (t70) cc_final: 0.7221 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1405
  time to fit residues: 11.0654
Evaluate side-chains
  46 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 154 optimal weight:    4.9990
   chunk 138 optimal weight:    3.9990
   chunk 76 optimal weight:    0.0980
   chunk 47 optimal weight:    5.9990
   chunk 93 optimal weight:    5.9990
   chunk 74 optimal weight:    0.0040
   chunk 143 optimal weight:    9.9990
   chunk 55 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9980
   chunk 106 optimal weight:    8.9990
   chunk 166 optimal weight:    9.9990
   overall best weight:    2.0196
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 224 ASN
A 309 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.134447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.125661 restraints weight = 8013.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.128218 restraints weight = 5051.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.130056 restraints weight = 3346.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3968
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.129034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.119210 restraints weight = 7183.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.121627 restraints weight = 4649.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.123465 restraints weight = 3174.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4581
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104  14868  Z= 0.276
  Angle     :  0.732  11.539  20322  Z= 0.391
  Chirality :  0.048   0.188   2112
  Planarity :  0.006   0.065   2694
  Dihedral  :  4.876  22.372   2079
  Min Nonbonded Distance : 1.751

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.18), residues: 1854
  helix:  0.04 (0.37), residues: 138
  sheet:  0.04 (0.20), residues: 606
  loop : -1.24 (0.18), residues: 1110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP D 127 
 HIS   0.003   0.001   HIS E  21 
 PHE   0.063   0.003   PHE B 264 
 TYR   0.022   0.002   TYR A 126 
 ARG   0.009   0.001   ARG F 247 

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

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

  3706 Ramachandran restraints generated.
    1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3706 Ramachandran restraints generated.
    1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.1231
  time to fit residues: 7.2680
Evaluate side-chains
  33 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.275 
Evaluate side-chains
  51 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  136 TRP cc_start: 0.6529 (m100) cc_final: 0.6177 (m100)
REVERT: A  169 VAL cc_start: 0.5799 (p) cc_final: 0.5373 (p)
REVERT: A  269 ARG cc_start: 0.6177 (ptp90) cc_final: 0.5720 (mmt90)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1622
  time to fit residues: 9.7710
Evaluate side-chains
  41 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 104 optimal weight:    6.9990
   chunk 169 optimal weight:    0.0470
   chunk 108 optimal weight:    0.4980
   chunk 84 optimal weight:   10.0000
   chunk 32 optimal weight:    0.4980
   chunk 34 optimal weight:    9.9990
   chunk 92 optimal weight:    0.1980
   chunk 8 optimal weight:    2.9990
   chunk 93 optimal weight:    6.9990
   chunk 161 optimal weight:    0.5980
   chunk 71 optimal weight:    0.0170
   overall best weight:    0.2516
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  54 GLN
** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 261 ASN

Total number of N/Q/H flips: 2

Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.134584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.125963 restraints weight = 7780.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.128431 restraints weight = 4984.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.130211 restraints weight = 3333.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3977
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.129594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.120347 restraints weight = 7801.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.122538 restraints weight = 5127.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.124176 restraints weight = 3533.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4541
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.109  14868  Z= 0.350
  Angle     :  0.846  10.100  20322  Z= 0.465
  Chirality :  0.052   0.299   2112
  Planarity :  0.013   0.275   2694
  Dihedral  :  5.352  35.457   2079
  Min Nonbonded Distance : 1.745

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  3.64 %
    Favored  : 96.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.17), residues: 1854
  helix: -0.88 (0.36), residues: 135
  sheet:  0.02 (0.21), residues: 516
  loop : -1.65 (0.16), residues: 1203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.004   TRP D 127 
 HIS   0.012   0.002   HIS B 215 
 PHE   0.066   0.005   PHE B 264 
 TYR   0.036   0.003   TYR C  35 
 ARG   0.045   0.003   ARG A  53 

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

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

  3706 Ramachandran restraints generated.
    1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3706 Ramachandran restraints generated.
    1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0804
  time to fit residues: 4.4487
Evaluate side-chains
  35 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.249 
Evaluate side-chains
  45 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 TRP cc_start: 0.6835 (p90) cc_final: 0.5430 (p90)
REVERT: A  136 TRP cc_start: 0.6414 (m100) cc_final: 0.6188 (m100)
REVERT: A  169 VAL cc_start: 0.5644 (p) cc_final: 0.5240 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 45
  average time/residue: 0.1576
  time to fit residues: 8.3792
Evaluate side-chains
  37 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 145 optimal weight:    8.9990
   chunk 166 optimal weight:    0.0060
   chunk 154 optimal weight:    0.4980
   chunk 49 optimal weight:    0.5980
   chunk 108 optimal weight:    6.9990
   chunk 164 optimal weight:    0.7980
   chunk 163 optimal weight:    0.0770
   chunk 157 optimal weight:    4.9990
   chunk 161 optimal weight:    5.9990
   chunk 132 optimal weight:    0.0670
   chunk 170 optimal weight:    0.5980
   overall best weight:    0.2492
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 261 ASN

Total number of N/Q/H flips: 1

Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.134269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.125994 restraints weight = 7768.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.128461 restraints weight = 4819.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.130141 restraints weight = 3136.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3983
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.130869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.120565 restraints weight = 7754.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.123138 restraints weight = 4956.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.125144 restraints weight = 3355.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4512
moved from start:          0.3368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.110  14868  Z= 0.352
  Angle     :  0.848  10.145  20322  Z= 0.465
  Chirality :  0.052   0.299   2112
  Planarity :  0.014   0.275   2694
  Dihedral  :  5.352  35.455   2079
  Min Nonbonded Distance : 0.718

Molprobity Statistics.
  All-atom Clashscore : 23.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.17), residues: 1854
  helix: -0.88 (0.36), residues: 135
  sheet:  0.02 (0.21), residues: 516
  loop : -1.65 (0.16), residues: 1203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.004   TRP C 127 
 HIS   0.012   0.002   HIS F 215 
 PHE   0.066   0.005   PHE B 264 
 TYR   0.036   0.003   TYR C  35 
 ARG   0.045   0.003   ARG C  53 

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

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

  3706 Ramachandran restraints generated.
    1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3706 Ramachandran restraints generated.
    1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0816
  time to fit residues: 4.5026
Evaluate side-chains
  33 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.249 
Evaluate side-chains
  43 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 TRP cc_start: 0.6886 (p90) cc_final: 0.5442 (p90)
REVERT: A  169 VAL cc_start: 0.5657 (p) cc_final: 0.5254 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.1203
  time to fit residues: 6.4202
Evaluate side-chains
  35 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 161 optimal weight:    1.9990
   chunk 134 optimal weight:    1.9990
   chunk 51 optimal weight:    0.4980
   chunk 144 optimal weight:    3.9990
   chunk 165 optimal weight:    7.9990
   chunk 135 optimal weight:    0.2980
   chunk 111 optimal weight:    0.2980
   chunk 149 optimal weight:    0.9980
   chunk 107 optimal weight:    0.0040
   chunk 182 optimal weight:    0.0040
   overall best weight:    0.2204
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  94 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.134983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.125919 restraints weight = 8071.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.128364 restraints weight = 5150.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.130217 restraints weight = 3468.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3974
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.132173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.121566 restraints weight = 7538.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.124274 restraints weight = 4836.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.126172 restraints weight = 3297.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4537
moved from start:          0.3647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.258  14868  Z= 0.418
  Angle     :  0.834  11.140  20322  Z= 0.458
  Chirality :  0.054   0.305   2112
  Planarity :  0.011   0.225   2694
  Dihedral  :  5.301  29.209   2079
  Min Nonbonded Distance : 1.489

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.85 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.17), residues: 1854
  helix: -1.04 (0.36), residues: 135
  sheet: -0.17 (0.20), residues: 561
  loop : -1.79 (0.16), residues: 1158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.004   TRP C 120 
 HIS   0.020   0.002   HIS C 298 
 PHE   0.163   0.006   PHE F 264 
 TYR   0.038   0.003   TYR D  35 
 ARG   0.044   0.003   ARG C  53 

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

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

  3706 Ramachandran restraints generated.
    1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3706 Ramachandran restraints generated.
    1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: B  218 VAL cc_start: 0.7076 (t) cc_final: 0.6810 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0935
  time to fit residues: 5.0275
Evaluate side-chains
  32 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.290 
Evaluate side-chains
  50 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 TRP cc_start: 0.6967 (p90) cc_final: 0.6101 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1292
  time to fit residues: 7.9919
Evaluate side-chains
  37 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 84 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 141 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0030
   chunk 100 optimal weight:    0.0980
   chunk 108 optimal weight:    0.0170
   chunk 119 optimal weight:    0.0570
   chunk 23 optimal weight:    0.0070
   chunk 30 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0060
   overall best weight:    0.0180
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  54 GLN
** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.135235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.127583 restraints weight = 7950.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.129917 restraints weight = 5024.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.131531 restraints weight = 3294.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3993
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.131932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.120997 restraints weight = 7026.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.123777 restraints weight = 4596.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.125741 restraints weight = 3133.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4511
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.135  14868  Z= 0.326
  Angle     :  0.827  11.995  20322  Z= 0.439
  Chirality :  0.053   0.270   2112
  Planarity :  0.011   0.212   2694
  Dihedral  :  5.192  25.158   2079
  Min Nonbonded Distance : 1.597

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.87 (0.17), residues: 1854
  helix: -1.06 (0.37), residues: 135
  sheet: -0.30 (0.20), residues: 546
  loop : -1.82 (0.16), residues: 1173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.004   TRP C 127 
 HIS   0.077   0.006   HIS D 298 
 PHE   0.139   0.005   PHE D 129 
 TYR   0.036   0.003   TYR D 145 
 ARG   0.043   0.003   ARG C  53 

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

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

  3706 Ramachandran restraints generated.
    1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3706 Ramachandran restraints generated.
    1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: B  218 VAL cc_start: 0.7063 (t) cc_final: 0.6809 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.1118
  time to fit residues: 5.4445
Evaluate side-chains
  30 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.269 
Evaluate side-chains
  44 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 TRP cc_start: 0.6903 (p90) cc_final: 0.6148 (p90)
REVERT: A  317 LYS cc_start: 0.7485 (pttp) cc_final: 0.7020 (pptt)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.1554
  time to fit residues: 8.2423
Evaluate side-chains
  36 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 124 optimal weight:    6.9990
   chunk 104 optimal weight:    6.9990
   chunk 8 optimal weight:    9.9990
   chunk 142 optimal weight:    7.9990
   chunk 58 optimal weight:    8.9990
   chunk 98 optimal weight:    7.9990
   chunk 105 optimal weight:    6.9990
   chunk 52 optimal weight:    4.9990
   chunk 146 optimal weight:    9.9990
   chunk 145 optimal weight:    9.9990
   overall best weight:    6.7990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  94 ASN
A 187 HIS
A 309 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.127659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.119906 restraints weight = 7750.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.122197 restraints weight = 4810.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.123743 restraints weight = 3116.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.126743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.116238 restraints weight = 7512.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.118900 restraints weight = 4870.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.120839 restraints weight = 3323.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4785
moved from start:          0.4903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.093  14868  Z= 0.432
  Angle     :  0.885  11.417  20322  Z= 0.476
  Chirality :  0.051   0.185   2112
  Planarity :  0.011   0.201   2694
  Dihedral  :  5.844  30.610   2079
  Min Nonbonded Distance : 1.772

Molprobity Statistics.
  All-atom Clashscore : 19.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.42 %
    Favored  : 97.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.31 (0.17), residues: 1854
  helix: -1.20 (0.37), residues: 135
  sheet: -0.70 (0.19), residues: 591
  loop : -2.13 (0.16), residues: 1128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.005   TRP C 120 
 HIS   0.043   0.004   HIS C 298 
 PHE   0.100   0.006   PHE A   5 
 TYR   0.038   0.004   TYR D 270 
 ARG   0.041   0.003   ARG D  53 

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

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

  3706 Ramachandran restraints generated.
    1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3706 Ramachandran restraints generated.
    1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
REVERT: B  218 VAL cc_start: 0.7325 (t) cc_final: 0.7068 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.1507
  time to fit residues: 7.0971
Evaluate side-chains
  30 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.255 
Evaluate side-chains
  52 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A  169 VAL cc_start: 0.5904 (p) cc_final: 0.5639 (p)
REVERT: A  188 ARG cc_start: 0.5331 (ptm160) cc_final: 0.4834 (ptm160)
REVERT: A  190 ILE cc_start: 0.6632 (mt) cc_final: 0.6431 (tt)
REVERT: A  192 SER cc_start: 0.8275 (p) cc_final: 0.6726 (p)
REVERT: A  203 PRO cc_start: 0.7229 (Cg_exo) cc_final: 0.6195 (Cg_endo)
  outliers start: 1
  outliers final: 0
  residues processed: 52
  average time/residue: 0.1392
  time to fit residues: 8.9807
Evaluate side-chains
  34 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 72 optimal weight:    0.0070
   chunk 126 optimal weight:    9.9990
   chunk 61 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 98 optimal weight:   10.0000
   chunk 74 optimal weight:    0.5980
   chunk 153 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 169 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0060
   chunk 117 optimal weight:    7.9990
   overall best weight:    1.4816
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 160 HIS

Total number of N/Q/H flips: 1

Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.129197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.121568 restraints weight = 7849.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.123789 restraints weight = 4894.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.125214 restraints weight = 3205.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.127663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.116322 restraints weight = 7553.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.119067 restraints weight = 4899.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.121140 restraints weight = 3367.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4742
moved from start:          0.5011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.254  14868  Z= 0.497
  Angle     :  0.928  11.538  20322  Z= 0.501
  Chirality :  0.059   0.549   2112
  Planarity :  0.015   0.281   2694
  Dihedral  :  5.950  33.532   2079
  Min Nonbonded Distance : 1.786

Molprobity Statistics.
  All-atom Clashscore : 24.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.43 (0.17), residues: 1854
  helix: -1.33 (0.37), residues: 135
  sheet: -0.70 (0.20), residues: 546
  loop : -2.22 (0.16), residues: 1173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.065   0.005   TRP D 127 
 HIS   0.029   0.005   HIS C 298 
 PHE   0.068   0.006   PHE E 264 
 TYR   0.137   0.005   TYR C 145 
 ARG   0.039   0.003   ARG C  53 

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

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

  3706 Ramachandran restraints generated.
    1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3706 Ramachandran restraints generated.
    1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
REVERT: B  218 VAL cc_start: 0.7365 (t) cc_final: 0.7015 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.1168
  time to fit residues: 5.4296
Evaluate side-chains
  29 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.283 
Evaluate side-chains
  42 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
REVERT: A  169 VAL cc_start: 0.5824 (p) cc_final: 0.5510 (p)
REVERT: A  188 ARG cc_start: 0.5403 (ptm160) cc_final: 0.4929 (ptm160)
REVERT: A  203 PRO cc_start: 0.7103 (Cg_exo) cc_final: 0.6143 (Cg_endo)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1388
  time to fit residues: 7.2507
Evaluate side-chains
  34 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 126 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0570
   chunk 48 optimal weight:    0.0980
   chunk 143 optimal weight:    8.9990
   chunk 104 optimal weight:    7.9990
   chunk 167 optimal weight:    3.9990
   chunk 146 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9980
   chunk 24 optimal weight:    8.9990
   chunk 83 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.8300
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  40 HIS
B 112 HIS
** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  94 ASN
A 187 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.130131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.122214 restraints weight = 7722.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.124537 restraints weight = 4832.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.126080 restraints weight = 3155.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3926
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.129807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.118351 restraints weight = 7315.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.121096 restraints weight = 4669.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.123199 restraints weight = 3198.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4716
moved from start:          0.5166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.122  14868  Z= 0.321
  Angle     :  0.854  11.008  20322  Z= 0.456
  Chirality :  0.056   0.384   2112
  Planarity :  0.012   0.183   2694
  Dihedral  :  5.816  28.979   2079
  Min Nonbonded Distance : 1.799

Molprobity Statistics.
  All-atom Clashscore : 18.59
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.44 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.53 (0.17), residues: 1854
  helix: -1.25 (0.37), residues: 135
  sheet: -0.79 (0.19), residues: 582
  loop : -2.33 (0.16), residues: 1137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.004   TRP C 120 
 HIS   0.029   0.004   HIS A 298 
 PHE   0.113   0.005   PHE D 108 
 TYR   0.053   0.004   TYR D  35 
 ARG   0.039   0.003   ARG C  53 

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

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

  3706 Ramachandran restraints generated.
    1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3706 Ramachandran restraints generated.
    1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  218 VAL cc_start: 0.7343 (t) cc_final: 0.7068 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1154
  time to fit residues: 5.7962
Evaluate side-chains
  29 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.284 
Evaluate side-chains
  41 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.1403
  time to fit residues: 7.1243
Evaluate side-chains
  33 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 94 optimal weight:    0.5980
   chunk 13 optimal weight:    7.9990
   chunk 181 optimal weight:    0.8980
   chunk 27 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9990
   chunk 20 optimal weight:    7.9990
   chunk 154 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0030
   chunk 3 optimal weight:    5.9990
   chunk 54 optimal weight:    8.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    0.6994
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  40 HIS
** B  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.131370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.123554 restraints weight = 7781.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.125679 restraints weight = 4871.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.127260 restraints weight = 3243.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.129976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.118756 restraints weight = 7527.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.121496 restraints weight = 4842.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.123524 restraints weight = 3327.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4707
moved from start:          0.5185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.095  14868  Z= 0.293
  Angle     :  0.811   9.690  20322  Z= 0.434
  Chirality :  0.052   0.212   2112
  Planarity :  0.012   0.179   2694
  Dihedral  :  5.808  33.662   2079
  Min Nonbonded Distance : 1.835

Molprobity Statistics.
  All-atom Clashscore : 16.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.17), residues: 1854
  helix: -1.22 (0.37), residues: 135
  sheet: -0.95 (0.19), residues: 603
  loop : -2.32 (0.17), residues: 1116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.004   TRP C 127 
 HIS   0.025   0.003   HIS C 298 
 PHE   0.067   0.004   PHE E 264 
 TYR   0.116   0.004   TYR A 145 
 ARG   0.039   0.003   ARG D  53 

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

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

  3706 Ramachandran restraints generated.
    1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3706 Ramachandran restraints generated.
    1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: B  218 VAL cc_start: 0.7221 (t) cc_final: 0.6999 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.0838
  time to fit residues: 4.2929
Evaluate side-chains
  30 residues out of total 243 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.252 
Evaluate side-chains
  40 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.1008
  time to fit residues: 5.2805
Evaluate side-chains
  33 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 183
   random chunks:
   chunk 145 optimal weight:    5.9990
   chunk 116 optimal weight:    0.0970
   chunk 17 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0670
   chunk 33 optimal weight:    0.3980
   chunk 30 optimal weight:    0.5980
   chunk 99 optimal weight:    0.0070
   chunk 68 optimal weight:    0.0030
   chunk 72 optimal weight:    2.9990
   chunk 106 optimal weight:    3.9990
   chunk 104 optimal weight:    5.9990
   overall best weight:    0.1144
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 261 ASN

Total number of N/Q/H flips: 1

Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.130573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.122389 restraints weight = 7645.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.124673 restraints weight = 4882.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.126328 restraints weight = 3250.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3926
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.130925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.120156 restraints weight = 7639.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.122840 restraints weight = 4893.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.124770 restraints weight = 3342.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4691
moved from start:          0.5234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.095  14868  Z= 0.294
  Angle     :  0.811   9.690  20322  Z= 0.434
  Chirality :  0.052   0.212   2112
  Planarity :  0.012   0.179   2694
  Dihedral  :  5.808  33.660   2079
  Min Nonbonded Distance : 1.742

Molprobity Statistics.
  All-atom Clashscore : 21.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.17), residues: 1854
  helix: -1.22 (0.37), residues: 135
  sheet: -0.95 (0.19), residues: 603
  loop : -2.32 (0.17), residues: 1116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.004   TRP A 127 
 HIS   0.025   0.003   HIS C 298 
 PHE   0.067   0.004   PHE B 264 
 TYR   0.116   0.004   TYR A 145 
 ARG   0.039   0.003   ARG D  53 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2634.45 seconds
wall clock time: 49 minutes 21.81 seconds (2961.81 seconds total)