Starting phenix.real_space_refine
on Wed Feb 12 19:29:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o6p_12739/02_2025/7o6p_12739.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o6p_12739/02_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_12739/02_2025/7o6p_12739.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o6p_12739/02_2025/7o6p_12739.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o6p_12739/02_2025/7o6p_12739.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o6p_12739/02_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-5592/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: 9.06, per 1000 atoms: 1.09
  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: 2.23
  Conformation dependent library (CDL) restraints added in 1.7 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: 0.95
  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: 2.30

  Time building geometry restraints manager: 2.57 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:             2.980
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     26.650
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.050
  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:12.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.670
-------------------------------------------------------------------------------
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  : 0.902 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 2
  residues processed: 113
  average time/residue: 2.0047
  time to fit residues: 235.6776
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  : 0.828 
-------------------------------------------------------------------------------
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 = 47)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.073383 restraints weight = 132234.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 4.84
r_work: 0.2917 rms_B_bonded: 4.53 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 = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8962
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  : 0.797 
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: 0.8848 (mmt90) cc_final: 0.8576 (mmm-85)
REVERT: D   92 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8534 (tttt)
  outliers start: 3
  outliers final: 0
  residues processed: 82
  average time/residue: 1.6995
  time to fit residues: 146.4419
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  : 0.806 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 49 optimal weight:    0.0980
   chunk 13 optimal weight:    0.9990
   chunk 35 optimal weight:    0.3980
   chunk 87 optimal weight:    0.5980
   chunk 86 optimal weight:    0.5980
   chunk 95 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
D 233 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.101653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.074284 restraints weight = 129756.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 4.79
r_work: 0.2939 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8941
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8168  Z= 0.178
  Angle     :  0.469   7.781  11080  Z= 0.255
  Chirality :  0.043   0.154   1264
  Planarity :  0.003   0.047   1468
  Dihedral  :  4.835  56.833   1180
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.16
  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:  1.34 (0.25), residues: 1117
  helix:  1.73 (0.22), residues: 535
  sheet:  0.45 (0.36), residues: 183
  loop :  0.06 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 221 
 HIS   0.003   0.001   HIS A 138 
 PHE   0.011   0.001   PHE C 133 
 TYR   0.018   0.002   TYR C 169 
 ARG   0.005   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
  92 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   20 ARG cc_start: 0.8813 (mmt90) cc_final: 0.8566 (mmm-85)
REVERT: C   92 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8551 (tmtt)
REVERT: D   92 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8672 (tmtt)
  outliers start: 9
  outliers final: 1
  residues processed: 86
  average time/residue: 1.6183
  time to fit residues: 146.5950
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  : 0.996 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 69 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   chunk 68 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 95 optimal weight:    0.6980
   chunk 29 optimal weight:    9.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.099467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.072099 restraints weight = 130325.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 4.75
r_work: 0.2897 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2897
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2897 r_free = 0.2897    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2897
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8971
moved from start:          0.1730

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= 0.288
  Angle     :  0.497   7.518  11080  Z= 0.271
  Chirality :  0.044   0.157   1264
  Planarity :  0.003   0.045   1468
  Dihedral  :  4.459  57.101   1176
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  9.74 %
    Favored  : 89.10 %
  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:  1.41 (0.25), residues: 1117
  helix:  1.76 (0.22), residues: 535
  sheet:  0.39 (0.36), residues: 185
  loop :  0.20 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 221 
 HIS   0.006   0.001   HIS D 138 
 PHE   0.012   0.002   PHE C 133 
 TYR   0.019   0.002   TYR C 169 
 ARG   0.004   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
  90 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8651 (tt0)
REVERT: B  186 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8678 (tt0)
REVERT: B  238 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8457 (pm20)
REVERT: C  186 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8656 (tt0)
REVERT: D  186 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8584 (tt0)
  outliers start: 10
  outliers final: 2
  residues processed: 82
  average time/residue: 1.7384
  time to fit residues: 149.7286
Evaluate side-chains
  86 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 4 optimal weight:    8.9990
   chunk 97 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3604 r_free = 0.3604 target = 0.099845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.072578 restraints weight = 125119.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 4.71
r_work: 0.2912 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2912
-------------------------------------------------------------------------------
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 = 0.19   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 = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2911
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8969
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8168  Z= 0.257
  Angle     :  0.480   8.694  11080  Z= 0.260
  Chirality :  0.043   0.152   1264
  Planarity :  0.003   0.045   1468
  Dihedral  :  3.917  17.886   1172
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 10.90 %
    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:  1.51 (0.25), residues: 1117
  helix:  1.84 (0.22), residues: 535
  sheet:  0.51 (0.37), residues: 183
  loop :  0.20 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 221 
 HIS   0.004   0.001   HIS A 138 
 PHE   0.012   0.001   PHE C 133 
 TYR   0.021   0.003   TYR C 169 
 ARG   0.005   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
  85 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8640 (tt0)
REVERT: B  186 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8654 (tt0)
REVERT: B  238 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8440 (pm20)
REVERT: C  106 SER cc_start: 0.9238 (OUTLIER) cc_final: 0.8996 (t)
REVERT: C  186 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8640 (tt0)
REVERT: D  186 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8563 (tt0)
  outliers start: 8
  outliers final: 1
  residues processed: 79
  average time/residue: 1.5847
  time to fit residues: 131.7891
Evaluate side-chains
  82 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 83 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 82 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 18 optimal weight:    0.3980
   chunk 11 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   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 = 0.3608 r_free = 0.3608 target = 0.100045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.072744 restraints weight = 138954.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 4.85
r_work: 0.2912 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.2912
-------------------------------------------------------------------------------
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 = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2907 r_free = 0.2907    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2907
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8971
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8168  Z= 0.232
  Angle     :  0.469   7.838  11080  Z= 0.254
  Chirality :  0.043   0.143   1264
  Planarity :  0.003   0.045   1468
  Dihedral  :  3.899  22.536   1172
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  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:  1.61 (0.26), residues: 1117
  helix:  1.91 (0.22), residues: 535
  sheet:  0.53 (0.37), residues: 183
  loop :  0.28 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 221 
 HIS   0.004   0.001   HIS C 138 
 PHE   0.011   0.001   PHE C 133 
 TYR   0.021   0.002   TYR C 169 
 ARG   0.003   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: 6
    poor density    : 76
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8658 (tt0)
REVERT: B  186 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8675 (tt0)
REVERT: B  238 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8456 (pm20)
REVERT: C  186 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8657 (tt0)
REVERT: D  186 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8561 (tt0)
REVERT: D  226 ARG cc_start: 0.7985 (mtm110) cc_final: 0.7735 (mtm110)
  outliers start: 6
  outliers final: 1
  residues processed: 76
  average time/residue: 1.6899
  time to fit residues: 135.3595
Evaluate side-chains
  81 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
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  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:    3.9990
   chunk 81 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 29 optimal weight:    9.9990
   chunk 96 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   chunk 92 optimal weight:    0.5980
   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 = 0.3599 r_free = 0.3599 target = 0.099456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.072206 restraints weight = 130623.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 4.74
r_work: 0.2902 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2902
-------------------------------------------------------------------------------
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 = 0.13   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 = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2902
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8972
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8168  Z= 0.273
  Angle     :  0.477   7.230  11080  Z= 0.261
  Chirality :  0.043   0.146   1264
  Planarity :  0.003   0.044   1468
  Dihedral  :  3.941  22.607   1172
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 11.02 %
    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:  1.58 (0.25), residues: 1117
  helix:  1.90 (0.22), residues: 535
  sheet:  0.42 (0.37), residues: 185
  loop :  0.31 (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 D 138 
 PHE   0.011   0.001   PHE C 133 
 TYR   0.023   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
  82 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8662 (tt0)
REVERT: B   45 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8774 (mttt)
REVERT: B  186 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8685 (tt0)
REVERT: B  238 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8462 (pm20)
REVERT: C  106 SER cc_start: 0.9277 (OUTLIER) cc_final: 0.9075 (t)
REVERT: C  186 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8668 (tt0)
REVERT: D  186 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8566 (tt0)
  outliers start: 7
  outliers final: 1
  residues processed: 77
  average time/residue: 1.7055
  time to fit residues: 138.0741
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  : 0.866 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0970
   chunk 61 optimal weight:    0.4980
   chunk 73 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 87 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0870
   chunk 92 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.4556

-------------------------------------------------------------------------------
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 = 0.3625 r_free = 0.3625 target = 0.101119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.073810 restraints weight = 124972.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 4.76
r_work: 0.2941 rms_B_bonded: 4.38 restraints_weight: 0.5000
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8944
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8168  Z= 0.176
  Angle     :  0.440   6.883  11080  Z= 0.239
  Chirality :  0.042   0.144   1264
  Planarity :  0.003   0.046   1468
  Dihedral  :  3.796  23.410   1172
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 11.02 %
    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:  1.75 (0.26), residues: 1117
  helix:  2.05 (0.22), residues: 535
  sheet:  0.50 (0.37), residues: 183
  loop :  0.38 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 221 
 HIS   0.004   0.001   HIS B 138 
 PHE   0.010   0.001   PHE B 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
  85 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8645 (tt0)
REVERT: B   45 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8729 (mttt)
REVERT: B  186 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8635 (tt0)
REVERT: B  238 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8453 (pm20)
REVERT: C  186 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8614 (tt0)
REVERT: D  186 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8565 (tt0)
  outliers start: 7
  outliers final: 1
  residues processed: 80
  average time/residue: 1.6092
  time to fit residues: 135.5383
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  : 0.822 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 37 optimal weight:    0.4980
   chunk 11 optimal weight:    0.5980
   chunk 74 optimal weight:    0.8980
   chunk 54 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 56 optimal weight:    0.4980
   chunk 82 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 98 optimal weight:    2.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3615 r_free = 0.3615 target = 0.100552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.073319 restraints weight = 127522.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 4.77
r_work: 0.2929 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2923
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.2923
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8958
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8168  Z= 0.206
  Angle     :  0.450   7.556  11080  Z= 0.245
  Chirality :  0.042   0.141   1264
  Planarity :  0.003   0.045   1468
  Dihedral  :  3.801  23.518   1172
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  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:  1.75 (0.26), residues: 1117
  helix:  2.02 (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   0.004   0.001   TRP A 221 
 HIS   0.004   0.001   HIS C 138 
 PHE   0.011   0.001   PHE C 133 
 TYR   0.022   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  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8658 (tt0)
REVERT: B   45 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8782 (mttt)
REVERT: B  186 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8658 (tt0)
REVERT: B  238 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8447 (pm20)
REVERT: C  186 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8647 (tt0)
REVERT: D  186 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8583 (tt0)
  outliers start: 6
  outliers final: 1
  residues processed: 79
  average time/residue: 1.6344
  time to fit residues: 136.1986
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  : 0.808 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3600 r_free = 0.3600 target = 0.099527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.072268 restraints weight = 134048.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 4.78
r_work: 0.2904 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2905
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2905 r_free = 0.2905    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.2905
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8969
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8168  Z= 0.265
  Angle     :  0.479   7.979  11080  Z= 0.261
  Chirality :  0.043   0.143   1264
  Planarity :  0.003   0.043   1468
  Dihedral  :  3.893  23.441   1172
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  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:  1.69 (0.26), residues: 1117
  helix:  1.95 (0.22), residues: 535
  sheet:  0.43 (0.37), residues: 185
  loop :  0.45 (0.33), residues: 397

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   0.010   0.001   PHE C 133 
 TYR   0.023   0.003   TYR D 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: 7
    poor density    : 76
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8689 (tt0)
REVERT: B   45 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8789 (mttt)
REVERT: B  186 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8686 (tt0)
REVERT: B  238 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8448 (pm20)
REVERT: C  186 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8672 (tt0)
REVERT: D  186 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8598 (tt0)
  outliers start: 7
  outliers final: 1
  residues processed: 78
  average time/residue: 1.7128
  time to fit residues: 140.5903
Evaluate side-chains
  82 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 86 optimal weight:    0.5980
   chunk 52 optimal weight:    0.1980
   chunk 43 optimal weight:    1.9990
   chunk 32 optimal weight:    0.4980
   chunk 80 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 31 optimal weight:    0.3980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.100718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.073501 restraints weight = 132291.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 4.79
r_work: 0.2933 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2929
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.2929
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8956
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8168  Z= 0.193
  Angle     :  0.450   7.578  11080  Z= 0.244
  Chirality :  0.042   0.141   1264
  Planarity :  0.003   0.045   1468
  Dihedral  :  3.785  23.074   1172
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  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:  1.80 (0.26), residues: 1117
  helix:  2.04 (0.22), residues: 535
  sheet:  0.50 (0.38), residues: 183
  loop :  0.49 (0.34), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 221 
 HIS   0.004   0.001   HIS C 138 
 PHE   0.011   0.001   PHE D 133 
 TYR   0.022   0.002   TYR D 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: 8040.44 seconds
wall clock time: 142 minutes 8.32 seconds (8528.32 seconds total)