Starting phenix.real_space_refine
on Wed Mar 12 20:06:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o6p_12739/03_2025/7o6p_12739.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o6p_12739/03_2025/7o6p_12739.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7o6p_12739/03_2025/7o6p_12739.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o6p_12739/03_2025/7o6p_12739.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o6p_12739/03_2025/7o6p_12739.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o6p_12739/03_2025/7o6p_12739.cif"
  }
  resolution = 2.04
  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=   0.004 sd=   0.042
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      52      5.16       5
     C    5014      2.51       5
     N    1451      2.21       5
     O    1759      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8276
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2010
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 256, 1913
          Classifications: {'peptide': 256}
          Link IDs: {'PTRANS': 8, 'TRANS': 247}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 256, 1913
          Classifications: {'peptide': 256}
          Link IDs: {'PTRANS': 8, 'TRANS': 247}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1837
    Chain: "B"
      Number of atoms: 1980
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 255, 1905
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 8, 'TRANS': 246}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 255, 1905
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 8, 'TRANS': 246}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1855
    Chain: "C"
      Number of atoms: 1991
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 254, 1901
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 8, 'TRANS': 245}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 254, 1901
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 8, 'TRANS': 245}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1833
    Chain: "D"
      Number of atoms: 2027
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 257, 1919
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 8, 'TRANS': 248}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 257, 1919
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 8, 'TRANS': 248}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1831
    Chain: "A"
      Number of atoms: 68
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 68, 68
          Classifications: {'water': 68}
          Link IDs: {None: 67}
    Chain: "B"
      Number of atoms: 71
      Number of conformers: 2
      Conformer: "B"
        Number of residues, atoms: 70, 70
          Classifications: {'water': 70}
          Link IDs: {None: 69}
      Conformer: "A"
        Number of residues, atoms: 70, 70
          Classifications: {'water': 70}
          Link IDs: {None: 69}
    Chain: "C"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 60, 60
          Classifications: {'water': 60}
          Link IDs: {None: 59}
    Chain: "D"
      Number of atoms: 69
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 69
          Classifications: {'water': 69}
          Link IDs: {None: 68}
  Residues with excluded nonbonded symmetry interactions: 43
    residue:
      pdb=" N  AARG A  20 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A  20 " occ=0.50
    residue:
      pdb=" N  ASER A  34 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER A  34 " occ=0.50
    residue:
      pdb=" N  AARG A  40 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A  40 " occ=0.50
    residue:
      pdb=" N  ALYS A  45 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS A  45 " occ=0.50
    residue:
      pdb=" N  AARG A  84 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A  84 " occ=0.50
    residue:
      pdb=" N  ALYS A 147 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS A 147 " occ=0.50
    residue:
      pdb=" N  ALYS A 181 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS A 181 " occ=0.50
    residue:
      pdb=" N  AARG A 225 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 225 " occ=0.50
    residue:
      pdb=" N  AGLU A 238 " occ=0.50
      ... (16 atoms not shown)
      pdb=" OE2BGLU A 238 " occ=0.50
    residue:
      pdb=" N  AARG A 257 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 257 " occ=0.50
    residue:
      pdb=" N  ALEU B  37 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CD2BLEU B  37 " occ=0.50
    residue:
      pdb=" N  ALYS B  83 " occ=0.50
      ... (16 atoms not shown)
      pdb=" NZ BLYS B  83 " occ=0.50
    ... (remaining 31 not shown)
  Time building chain proxies: 9.44, per 1000 atoms: 1.14
  Number of scatterers: 8276
  At special positions: 0
  Unit cell: (81.536, 93.184, 79.04, 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      52     16.00
     O    1759      8.00
     N    1451      7.00
     C    5014      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=0, symmetry=0
  Time building additional restraints: 2.18
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1914

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 4 sheets defined
      53.9% alpha, 12.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 42
      removed outlier: 3.507A  pdb=" N  ASER A  34 " --> pdb=" O   GLY A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 3.558A  pdb=" N   CYS A  60 " --> pdb=" O   GLY A  56 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLY A  64 " --> pdb=" O   CYS A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 94
    Processing helix  chain 'A' and resid 112 through 116
    Processing helix  chain 'A' and resid 117 through 129
    Processing helix  chain 'A' and resid 129 through 147
      removed outlier: 3.726A  pdb=" N   ILE A 142 " --> pdb=" O   HIS A 138 " (cutoff:3.500A)
      Proline residue:  A 145  - end of helix
    Processing helix  chain 'A' and resid 156 through 160
    Processing helix  chain 'A' and resid 166 through 188
    Processing helix  chain 'A' and resid 220 through 231
    Processing helix  chain 'A' and resid 240 through 253
      removed outlier: 3.610A  pdb=" N   VAL A 244 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 257
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 52 through 64
      removed outlier: 3.842A  pdb=" N   GLN B  57 " --> pdb=" O   ASP B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 94
    Processing helix  chain 'B' and resid 112 through 116
    Processing helix  chain 'B' and resid 117 through 129
    Processing helix  chain 'B' and resid 129 through 147
      removed outlier: 3.727A  pdb=" N   ILE B 142 " --> pdb=" O   HIS B 138 " (cutoff:3.500A)
      Proline residue:  B 145  - end of helix
    Processing helix  chain 'B' and resid 156 through 160
    Processing helix  chain 'B' and resid 166 through 188
    Processing helix  chain 'B' and resid 221 through 231
    Processing helix  chain 'B' and resid 240 through 253
      removed outlier: 3.606A  pdb=" N   VAL B 244 " --> pdb=" O   THR B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 257
    Processing helix  chain 'C' and resid 30 through 42
    Processing helix  chain 'C' and resid 52 through 64
      removed outlier: 3.871A  pdb=" N   ARG C  58 " --> pdb=" O   ASN C  54 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   CYS C  60 " --> pdb=" O   GLY C  56 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 94
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'C' and resid 117 through 129
    Processing helix  chain 'C' and resid 129 through 147
      removed outlier: 3.730A  pdb=" N   ILE C 142 " --> pdb=" O   HIS C 138 " (cutoff:3.500A)
      Proline residue:  C 145  - end of helix
    Processing helix  chain 'C' and resid 156 through 160
    Processing helix  chain 'C' and resid 166 through 188
    Processing helix  chain 'C' and resid 220 through 231
    Processing helix  chain 'C' and resid 240 through 253
      removed outlier: 3.597A  pdb=" N   VAL C 244 " --> pdb=" O   THR C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 254 through 257
    Processing helix  chain 'D' and resid 30 through 42
    Processing helix  chain 'D' and resid 52 through 64
      removed outlier: 3.720A  pdb=" N   GLY D  64 " --> pdb=" O   CYS D  60 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 94
    Processing helix  chain 'D' and resid 112 through 116
    Processing helix  chain 'D' and resid 117 through 129
    Processing helix  chain 'D' and resid 129 through 147
      removed outlier: 3.732A  pdb=" N   ILE D 142 " --> pdb=" O   HIS D 138 " (cutoff:3.500A)
      Proline residue:  D 145  - end of helix
    Processing helix  chain 'D' and resid 156 through 160
    Processing helix  chain 'D' and resid 166 through 188
    Processing helix  chain 'D' and resid 220 through 231
    Processing helix  chain 'D' and resid 240 through 253
      removed outlier: 3.619A  pdb=" N   VAL D 244 " --> pdb=" O   THR D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 254 through 257
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 73
      removed outlier: 6.552A  pdb=" N   VAL A  21 " --> pdb=" O   ILE A  98 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   VAL A 100 " --> pdb=" O   VAL A  21 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   LEU A  23 " --> pdb=" O   VAL A 100 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   MET A  99 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   ILE A 154 " --> pdb=" O   MET A  99 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   ASN A 101 " --> pdb=" O   ILE A 154 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   MET A 262 " --> pdb=" O   VAL A 194 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 69 through 73
      removed outlier: 6.537A  pdb=" N   VAL B  21 " --> pdb=" O   ILE B  98 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   VAL B 100 " --> pdb=" O   VAL B  21 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LEU B  23 " --> pdb=" O   VAL B 100 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   MET B  99 " --> pdb=" O   ILE B 152 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   ILE B 154 " --> pdb=" O   MET B  99 " (cutoff:3.500A)
      removed outlier: 7.411A  pdb=" N   ASN B 101 " --> pdb=" O   ILE B 154 " (cutoff:3.500A)
      removed outlier: 9.756A  pdb=" N   MET B 262 " --> pdb=" O   ILE B 192 " (cutoff:3.500A)
      removed outlier: 7.687A  pdb=" N   VAL B 194 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 8.615A  pdb=" N   LEU B 264 " --> pdb=" O   VAL B 194 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   CYS B 196 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
      removed outlier: 7.651A  pdb=" N   VAL B 266 " --> pdb=" O   CYS B 196 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   SER B 198 " --> pdb=" O   VAL B 266 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 69 through 73
      removed outlier: 6.563A  pdb=" N   VAL C  21 " --> pdb=" O   ILE C  98 " (cutoff:3.500A)
      removed outlier: 8.006A  pdb=" N   VAL C 100 " --> pdb=" O   VAL C  21 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   LEU C  23 " --> pdb=" O   VAL C 100 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   MET C  99 " --> pdb=" O   ILE C 152 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   ILE C 154 " --> pdb=" O   MET C  99 " (cutoff:3.500A)
      removed outlier: 7.412A  pdb=" N   ASN C 101 " --> pdb=" O   ILE C 154 " (cutoff:3.500A)
      removed outlier: 8.629A  pdb=" N   LEU C 264 " --> pdb=" O   VAL C 194 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   CYS C 196 " --> pdb=" O   LEU C 264 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   VAL C 266 " --> pdb=" O   CYS C 196 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   SER C 198 " --> pdb=" O   VAL C 266 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 69 through 73
      removed outlier: 6.558A  pdb=" N   VAL D  21 " --> pdb=" O   ILE D  98 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   VAL D 100 " --> pdb=" O   VAL D  21 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   LEU D  23 " --> pdb=" O   VAL D 100 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   MET D  99 " --> pdb=" O   ILE D 152 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   ILE D 154 " --> pdb=" O   MET D  99 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   ASN D 101 " --> pdb=" O   ILE D 154 " (cutoff:3.500A)
      removed outlier: 8.615A  pdb=" N   LEU D 264 " --> pdb=" O   VAL D 194 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   CYS D 196 " --> pdb=" O   LEU D 264 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   VAL D 266 " --> pdb=" O   CYS D 196 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   SER D 198 " --> pdb=" O   VAL D 266 " (cutoff:3.500A)

    460 hydrogen bonds defined for protein.
    1333 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.47

  Time building geometry restraints manager: 2.56 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: 2778
        1.34 -     1.46: 1652
        1.46 -     1.58: 3658
        1.58 -     1.70: 0
        1.70 -     1.81: 80
  Bond restraints: 8168
  Sorted by residual:
  bond pdb=" CB ALYS D 189 "
       pdb=" CG ALYS D 189 "
    ideal  model  delta    sigma   weight residual
    1.520  1.470  0.050 3.00e-02 1.11e+03 2.78e+00
  bond pdb=" CA  GLN D  52 "
       pdb=" C   GLN D  52 "
    ideal  model  delta    sigma   weight residual
    1.532  1.520  0.013 9.60e-03 1.09e+04 1.80e+00
  bond pdb=" CG1 ILE D  98 "
       pdb=" CD1 ILE D  98 "
    ideal  model  delta    sigma   weight residual
    1.513  1.463  0.050 3.90e-02 6.57e+02 1.62e+00
  bond pdb=" CG1 ILE B  98 "
       pdb=" CD1 ILE B  98 "
    ideal  model  delta    sigma   weight residual
    1.513  1.464  0.049 3.90e-02 6.57e+02 1.57e+00
  bond pdb=" CG1 ILE A  98 "
       pdb=" CD1 ILE A  98 "
    ideal  model  delta    sigma   weight residual
    1.513  1.464  0.049 3.90e-02 6.57e+02 1.56e+00
  ... (remaining 8163 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.06: 10294
        1.06 -     2.11: 636
        2.11 -     3.17: 121
        3.17 -     4.23: 23
        4.23 -     5.28: 6
  Bond angle restraints: 11080
  Sorted by residual:
  angle pdb=" CA  SER B 155 "
        pdb=" C   SER B 155 "
        pdb=" N   SER B 156 "
      ideal   model   delta    sigma   weight residual
     117.21  120.45   -3.24 1.42e+00 4.96e-01 5.22e+00
  angle pdb=" CA  SER A 155 "
        pdb=" C   SER A 155 "
        pdb=" N   SER A 156 "
      ideal   model   delta    sigma   weight residual
     117.21  120.45   -3.24 1.42e+00 4.96e-01 5.20e+00
  angle pdb=" CA  SER C 155 "
        pdb=" C   SER C 155 "
        pdb=" N   SER C 156 "
      ideal   model   delta    sigma   weight residual
     117.21  120.43   -3.22 1.42e+00 4.96e-01 5.13e+00
  angle pdb=" CA  SER B 155 "
        pdb=" C   SER B 155 "
        pdb=" O   SER B 155 "
      ideal   model   delta    sigma   weight residual
     120.84  117.86    2.98 1.33e+00 5.65e-01 5.01e+00
  angle pdb=" C   ALA B 256 "
        pdb=" N  BARG B 257 "
        pdb=" CA BARG B 257 "
      ideal   model   delta    sigma   weight residual
     120.38  123.64   -3.26 1.46e+00 4.69e-01 4.99e+00
  ... (remaining 11075 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.21: 4535
       16.21 -    32.42: 316
       32.42 -    48.63: 48
       48.63 -    64.84: 12
       64.84 -    81.05: 5
  Dihedral angle restraints: 4916
    sinusoidal: 1901
      harmonic: 3015
  Sorted by residual:
  dihedral pdb=" CA  PRO A 199 "
           pdb=" C   PRO A 199 "
           pdb=" N   TYR A 200 "
           pdb=" CA  TYR A 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.59   16.41     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  PRO C 199 "
           pdb=" C   PRO C 199 "
           pdb=" N   TYR C 200 "
           pdb=" CA  TYR C 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.86   16.14     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CA  CYS A  60 "
           pdb=" C   CYS A  60 "
           pdb=" N   GLU A  61 "
           pdb=" CA  GLU A  61 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.94   16.06     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 4913 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 458
       0.027 -    0.054: 446
       0.054 -    0.081: 244
       0.081 -    0.108: 83
       0.108 -    0.135: 33
  Chirality restraints: 1264
  Sorted by residual:
  chirality pdb=" CB  ILE A 192 "
            pdb=" CA  ILE A 192 "
            pdb=" CG1 ILE A 192 "
            pdb=" CG2 ILE A 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.59e-01
  chirality pdb=" CB  ILE C 192 "
            pdb=" CA  ILE C 192 "
            pdb=" CG1 ILE C 192 "
            pdb=" CG2 ILE C 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.43e-01
  chirality pdb=" CB  ILE D 192 "
            pdb=" CA  ILE D 192 "
            pdb=" CG1 ILE D 192 "
            pdb=" CG2 ILE D 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.29e-01
  ... (remaining 1261 not shown)

  Planarity restraints: 1468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 198 "    0.035 5.00e-02 4.00e+02   5.22e-02 4.37e+00
        pdb=" N   PRO B 199 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO B 199 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 199 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D 198 "   -0.034 5.00e-02 4.00e+02   5.07e-02 4.12e+00
        pdb=" N   PRO D 199 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO D 199 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO D 199 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 198 "    0.033 5.00e-02 4.00e+02   4.96e-02 3.94e+00
        pdb=" N   PRO A 199 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 199 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 199 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1465 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 247
        2.69 -     3.24: 8750
        3.24 -     3.80: 14430
        3.80 -     4.35: 20153
        4.35 -     4.90: 31567
  Nonbonded interactions: 75147
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 112 "
            pdb=" O   HOH A 301 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" OD2 ASP D 112 "
            pdb=" O   HOH D 301 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" OD2 ASP C 112 "
            pdb=" O   HOH C 301 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" O   VAL C 237 "
            pdb=" O   HOH C 302 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" O   VAL A 237 "
            pdb=" O   HOH A 302 "
     model   vdw
     2.180 3.040
  ... (remaining 75142 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 13 through 19 or resid 21 through 33 or resid 35 through 3 \ 
6 or resid 38 through 39 or resid 41 through 44 or resid 46 through 82 or resid  \ 
85 through 89 or resid 91 through 116 or resid 118 through 146 or resid 149 thro \ 
ugh 180 or resid 182 through 188 or resid 190 through 202 or resid 220 through 2 \ 
24 or resid 226 through 237 or resid 239 through 256 or resid 258 through 282))
  selection = (chain 'B' and (resid 13 through 19 or resid 21 through 33 or resid 35 through 3 \ 
6 or resid 38 through 39 or resid 41 through 44 or resid 46 through 82 or resid  \ 
85 through 89 or resid 91 through 116 or resid 118 through 146 or resid 149 thro \ 
ugh 180 or resid 182 through 188 or resid 190 through 202 or resid 220 through 2 \ 
24 or resid 226 through 237 or resid 239 through 256 or resid 258 through 282))
  selection = (chain 'C' and (resid 13 through 19 or resid 21 through 33 or resid 35 through 3 \ 
6 or resid 38 through 39 or resid 41 through 44 or resid 46 through 82 or resid  \ 
85 through 89 or resid 91 through 116 or resid 118 through 146 or resid 149 thro \ 
ugh 180 or resid 182 through 188 or resid 190 through 202 or resid 220 through 2 \ 
24 or resid 226 through 237 or resid 239 through 256 or resid 258 through 282))
  selection = (chain 'D' and (resid 13 through 19 or resid 21 through 33 or resid 35 through 3 \ 
6 or resid 38 through 39 or resid 41 through 44 or resid 46 through 82 or resid  \ 
85 through 89 or resid 91 through 116 or resid 118 through 146 or resid 149 thro \ 
ugh 180 or resid 182 through 188 or resid 190 through 202 or resid 220 through 2 \ 
24 or resid 226 through 237 or resid 239 through 256 or resid 258 through 282))
}

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=0.50 max=1.00 mean=0.96
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:             4.510
  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:          0.340
  Check model and map are aligned:         0.050
  Set scattering table:                    0.090
  Process input model:                     28.050
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.060
  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:13.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
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      :  0.008   0.050   8168  Z= 0.537
  Angle     :  0.594   5.284  11080  Z= 0.334
  Chirality :  0.049   0.135   1264
  Planarity :  0.005   0.052   1468
  Dihedral  : 11.733  81.046   3002
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  5.10 %
    Favored  : 93.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.23), residues: 1117
  helix: -0.01 (0.22), residues: 511
  sheet:  0.38 (0.39), residues: 176
  loop : -0.96 (0.26), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 221 
 HIS   0.012   0.002   HIS A 138 
 PHE   0.016   0.003   PHE C 133 
 TYR   0.014   0.003   TYR C 200 
 ARG   0.003   0.001   ARG C  16 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 2
  residues processed: 113
  average time/residue: 2.0634
  time to fit residues: 242.5899
Evaluate side-chains
  79 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LYS
Chi-restraints excluded: chain D residue   92 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0870
   chunk 51 optimal weight:    0.3980
   chunk 40 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
A 235 GLN
B 235 GLN
C 235 GLN
D 233 ASN
D 235 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.100995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.073381 restraints weight = 132234.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 4.84
r_work: 0.2917 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2911
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2911 r_free = 0.2911    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2911 r_free = 0.2911    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2911
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8961
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8168  Z= 0.226
  Angle     :  0.522   9.058  11080  Z= 0.287
  Chirality :  0.044   0.146   1264
  Planarity :  0.004   0.048   1468
  Dihedral  :  5.101  55.886   1180
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  9.74 %
    Favored  : 89.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.25), residues: 1117
  helix:  1.31 (0.22), residues: 535
  sheet:  0.49 (0.37), residues: 180
  loop : -0.34 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 221 
 HIS   0.003   0.001   HIS D 138 
 PHE   0.011   0.002   PHE C 133 
 TYR   0.017   0.002   TYR C 169 
 ARG   0.006   0.001   ARG B  20 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8567 (tttt)
REVERT: B   20 ARG cc_start: 0.8850 (mmt90) cc_final: 0.8578 (mmm-85)
REVERT: D   92 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8535 (tttt)
  outliers start: 3
  outliers final: 0
  residues processed: 82
  average time/residue: 2.0561
  time to fit residues: 177.5265
Evaluate side-chains
  74 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 1.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LYS
Chi-restraints excluded: chain D residue   92 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 87 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9990
   chunk 95 optimal weight:    0.7980
   chunk 64 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
D 233 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.100061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.072702 restraints weight = 129177.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 4.76
r_work: 0.2908 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2909
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8964
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8168  Z= 0.255
  Angle     :  0.498   8.396  11080  Z= 0.272
  Chirality :  0.044   0.152   1264
  Planarity :  0.003   0.047   1468
  Dihedral  :  4.944  57.015   1180
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.63 %
    Favored  : 89.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.25), residues: 1117
  helix:  1.64 (0.22), residues: 535
  sheet:  0.41 (0.36), residues: 184
  loop :  0.02 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 221 
 HIS   0.005   0.001   HIS A 138 
 PHE   0.012   0.001   PHE B 133 
 TYR   0.018   0.002   TYR C 169 
 ARG   0.004   0.000   ARG B  20 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   20 ARG cc_start: 0.8826 (mmt90) cc_final: 0.8576 (mmm-85)
REVERT: B  238 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8468 (pm20)
REVERT: C   92 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8575 (tmtt)
REVERT: D   92 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8681 (tmtt)
  outliers start: 9
  outliers final: 1
  residues processed: 85
  average time/residue: 1.5400
  time to fit residues: 137.9128
Evaluate side-chains
  84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   92 LYS
Chi-restraints excluded: chain D residue   92 LYS
Chi-restraints excluded: chain D residue  161 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 93 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 95 optimal weight:    0.4980
   chunk 29 optimal weight:    9.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3587 r_free = 0.3587 target = 0.098917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.071592 restraints weight = 130095.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 4.72
r_work: 0.2887 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2888
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2888
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8978
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8168  Z= 0.334
  Angle     :  0.517   8.768  11080  Z= 0.281
  Chirality :  0.044   0.139   1264
  Planarity :  0.004   0.047   1468
  Dihedral  :  4.538  57.460   1176
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  9.98 %
    Favored  : 88.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.25), residues: 1117
  helix:  1.69 (0.22), residues: 535
  sheet:  0.41 (0.36), residues: 184
  loop :  0.11 (0.33), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 221 
 HIS   0.006   0.001   HIS C 138 
 PHE   0.012   0.002   PHE C 133 
 TYR   0.021   0.003   TYR C 169 
 ARG   0.003   0.000   ARG B  20 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8672 (tt0)
REVERT: B  186 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8680 (tt0)
REVERT: B  238 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8468 (pm20)
REVERT: C  186 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8657 (tt0)
REVERT: D  186 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8584 (tt0)
  outliers start: 10
  outliers final: 2
  residues processed: 77
  average time/residue: 1.6446
  time to fit residues: 133.5821
Evaluate side-chains
  79 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain B residue   92 LYS
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain D residue  161 MET
Chi-restraints excluded: chain D residue  186 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 4 optimal weight:    7.9990
   chunk 97 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 96 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3598 r_free = 0.3598 target = 0.099506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.072282 restraints weight = 125133.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 4.68
r_work: 0.2905 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2906
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2906 r_free = 0.2906    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2905
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8968
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8168  Z= 0.273
  Angle     :  0.485   8.637  11080  Z= 0.263
  Chirality :  0.043   0.139   1264
  Planarity :  0.003   0.045   1468
  Dihedral  :  3.972  18.483   1172
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 10.79 %
    Favored  : 88.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.25), residues: 1117
  helix:  1.80 (0.22), residues: 535
  sheet:  0.44 (0.37), residues: 185
  loop :  0.18 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 221 
 HIS   0.005   0.001   HIS C 138 
 PHE   0.012   0.001   PHE C 133 
 TYR   0.022   0.003   TYR C 169 
 ARG   0.004   0.000   ARG B  20 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8665 (tt0)
REVERT: B  186 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8664 (tt0)
REVERT: B  238 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8465 (pm20)
REVERT: C  106 SER cc_start: 0.9229 (OUTLIER) cc_final: 0.8990 (t)
REVERT: C  186 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8656 (tt0)
REVERT: D  186 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8589 (tt0)
REVERT: D  226 ARG cc_start: 0.7955 (mtm110) cc_final: 0.7752 (mtm110)
  outliers start: 7
  outliers final: 1
  residues processed: 76
  average time/residue: 1.6487
  time to fit residues: 131.9021
Evaluate side-chains
  80 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain D residue  161 MET
Chi-restraints excluded: chain D residue  186 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 82 optimal weight:    0.6980
   chunk 72 optimal weight:    0.6980
   chunk 66 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3606 r_free = 0.3606 target = 0.100028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.072714 restraints weight = 139310.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 4.83
r_work: 0.2910 rms_B_bonded: 4.50 restraints_weight: 0.5000
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2908
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2908
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8972
moved from start:          0.1928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8168  Z= 0.232
  Angle     :  0.466   8.706  11080  Z= 0.253
  Chirality :  0.043   0.137   1264
  Planarity :  0.003   0.046   1468
  Dihedral  :  3.890  18.451   1172
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 11.14 %
    Favored  : 88.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.25), residues: 1117
  helix:  1.91 (0.22), residues: 535
  sheet:  0.46 (0.37), residues: 185
  loop :  0.28 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 221 
 HIS   0.004   0.001   HIS D 138 
 PHE   0.012   0.001   PHE C 133 
 TYR   0.021   0.003   TYR C 169 
 ARG   0.004   0.000   ARG B  20 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8686 (tt0)
REVERT: B   45 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8776 (mttt)
REVERT: B  186 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8669 (tt0)
REVERT: B  238 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8450 (pm20)
REVERT: C  106 SER cc_start: 0.9286 (OUTLIER) cc_final: 0.9063 (t)
REVERT: C  186 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8659 (tt0)
REVERT: D  186 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8577 (tt0)
  outliers start: 7
  outliers final: 1
  residues processed: 77
  average time/residue: 1.6142
  time to fit residues: 130.8378
Evaluate side-chains
  81 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain D residue  161 MET
Chi-restraints excluded: chain D residue  186 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 81 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 96 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3596 r_free = 0.3596 target = 0.099372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.072092 restraints weight = 130597.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 4.75
r_work: 0.2901 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2902
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2902 r_free = 0.2902    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2902 r_free = 0.2902    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2902
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8971
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8168  Z= 0.270
  Angle     :  0.484   9.634  11080  Z= 0.262
  Chirality :  0.043   0.156   1264
  Planarity :  0.003   0.045   1468
  Dihedral  :  3.923  19.465   1172
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 11.02 %
    Favored  : 88.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.25), residues: 1117
  helix:  1.87 (0.22), residues: 535
  sheet:  0.43 (0.37), residues: 185
  loop :  0.28 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 221 
 HIS   0.005   0.001   HIS A 138 
 PHE   0.011   0.001   PHE B 133 
 TYR   0.022   0.003   TYR C 169 
 ARG   0.003   0.000   ARG B  20 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8667 (tt0)
REVERT: B   45 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8741 (mttt)
REVERT: B  186 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8684 (tt0)
REVERT: B  238 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8451 (pm20)
REVERT: C  186 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8673 (tt0)
REVERT: D  186 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8588 (tt0)
  outliers start: 8
  outliers final: 1
  residues processed: 75
  average time/residue: 1.7977
  time to fit residues: 141.4220
Evaluate side-chains
  79 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain D residue  161 MET
Chi-restraints excluded: chain D residue  186 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 96 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 61 optimal weight:    0.2980
   chunk 73 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 6 optimal weight:    0.3980
   chunk 88 optimal weight:    0.0570
   chunk 92 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.3898

-------------------------------------------------------------------------------
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 = 0.3626 r_free = 0.3626 target = 0.101307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.074184 restraints weight = 125404.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 4.74
r_work: 0.2951 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2943
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2943 r_free = 0.2943    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2943 r_free = 0.2943    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.2943
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8945
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8168  Z= 0.159
  Angle     :  0.443   8.407  11080  Z= 0.239
  Chirality :  0.042   0.156   1264
  Planarity :  0.003   0.047   1468
  Dihedral  :  3.763  21.341   1172
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 11.14 %
    Favored  : 88.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.26), residues: 1117
  helix:  2.04 (0.22), residues: 535
  sheet:  0.48 (0.38), residues: 183
  loop :  0.37 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 221 
 HIS   0.003   0.001   HIS A 138 
 PHE   0.010   0.001   PHE D 133 
 TYR   0.022   0.002   TYR C 169 
 ARG   0.004   0.000   ARG B  20 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8648 (tt0)
REVERT: B   45 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8733 (mttt)
REVERT: B  186 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8648 (tt0)
REVERT: B  238 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8438 (pm20)
REVERT: C  186 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8608 (tt0)
REVERT: D  186 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8552 (tt0)
  outliers start: 6
  outliers final: 1
  residues processed: 79
  average time/residue: 1.6669
  time to fit residues: 138.4565
Evaluate side-chains
  84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain D residue  161 MET
Chi-restraints excluded: chain D residue  186 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 97 optimal weight:    0.6980
   chunk 37 optimal weight:    0.3980
   chunk 11 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0670
   chunk 56 optimal weight:    0.8980
   chunk 82 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.5118

-------------------------------------------------------------------------------
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 = 0.3619 r_free = 0.3619 target = 0.100782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.073588 restraints weight = 127997.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 4.76
r_work: 0.2932 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2932
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.2932
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8949
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8168  Z= 0.190
  Angle     :  0.448   8.165  11080  Z= 0.242
  Chirality :  0.042   0.151   1264
  Planarity :  0.003   0.046   1468
  Dihedral  :  3.759  22.852   1172
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 11.25 %
    Favored  : 88.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.26), residues: 1117
  helix:  2.03 (0.22), residues: 535
  sheet:  0.49 (0.38), residues: 183
  loop :  0.41 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 221 
 HIS   0.004   0.001   HIS B 138 
 PHE   0.011   0.001   PHE C 133 
 TYR   0.020   0.002   TYR D 169 
 ARG   0.003   0.000   ARG B  20 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8671 (tt0)
REVERT: B   45 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8767 (mttt)
REVERT: B  186 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8651 (tt0)
REVERT: B  238 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8445 (pm20)
REVERT: C  186 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8642 (tt0)
REVERT: D  186 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8573 (tt0)
  outliers start: 6
  outliers final: 1
  residues processed: 79
  average time/residue: 1.6034
  time to fit residues: 133.4189
Evaluate side-chains
  84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain D residue  161 MET
Chi-restraints excluded: chain D residue  186 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 93 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 67 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3603 r_free = 0.3603 target = 0.099785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.072523 restraints weight = 134279.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 4.78
r_work: 0.2910 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2909
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.2909
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8965
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8168  Z= 0.255
  Angle     :  0.478   8.847  11080  Z= 0.259
  Chirality :  0.043   0.156   1264
  Planarity :  0.003   0.044   1468
  Dihedral  :  3.862  23.179   1172
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 11.37 %
    Favored  : 87.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.26), residues: 1117
  helix:  1.96 (0.22), residues: 535
  sheet:  0.51 (0.38), residues: 183
  loop :  0.42 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 221 
 HIS   0.005   0.001   HIS C 138 
 PHE   0.011   0.001   PHE C 133 
 TYR   0.024   0.003   TYR C 169 
 ARG   0.003   0.000   ARG B  20 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8689 (tt0)
REVERT: B   45 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8784 (mttt)
REVERT: B  186 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8679 (tt0)
REVERT: B  238 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8444 (pm20)
REVERT: C  186 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8663 (tt0)
REVERT: D  186 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8586 (tt0)
  outliers start: 6
  outliers final: 1
  residues processed: 78
  average time/residue: 1.6449
  time to fit residues: 135.2768
Evaluate side-chains
  83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain B residue   45 LYS
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain C residue  186 GLU
Chi-restraints excluded: chain D residue  161 MET
Chi-restraints excluded: chain D residue  186 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 80 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3605 r_free = 0.3605 target = 0.099868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.072638 restraints weight = 131871.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 4.78
r_work: 0.2912 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2913
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2913 r_free = 0.2913    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.2913
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8962
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8168  Z= 0.243
  Angle     :  0.465   6.969  11080  Z= 0.254
  Chirality :  0.043   0.150   1264
  Planarity :  0.003   0.045   1468
  Dihedral  :  3.866  23.492   1172
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 11.25 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.26), residues: 1117
  helix:  1.97 (0.22), residues: 535
  sheet:  0.49 (0.37), residues: 183
  loop :  0.43 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 221 
 HIS   0.004   0.001   HIS C 138 
 PHE   0.011   0.001   PHE B 133 
 TYR   0.024   0.003   TYR C 169 
 ARG   0.003   0.000   ARG B  20 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8426.29 seconds
wall clock time: 146 minutes 36.70 seconds (8796.70 seconds total)