Starting phenix.real_space_refine
on Wed Mar 12 13:22:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ej7_31154/03_2025/7ej7_31154_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ej7_31154/03_2025/7ej7_31154.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ej7_31154/03_2025/7ej7_31154.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ej7_31154/03_2025/7ej7_31154.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ej7_31154/03_2025/7ej7_31154_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ej7_31154/03_2025/7ej7_31154_trim.cif"
  }
  resolution = 3.41
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
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: 6
    Type Number    sf(0)   Gaussians
     P      27      5.49       5
     Mg      3      5.21       5
     S      39      5.16       5
     C    4764      2.51       5
     N    1371      2.21       5
     O    1569      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7773
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 2436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2436
          Classifications: {'peptide': 316}
          Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 306}
    Chain: "A"
      Number of atoms: 2436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2436
          Classifications: {'peptide': 316}
          Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 306}
    Chain: "C"
      Number of atoms: 2436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2436
          Classifications: {'peptide': 316}
          Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 306}
    Chain: "D"
      Number of atoms: 180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 180
          Classifications: {'DNA': 9}
          Link IDs: {'rna3p': 8}
    Chain: "E"
      Number of atoms: 189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 189
          Classifications: {'DNA': 9}
          Link IDs: {'rna3p': 8}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 63
          Unusual residues: {' MG': 1, 'ATP': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 6.09, per 1000 atoms: 0.78
  Number of scatterers: 7773
  At special positions: 0
  Unit cell: (84.05, 96.35, 111.725, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      39     16.00
     P      27     15.00
     Mg      3     11.99
     O    1569      8.00
     N    1371      7.00
     C    4764      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=13, symmetry=0
  Number of additional bonds: simple=13, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.49
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1716

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 3 sheets defined
      46.5% alpha, 14.9% beta
      7 base pairs and 10 stacking pairs defined.
    Time for finding SS restraints: 2.69
  Creating SS restraints...
    Processing helix  chain 'B' and resid 20 through 25
      removed outlier: 3.789A  pdb=" N   ASN B  24 " --> pdb=" O   GLU B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 38
    Processing helix  chain 'B' and resid 43 through 48
    Processing helix  chain 'B' and resid 50 through 55
    Processing helix  chain 'B' and resid 62 through 76
      removed outlier: 3.594A  pdb=" N   ILE B  76 " --> pdb=" O   ALA B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 90
    Processing helix  chain 'B' and resid 100 through 107
    Processing helix  chain 'B' and resid 128 through 138
      removed outlier: 3.836A  pdb=" N   HIS B 132 " --> pdb=" O   THR B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 145
    Processing helix  chain 'B' and resid 161 through 172
      removed outlier: 3.600A  pdb=" N   ILE B 165 " --> pdb=" O   ARG B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 182
    Processing helix  chain 'B' and resid 190 through 205
      removed outlier: 3.709A  pdb=" N   VAL B 198 " --> pdb=" O   GLN B 194 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLU B 199 " --> pdb=" O   MET B 195 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLN B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   GLU B 203 " --> pdb=" O   GLU B 199 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   GLU B 204 " --> pdb=" O   GLN B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 226
    Processing helix  chain 'B' and resid 231 through 253
      removed outlier: 3.597A  pdb=" N   LYS B 238 " --> pdb=" O   GLU B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 291
      removed outlier: 3.856A  pdb=" N   LEU B 287 " --> pdb=" O   GLY B 283 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA B 288 " --> pdb=" O   GLY B 284 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ALA B 290 " --> pdb=" O   VAL B 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 20 through 25
      removed outlier: 3.790A  pdb=" N   ASN A  24 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 38
    Processing helix  chain 'A' and resid 43 through 48
    Processing helix  chain 'A' and resid 50 through 55
    Processing helix  chain 'A' and resid 62 through 76
      removed outlier: 3.593A  pdb=" N   ILE A  76 " --> pdb=" O   ALA A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 90
    Processing helix  chain 'A' and resid 100 through 107
    Processing helix  chain 'A' and resid 128 through 138
      removed outlier: 4.076A  pdb=" N   HIS A 132 " --> pdb=" O   THR A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 145
    Processing helix  chain 'A' and resid 161 through 172
      removed outlier: 3.601A  pdb=" N   ILE A 165 " --> pdb=" O   ARG A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 182
    Processing helix  chain 'A' and resid 190 through 205
      removed outlier: 3.710A  pdb=" N   VAL A 198 " --> pdb=" O   GLN A 194 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLU A 199 " --> pdb=" O   MET A 195 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLN A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLU A 203 " --> pdb=" O   GLU A 199 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   GLU A 204 " --> pdb=" O   GLN A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 226
    Processing helix  chain 'A' and resid 231 through 253
      removed outlier: 3.597A  pdb=" N   LYS A 238 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 291
      removed outlier: 3.855A  pdb=" N   LEU A 287 " --> pdb=" O   GLY A 283 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ALA A 288 " --> pdb=" O   GLY A 284 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA A 290 " --> pdb=" O   VAL A 286 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 25
      removed outlier: 3.789A  pdb=" N   ASN C  24 " --> pdb=" O   GLU C  21 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 38
    Processing helix  chain 'C' and resid 43 through 48
    Processing helix  chain 'C' and resid 50 through 55
    Processing helix  chain 'C' and resid 62 through 76
      removed outlier: 3.594A  pdb=" N   ILE C  76 " --> pdb=" O   ALA C  72 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 90
    Processing helix  chain 'C' and resid 100 through 107
    Processing helix  chain 'C' and resid 128 through 138
      removed outlier: 4.075A  pdb=" N   HIS C 132 " --> pdb=" O   THR C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 141 through 145
    Processing helix  chain 'C' and resid 161 through 172
      removed outlier: 3.601A  pdb=" N   ILE C 165 " --> pdb=" O   ARG C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 175 through 182
    Processing helix  chain 'C' and resid 190 through 205
      removed outlier: 3.710A  pdb=" N   VAL C 198 " --> pdb=" O   GLN C 194 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLU C 199 " --> pdb=" O   MET C 195 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLN C 200 " --> pdb=" O   GLU C 196 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLU C 203 " --> pdb=" O   GLU C 199 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   GLU C 204 " --> pdb=" O   GLN C 200 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 226
    Processing helix  chain 'C' and resid 231 through 253
      removed outlier: 3.596A  pdb=" N   LYS C 238 " --> pdb=" O   GLU C 234 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 283 through 291
      removed outlier: 3.855A  pdb=" N   LEU C 287 " --> pdb=" O   GLY C 283 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA C 288 " --> pdb=" O   GLY C 284 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ALA C 290 " --> pdb=" O   VAL C 286 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 183 through 187
      removed outlier: 7.596A  pdb=" N   LYS B 150 " --> pdb=" O   ARG B 211 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ILE B 213 " --> pdb=" O   LYS B 150 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ALA B 152 " --> pdb=" O   ILE B 213 " (cutoff:3.500A)
      removed outlier: 5.693A  pdb=" N   VAL B 215 " --> pdb=" O   ALA B 152 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   ILE B 154 " --> pdb=" O   VAL B 215 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   ARG B 211 " --> pdb=" O   ALA B 256 " (cutoff:3.500A)
      removed outlier: 7.908A  pdb=" N   PHE B 258 " --> pdb=" O   ARG B 211 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ILE B 213 " --> pdb=" O   PHE B 258 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   THR B 260 " --> pdb=" O   ILE B 213 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   VAL B 215 " --> pdb=" O   THR B 260 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   SER B 115 " --> pdb=" O   VAL B 257 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   LEU B 259 " --> pdb=" O   SER B 115 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   THR B 117 " --> pdb=" O   LEU B 259 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   ASN B 261 " --> pdb=" O   THR B 117 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   VAL B 119 " --> pdb=" O   ASN B 261 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   ARG B 294 " --> pdb=" O   GLN B 310 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   GLU B 304 " --> pdb=" O   GLY B 300 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   GLY B 328 " --> pdb=" O   GLY B 325 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 187
      removed outlier: 7.596A  pdb=" N   LYS A 150 " --> pdb=" O   ARG A 211 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ILE A 213 " --> pdb=" O   LYS A 150 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ALA A 152 " --> pdb=" O   ILE A 213 " (cutoff:3.500A)
      removed outlier: 5.693A  pdb=" N   VAL A 215 " --> pdb=" O   ALA A 152 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   ILE A 154 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   ARG A 211 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
      removed outlier: 7.908A  pdb=" N   PHE A 258 " --> pdb=" O   ARG A 211 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ILE A 213 " --> pdb=" O   PHE A 258 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   THR A 260 " --> pdb=" O   ILE A 213 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   VAL A 215 " --> pdb=" O   THR A 260 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   SER A 115 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   LEU A 259 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   THR A 117 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   ASN A 261 " --> pdb=" O   THR A 117 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   VAL A 119 " --> pdb=" O   ASN A 261 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   ARG A 294 " --> pdb=" O   GLN A 310 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   GLU A 304 " --> pdb=" O   GLY A 300 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   GLY A 328 " --> pdb=" O   GLY A 325 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 183 through 187
      removed outlier: 7.596A  pdb=" N   LYS C 150 " --> pdb=" O   ARG C 211 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ILE C 213 " --> pdb=" O   LYS C 150 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ALA C 152 " --> pdb=" O   ILE C 213 " (cutoff:3.500A)
      removed outlier: 5.693A  pdb=" N   VAL C 215 " --> pdb=" O   ALA C 152 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   ILE C 154 " --> pdb=" O   VAL C 215 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   ARG C 211 " --> pdb=" O   ALA C 256 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   PHE C 258 " --> pdb=" O   ARG C 211 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ILE C 213 " --> pdb=" O   PHE C 258 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   THR C 260 " --> pdb=" O   ILE C 213 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   VAL C 215 " --> pdb=" O   THR C 260 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   SER C 115 " --> pdb=" O   VAL C 257 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   LEU C 259 " --> pdb=" O   SER C 115 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   THR C 117 " --> pdb=" O   LEU C 259 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   ASN C 261 " --> pdb=" O   THR C 117 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   VAL C 119 " --> pdb=" O   ASN C 261 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   ARG C 294 " --> pdb=" O   GLN C 310 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   GLU C 304 " --> pdb=" O   GLY C 300 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLY C 328 " --> pdb=" O   GLY C 325 " (cutoff:3.500A)

    294 hydrogen bonds defined for protein.
    837 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      14 hydrogen bonds
      28 hydrogen bond angles
      0 basepair planarities
      7 basepair parallelities
      10 stacking parallelities
  Total time for adding SS restraints: 2.26

  Time building geometry restraints manager: 2.83 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1293
        1.30 -     1.42: 1934
        1.42 -     1.55: 4576
        1.55 -     1.68: 49
        1.68 -     1.80: 60
  Bond restraints: 7912
  Sorted by residual:
  bond pdb=" C4  ATP C 402 "
       pdb=" C5  ATP C 402 "
    ideal  model  delta    sigma   weight residual
    1.388  1.462 -0.074 1.00e-02 1.00e+04 5.44e+01
  bond pdb=" C4  ATP C 401 "
       pdb=" C5  ATP C 401 "
    ideal  model  delta    sigma   weight residual
    1.388  1.461 -0.073 1.00e-02 1.00e+04 5.35e+01
  bond pdb=" C4  ATP B 602 "
       pdb=" C5  ATP B 602 "
    ideal  model  delta    sigma   weight residual
    1.388  1.461 -0.073 1.00e-02 1.00e+04 5.34e+01
  bond pdb=" C5  ATP C 402 "
       pdb=" C6  ATP C 402 "
    ideal  model  delta    sigma   weight residual
    1.409  1.482 -0.073 1.00e-02 1.00e+04 5.30e+01
  bond pdb=" C5  ATP B 602 "
       pdb=" C6  ATP B 602 "
    ideal  model  delta    sigma   weight residual
    1.409  1.481 -0.072 1.00e-02 1.00e+04 5.18e+01
  ... (remaining 7907 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.62: 10657
        3.62 -     7.25: 72
        7.25 -    10.87: 9
       10.87 -    14.50: 0
       14.50 -    18.12: 6
  Bond angle restraints: 10744
  Sorted by residual:
  angle pdb=" PA  ATP C 402 "
        pdb=" O3A ATP C 402 "
        pdb=" PB  ATP C 402 "
      ideal   model   delta    sigma   weight residual
     136.83  118.71   18.12 1.00e+00 1.00e+00 3.28e+02
  angle pdb=" PA  ATP B 602 "
        pdb=" O3A ATP B 602 "
        pdb=" PB  ATP B 602 "
      ideal   model   delta    sigma   weight residual
     136.83  118.74   18.09 1.00e+00 1.00e+00 3.27e+02
  angle pdb=" PA  ATP C 401 "
        pdb=" O3A ATP C 401 "
        pdb=" PB  ATP C 401 "
      ideal   model   delta    sigma   weight residual
     136.83  118.74   18.09 1.00e+00 1.00e+00 3.27e+02
  angle pdb=" PB  ATP B 602 "
        pdb=" O3B ATP B 602 "
        pdb=" PG  ATP B 602 "
      ideal   model   delta    sigma   weight residual
     139.87  123.70   16.17 1.00e+00 1.00e+00 2.62e+02
  angle pdb=" PB  ATP C 401 "
        pdb=" O3B ATP C 401 "
        pdb=" PG  ATP C 401 "
      ideal   model   delta    sigma   weight residual
     139.87  123.74   16.13 1.00e+00 1.00e+00 2.60e+02
  ... (remaining 10739 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.75: 4104
       16.75 -    33.50: 516
       33.50 -    50.25: 155
       50.25 -    67.01: 40
       67.01 -    83.76: 33
  Dihedral angle restraints: 4848
    sinusoidal: 2160
      harmonic: 2688
  Sorted by residual:
  dihedral pdb=" CA  ASN B  28 "
           pdb=" C   ASN B  28 "
           pdb=" N   ALA B  29 "
           pdb=" CA  ALA B  29 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.70  -26.30     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  ASN C  28 "
           pdb=" C   ASN C  28 "
           pdb=" N   ALA C  29 "
           pdb=" CA  ALA C  29 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.71  -26.29     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  ASN A  28 "
           pdb=" C   ASN A  28 "
           pdb=" N   ALA A  29 "
           pdb=" CA  ALA A  29 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.72  -26.28     0      5.00e+00 4.00e-02 2.76e+01
  ... (remaining 4845 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 843
       0.037 -    0.074: 267
       0.074 -    0.111: 78
       0.111 -    0.147: 24
       0.147 -    0.184: 6
  Chirality restraints: 1218
  Sorted by residual:
  chirality pdb=" CA  ASP A 216 "
            pdb=" N   ASP A 216 "
            pdb=" C   ASP A 216 "
            pdb=" CB  ASP A 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.50e-01
  chirality pdb=" CA  ASP C 216 "
            pdb=" N   ASP C 216 "
            pdb=" C   ASP C 216 "
            pdb=" CB  ASP C 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.73e-01
  chirality pdb=" CA  ASP B 216 "
            pdb=" N   ASP B 216 "
            pdb=" C   ASP B 216 "
            pdb=" CB  ASP B 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.68e-01
  ... (remaining 1215 not shown)

  Planarity restraints: 1323
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET C 315 "   -0.014 2.00e-02 2.50e+03   2.86e-02 8.18e+00
        pdb=" C   MET C 315 "    0.049 2.00e-02 2.50e+03
        pdb=" O   MET C 315 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   PRO C 316 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 315 "    0.014 2.00e-02 2.50e+03   2.84e-02 8.05e+00
        pdb=" C   MET A 315 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   MET A 315 "    0.018 2.00e-02 2.50e+03
        pdb=" N   PRO A 316 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 315 "   -0.014 2.00e-02 2.50e+03   2.83e-02 8.03e+00
        pdb=" C   MET B 315 "    0.049 2.00e-02 2.50e+03
        pdb=" O   MET B 315 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   PRO B 316 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1320 not shown)

  Histogram of nonbonded interaction distances:
        1.86 -     2.47: 78
        2.47 -     3.08: 6331
        3.08 -     3.68: 11314
        3.68 -     4.29: 17663
        4.29 -     4.90: 29004
  Nonbonded interactions: 64390
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 316 "
            pdb=" O2' ATP B 602 "
     model   vdw
     1.860 3.040
  nonbonded pdb=" O   PRO C 316 "
            pdb=" O2' ATP C 401 "
     model   vdw
     1.901 3.040
  nonbonded pdb=" O2G ATP C 402 "
            pdb="MG    MG C 403 "
     model   vdw
     1.913 2.170
  nonbonded pdb="MG    MG B 601 "
            pdb=" O2G ATP C 401 "
     model   vdw
     1.913 2.170
  nonbonded pdb=" O2G ATP B 602 "
            pdb="MG    MG A 601 "
     model   vdw
     1.913 2.170
  ... (remaining 64385 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 16 through 334)
  selection = (chain 'B' and resid 16 through 334)
  selection = (chain 'C' and resid 16 through 334)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.940
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
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      :  0.006   0.074   7912  Z= 0.382
  Angle     :  0.915  18.124  10744  Z= 0.680
  Chirality :  0.043   0.184   1218
  Planarity :  0.004   0.044   1323
  Dihedral  : 18.099  83.758   3132
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 43.57
  Ramachandran Plot:
    Outliers :  0.96 %
    Allowed  : 10.83 %
    Favored  : 88.22 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  4.64 %
    Favored  : 93.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    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: -4.75 (0.22), residues: 942
  helix: -3.33 (0.19), residues: 381
  sheet: -0.20 (0.45), residues: 150
  loop : -4.17 (0.21), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 193 
 PHE   0.007   0.001   PHE C 160 
 TYR   0.006   0.001   TYR B  41 
 ARG   0.003   0.000   ARG A 142 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
REVERT: B   24 ASN cc_start: 0.8704 (p0) cc_final: 0.8486 (p0)
REVERT: B   61 SER cc_start: 0.6819 (OUTLIER) cc_final: 0.6156 (m)
REVERT: A   61 SER cc_start: 0.6980 (OUTLIER) cc_final: 0.6729 (m)
REVERT: C   61 SER cc_start: 0.6506 (OUTLIER) cc_final: 0.6167 (m)
  outliers start: 14
  outliers final: 2
  residues processed: 111
  average time/residue: 0.2346
  time to fit residues: 34.2720
Evaluate side-chains
  68 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain A residue   61 SER
Chi-restraints excluded: chain A residue  164 ARG
Chi-restraints excluded: chain C residue   61 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 70 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0070
   chunk 72 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
B  28 ASN
B  44 ASN
B 182 ASN
B 236 GLN
A 182 ASN
A 236 GLN
C  44 ASN
C 182 ASN
C 236 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.101511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.077177 restraints weight = 14022.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 2.65
r_work: 0.2786 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7912  Z= 0.196
  Angle     :  0.658   8.614  10744  Z= 0.344
  Chirality :  0.046   0.142   1218
  Planarity :  0.004   0.030   1323
  Dihedral  : 16.828  78.714   1349
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  :  9.24 %
    Favored  : 90.13 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 10.65 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

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: -2.90 (0.25), residues: 942
  helix: -1.34 (0.24), residues: 426
  sheet:  0.79 (0.44), residues: 159
  loop : -4.00 (0.24), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 193 
 PHE   0.011   0.001   PHE A 160 
 TYR   0.014   0.001   TYR C  41 
 ARG   0.004   0.001   ARG B 229 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  254 ASN cc_start: 0.9473 (t0) cc_final: 0.9174 (t0)
REVERT: B  272 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6710 (mp)
REVERT: A   89 ILE cc_start: 0.9028 (tt) cc_final: 0.8686 (mt)
  outliers start: 17
  outliers final: 8
  residues processed: 109
  average time/residue: 0.2238
  time to fit residues: 32.2261
Evaluate side-chains
  77 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain A residue  164 ARG
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  314 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 8 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 28 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 63 optimal weight:    7.9990
   chunk 76 optimal weight:    0.0370
   chunk 12 optimal weight:    6.9990
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.9262

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.101451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.076835 restraints weight = 14100.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 2.70
r_work: 0.2792 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7912  Z= 0.193
  Angle     :  0.601   8.181  10744  Z= 0.316
  Chirality :  0.045   0.136   1218
  Planarity :  0.004   0.029   1323
  Dihedral  : 16.471  78.153   1346
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  9.02 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 14.54 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    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: -1.89 (0.27), residues: 942
  helix: -0.27 (0.25), residues: 426
  sheet:  1.14 (0.43), residues: 165
  loop : -3.84 (0.25), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 193 
 PHE   0.008   0.001   PHE C 160 
 TYR   0.012   0.001   TYR C  41 
 ARG   0.004   0.000   ARG B 229 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  148 GLU cc_start: 0.7486 (mp0) cc_final: 0.7192 (pm20)
REVERT: A   89 ILE cc_start: 0.9082 (tt) cc_final: 0.8800 (mt)
REVERT: A  144 MET cc_start: 0.8641 (mtt) cc_final: 0.8391 (mtt)
REVERT: C   56 LYS cc_start: 0.8706 (mmtp) cc_final: 0.8488 (mmtp)
REVERT: C  144 MET cc_start: 0.8512 (mtt) cc_final: 0.8082 (mtp)
  outliers start: 15
  outliers final: 13
  residues processed: 90
  average time/residue: 0.2288
  time to fit residues: 27.5926
Evaluate side-chains
  81 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  231 GLU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  164 ARG
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  314 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 32 optimal weight:   10.0000
   chunk 17 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0980
   chunk 26 optimal weight:    5.9990
   chunk 64 optimal weight:    0.7980
   chunk 76 optimal weight:    4.9990
   chunk 81 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 19 optimal weight:    0.2980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.102972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.078293 restraints weight = 14098.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 2.71
r_work: 0.2812 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.3019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7912  Z= 0.159
  Angle     :  0.550   4.998  10744  Z= 0.293
  Chirality :  0.043   0.128   1218
  Planarity :  0.003   0.028   1323
  Dihedral  : 16.172  74.461   1346
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  9.13 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 14.16 %
    Favored  : 82.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    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: -1.38 (0.27), residues: 942
  helix:  0.18 (0.26), residues: 426
  sheet:  1.54 (0.42), residues: 159
  loop : -3.62 (0.25), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 289 
 PHE   0.007   0.001   PHE B 120 
 TYR   0.017   0.001   TYR B  41 
 ARG   0.003   0.000   ARG B 229 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   64 LYS cc_start: 0.8552 (mtmm) cc_final: 0.8347 (ptpp)
REVERT: B  296 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9149 (tp)
REVERT: A   89 ILE cc_start: 0.9074 (tt) cc_final: 0.8778 (mt)
REVERT: A  144 MET cc_start: 0.8621 (mtt) cc_final: 0.8410 (mtt)
REVERT: C   56 LYS cc_start: 0.8699 (mmtp) cc_final: 0.8445 (mmtp)
REVERT: C  287 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9222 (tp)
  outliers start: 23
  outliers final: 15
  residues processed: 100
  average time/residue: 0.2526
  time to fit residues: 32.7027
Evaluate side-chains
  88 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   94 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  231 GLU
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  164 ARG
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  231 GLU
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  314 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 64 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   chunk 29 optimal weight:    8.9990
   chunk 90 optimal weight:    7.9990
   chunk 88 optimal weight:    0.4980
   chunk 89 optimal weight:    0.7980
   chunk 60 optimal weight:    0.4980
   chunk 66 optimal weight:    4.9990
   overall best weight:    0.7584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.102785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.077983 restraints weight = 14083.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 2.72
r_work: 0.2805 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.3209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7912  Z= 0.166
  Angle     :  0.533   5.287  10744  Z= 0.285
  Chirality :  0.043   0.129   1218
  Planarity :  0.003   0.028   1323
  Dihedral  : 15.890  74.078   1346
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  9.13 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 14.29 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    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: -1.17 (0.27), residues: 942
  helix:  0.31 (0.26), residues: 426
  sheet:  1.65 (0.42), residues: 159
  loop : -3.45 (0.25), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS B 285 
 PHE   0.006   0.001   PHE C 120 
 TYR   0.010   0.001   TYR C  41 
 ARG   0.002   0.000   ARG B 229 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 77
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  296 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9136 (tp)
REVERT: B  318 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7351 (mtmt)
REVERT: A   89 ILE cc_start: 0.9066 (tt) cc_final: 0.8795 (mt)
REVERT: A  144 MET cc_start: 0.8596 (mtt) cc_final: 0.8368 (mtt)
REVERT: C   34 LYS cc_start: 0.8829 (mtmm) cc_final: 0.8543 (mtmm)
REVERT: C   56 LYS cc_start: 0.8681 (mmtp) cc_final: 0.8431 (mmtm)
  outliers start: 31
  outliers final: 13
  residues processed: 100
  average time/residue: 0.2453
  time to fit residues: 32.1642
Evaluate side-chains
  85 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   94 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain B residue  318 LYS
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  231 GLU
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  314 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 87 optimal weight:    0.1980
   chunk 53 optimal weight:    0.6980
   chunk 77 optimal weight:    0.0000
   chunk 55 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 44 optimal weight:    6.9990
   chunk 61 optimal weight:    3.9990
   chunk 12 optimal weight:    0.3980
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.6586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.103594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.078769 restraints weight = 14011.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 2.69
r_work: 0.2822 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.3408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7912  Z= 0.165
  Angle     :  0.532   4.863  10744  Z= 0.283
  Chirality :  0.043   0.129   1218
  Planarity :  0.003   0.029   1323
  Dihedral  : 15.789  78.337   1342
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  9.13 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 16.17 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.28), residues: 942
  helix:  0.42 (0.26), residues: 426
  sheet:  1.68 (0.42), residues: 159
  loop : -3.24 (0.26), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 289 
 PHE   0.006   0.001   PHE B 120 
 TYR   0.008   0.001   TYR C  41 
 ARG   0.002   0.000   ARG B 164 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 LYS cc_start: 0.8418 (mmtm) cc_final: 0.8209 (mmtm)
REVERT: B  104 ASP cc_start: 0.8415 (m-30) cc_final: 0.8020 (m-30)
REVERT: B  144 MET cc_start: 0.8667 (mtt) cc_final: 0.8347 (mtm)
REVERT: B  296 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9101 (tp)
REVERT: C   34 LYS cc_start: 0.8804 (mtmm) cc_final: 0.8508 (mtmm)
REVERT: C   56 LYS cc_start: 0.8706 (mmtp) cc_final: 0.8503 (mmtp)
REVERT: C  104 ASP cc_start: 0.8021 (m-30) cc_final: 0.7342 (m-30)
  outliers start: 22
  outliers final: 14
  residues processed: 94
  average time/residue: 0.2497
  time to fit residues: 30.4975
Evaluate side-chains
  88 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   94 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  231 GLU
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  314 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 79 optimal weight:    0.5980
   chunk 4 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0570
   chunk 57 optimal weight:    5.9990
   chunk 52 optimal weight:    5.9990
   chunk 11 optimal weight:    0.5980
   chunk 22 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    1.0502

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

Flipped N/Q/H residues before XYZ refinement:
B 242 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.102343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.077310 restraints weight = 14116.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 2.73
r_work: 0.2795 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.3399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7912  Z= 0.194
  Angle     :  0.541   7.286  10744  Z= 0.286
  Chirality :  0.043   0.132   1218
  Planarity :  0.003   0.029   1323
  Dihedral  : 15.796  80.502   1342
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  9.13 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.54 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.28), residues: 942
  helix:  0.43 (0.26), residues: 429
  sheet:  1.59 (0.42), residues: 165
  loop : -3.26 (0.27), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 285 
 PHE   0.007   0.001   PHE C 120 
 TYR   0.015   0.001   TYR B  41 
 ARG   0.002   0.000   ARG B 229 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 LYS cc_start: 0.8479 (mmtm) cc_final: 0.8272 (mmtm)
REVERT: B  104 ASP cc_start: 0.8451 (m-30) cc_final: 0.8065 (m-30)
REVERT: B  296 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9110 (tp)
REVERT: C   34 LYS cc_start: 0.8863 (mtmm) cc_final: 0.8588 (mtmm)
REVERT: C   56 LYS cc_start: 0.8663 (mmtp) cc_final: 0.8429 (mmtp)
REVERT: C  104 ASP cc_start: 0.8074 (m-30) cc_final: 0.7418 (m-30)
  outliers start: 23
  outliers final: 16
  residues processed: 92
  average time/residue: 0.2474
  time to fit residues: 29.9846
Evaluate side-chains
  88 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   94 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain A residue   94 TYR
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  231 GLU
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  314 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 29 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 31 optimal weight:   10.0000
   chunk 69 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 61 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
B 242 HIS
A 242 HIS
C 242 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.098183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.073013 restraints weight = 14355.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 2.70
r_work: 0.2707 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   7912  Z= 0.336
  Angle     :  0.618   7.285  10744  Z= 0.326
  Chirality :  0.046   0.141   1218
  Planarity :  0.004   0.031   1323
  Dihedral  : 16.187  78.509   1342
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  9.55 %
    Favored  : 89.92 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 16.54 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    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 (0.28), residues: 942
  helix:  0.38 (0.26), residues: 429
  sheet:  1.30 (0.42), residues: 168
  loop : -3.18 (0.28), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 242 
 PHE   0.009   0.001   PHE B 120 
 TYR   0.013   0.001   TYR C  41 
 ARG   0.003   0.000   ARG A 164 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 66
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   56 LYS cc_start: 0.8529 (mmtm) cc_final: 0.8324 (mmtm)
REVERT: B  104 ASP cc_start: 0.8547 (m-30) cc_final: 0.8157 (m-30)
REVERT: A  144 MET cc_start: 0.8672 (mtt) cc_final: 0.8353 (mpp)
REVERT: C   34 LYS cc_start: 0.8919 (mtmm) cc_final: 0.8614 (mtmm)
REVERT: C   56 LYS cc_start: 0.8654 (mmtp) cc_final: 0.8373 (mmtm)
REVERT: C  104 ASP cc_start: 0.8221 (m-30) cc_final: 0.7685 (m-30)
  outliers start: 27
  outliers final: 18
  residues processed: 86
  average time/residue: 0.2237
  time to fit residues: 25.9805
Evaluate side-chains
  80 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   94 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  231 GLU
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  148 GLU
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  314 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 68 optimal weight:    7.9990
   chunk 66 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   chunk 33 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
B 242 HIS
A 242 HIS
C 242 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.098282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.072621 restraints weight = 14576.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.2844 rms_B_bonded: 2.77
r_work: 0.2695 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.3187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7912  Z= 0.335
  Angle     :  0.616   7.170  10744  Z= 0.325
  Chirality :  0.046   0.137   1218
  Planarity :  0.004   0.030   1323
  Dihedral  : 16.336  80.235   1342
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  9.34 %
    Favored  : 90.13 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 17.42 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.28), residues: 942
  helix:  0.43 (0.26), residues: 429
  sheet:  1.15 (0.43), residues: 168
  loop : -3.10 (0.29), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 242 
 PHE   0.010   0.001   PHE B 120 
 TYR   0.014   0.001   TYR C  41 
 ARG   0.002   0.000   ARG A  90 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 66
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  104 ASP cc_start: 0.8558 (m-30) cc_final: 0.8201 (m-30)
REVERT: B  144 MET cc_start: 0.8795 (mtt) cc_final: 0.8579 (mtp)
REVERT: C   34 LYS cc_start: 0.8956 (mtmm) cc_final: 0.8680 (mtmm)
REVERT: C   56 LYS cc_start: 0.8642 (mmtp) cc_final: 0.8408 (mmtp)
REVERT: C  104 ASP cc_start: 0.8253 (m-30) cc_final: 0.7706 (m-30)
  outliers start: 25
  outliers final: 20
  residues processed: 85
  average time/residue: 0.2298
  time to fit residues: 26.5114
Evaluate side-chains
  84 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   94 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  115 SER
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  148 GLU
Chi-restraints excluded: chain A residue  216 ASP
Chi-restraints excluded: chain A residue  231 GLU
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  148 GLU
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  314 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 91 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9980
   chunk 5 optimal weight:    8.9990
   chunk 66 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0670
   chunk 11 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
B 242 HIS
A 242 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.102511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.078063 restraints weight = 14150.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 2.64
r_work: 0.2817 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.3502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7912  Z= 0.171
  Angle     :  0.562   7.197  10744  Z= 0.297
  Chirality :  0.043   0.133   1218
  Planarity :  0.003   0.031   1323
  Dihedral  : 15.985  79.407   1342
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  9.13 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 17.92 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.28), residues: 942
  helix:  0.60 (0.27), residues: 429
  sheet:  1.16 (0.42), residues: 168
  loop : -3.01 (0.29), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 289 
 PHE   0.006   0.001   PHE B 120 
 TYR   0.011   0.001   TYR C  41 
 ARG   0.003   0.000   ARG B 164 

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  104 ASP cc_start: 0.8327 (m-30) cc_final: 0.8003 (m-30)
REVERT: B  144 MET cc_start: 0.8719 (mtt) cc_final: 0.8419 (mpp)
REVERT: C   34 LYS cc_start: 0.8837 (mtmm) cc_final: 0.8554 (mtmm)
REVERT: C   56 LYS cc_start: 0.8723 (mmtp) cc_final: 0.8506 (mmtp)
REVERT: C  104 ASP cc_start: 0.8114 (m-30) cc_final: 0.7408 (m-30)
  outliers start: 20
  outliers final: 14
  residues processed: 80
  average time/residue: 0.2354
  time to fit residues: 25.2546
Evaluate side-chains
  80 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   94 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  231 GLU
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  312 SER
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  314 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 92 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 32 optimal weight:   20.0000
   chunk 85 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0010
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
B 242 HIS
A 242 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.103277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.078615 restraints weight = 14114.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 2.66
r_work: 0.2815 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.3677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7912  Z= 0.175
  Angle     :  0.556   7.523  10744  Z= 0.293
  Chirality :  0.043   0.130   1218
  Planarity :  0.003   0.031   1323
  Dihedral  : 15.826  83.303   1342
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  8.92 %
    Favored  : 90.55 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 17.92 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.33 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.28), residues: 942
  helix:  0.65 (0.27), residues: 429
  sheet:  1.19 (0.42), residues: 168
  loop : -2.99 (0.29), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS B 285 
 PHE   0.007   0.001   PHE B 120 
 TYR   0.010   0.001   TYR C  41 
 ARG   0.003   0.000   ARG B 164 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3313.06 seconds
wall clock time: 57 minutes 45.83 seconds (3465.83 seconds total)