Starting phenix.real_space_refine
on Wed Mar  4 20:07:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pkb_13467/03_2026/7pkb_13467.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pkb_13467/03_2026/7pkb_13467.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pkb_13467/03_2026/7pkb_13467.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pkb_13467/03_2026/7pkb_13467.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pkb_13467/03_2026/7pkb_13467.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pkb_13467/03_2026/7pkb_13467.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca     10      9.91       5
     S      20      5.16       5
     C    5290      2.51       5
     N    1305      2.21       5
     O    1550      1.98       5
     H    7970      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16145
  Number of models: 1
  Model: ""
    Number of chains: 15
    Chain: "E"
      Number of atoms: 3224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3224
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "D"
      Number of atoms: 3224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3224
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "C"
      Number of atoms: 3224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3224
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "B"
      Number of atoms: 3224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3224
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "A"
      Number of atoms: 3224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3224
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
    Chain: "D"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
    Chain: "C"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Classifications: {'water': 1}
  Time building chain proxies: 2.45, per 1000 atoms: 0.15
  Number of scatterers: 16145
  At special positions: 0
  Unit cell: (113.696, 115.368, 53.504, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca     10     19.99
     S      20     16.00
     O    1550      8.00
     N    1305      7.00
     C    5290      6.00
     H    7970      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  36 " - pdb=" SG  CYS E  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  36 " - pdb=" SG  CYS D  97 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  36 " - pdb=" SG  CYS C  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  36 " - pdb=" SG  CYS B  97 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  36 " - pdb=" SG  CYS A  97 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.31
  Conformation dependent library (CDL) restraints added in 379.1 milliseconds
  

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1890

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 15 sheets defined
      12.1% alpha, 37.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'E' and resid 42 through 46
      removed outlier: 4.037A  pdb=" N   SER E  45 " --> pdb=" O   GLU E  42 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 147 through 151
    Processing helix  chain 'E' and resid 167 through 176
    Processing helix  chain 'E' and resid 186 through 190
      removed outlier: 3.996A  pdb=" N   LEU E 190 " --> pdb=" O   TRP E 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 42 through 46
      removed outlier: 4.019A  pdb=" N   SER D  45 " --> pdb=" O   GLU D  42 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 147 through 151
    Processing helix  chain 'D' and resid 167 through 176
    Processing helix  chain 'D' and resid 186 through 190
      removed outlier: 4.073A  pdb=" N   LEU D 190 " --> pdb=" O   TRP D 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 46
      removed outlier: 4.050A  pdb=" N   SER C  45 " --> pdb=" O   GLU C  42 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 151
    Processing helix  chain 'C' and resid 167 through 176
    Processing helix  chain 'C' and resid 186 through 190
      removed outlier: 4.004A  pdb=" N   LEU C 190 " --> pdb=" O   TRP C 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 46
      removed outlier: 4.040A  pdb=" N   SER B  45 " --> pdb=" O   GLU B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 151
    Processing helix  chain 'B' and resid 167 through 176
    Processing helix  chain 'B' and resid 186 through 190
      removed outlier: 3.987A  pdb=" N   LEU B 190 " --> pdb=" O   TRP B 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 46
      removed outlier: 4.248A  pdb=" N   SER A  45 " --> pdb=" O   GLU A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 151
    Processing helix  chain 'A' and resid 167 through 176
    Processing helix  chain 'A' and resid 186 through 190
      removed outlier: 3.856A  pdb=" N   LEU A 190 " --> pdb=" O   TRP A 187 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 114 through 115
    Processing sheet with id=AA2, first strand: chain 'E' and resid 114 through 115
      removed outlier: 3.513A  pdb=" N   ILE E 106 " --> pdb=" O   GLU E 101 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   THR E  34 " --> pdb=" O   MET E 161 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   MET E 161 " --> pdb=" O   THR E  34 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   CYS E  36 " --> pdb=" O   VAL E 159 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   VAL E 159 " --> pdb=" O   CYS E  36 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   ASN E 158 " --> pdb=" O   LYS E   7 " (cutoff:3.500A)
      removed outlier: 10.009A  pdb=" N   LYS E   7 " --> pdb=" O   ASN E 158 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 80 through 85
      removed outlier: 3.507A  pdb=" N   TYR E  73 " --> pdb=" O   PHE E  84 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   TRP E  67 " --> pdb=" O   SER E  50 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   SER E  50 " --> pdb=" O   TRP E  67 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ILE E 133 " --> pdb=" O   LEU E  22 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 114 through 115
    Processing sheet with id=AA5, first strand: chain 'D' and resid 114 through 115
      removed outlier: 3.571A  pdb=" N   ILE D 106 " --> pdb=" O   GLU D 101 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   THR D  34 " --> pdb=" O   MET D 161 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   MET D 161 " --> pdb=" O   THR D  34 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   CYS D  36 " --> pdb=" O   VAL D 159 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   VAL D 159 " --> pdb=" O   CYS D  36 " (cutoff:3.500A)
      removed outlier: 4.869A  pdb=" N   ASN D 158 " --> pdb=" O   LYS D   7 " (cutoff:3.500A)
      removed outlier: 10.047A  pdb=" N   LYS D   7 " --> pdb=" O   ASN D 158 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 80 through 85
      removed outlier: 6.183A  pdb=" N   ASN D  61 " --> pdb=" O   THR D  56 " (cutoff:3.500A)
      removed outlier: 7.410A  pdb=" N   THR D  56 " --> pdb=" O   ASN D  61 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   TRP D  67 " --> pdb=" O   SER D  50 " (cutoff:3.500A)
      removed outlier: 5.596A  pdb=" N   SER D  50 " --> pdb=" O   TRP D  67 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ILE D 133 " --> pdb=" O   LEU D  22 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 114 through 115
    Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 115
      removed outlier: 3.525A  pdb=" N   ILE C 106 " --> pdb=" O   GLU C 101 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   THR C  34 " --> pdb=" O   MET C 161 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   MET C 161 " --> pdb=" O   THR C  34 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   CYS C  36 " --> pdb=" O   VAL C 159 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   VAL C 159 " --> pdb=" O   CYS C  36 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   ASN C 158 " --> pdb=" O   LYS C   7 " (cutoff:3.500A)
      removed outlier: 10.073A  pdb=" N   LYS C   7 " --> pdb=" O   ASN C 158 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 85
      removed outlier: 3.631A  pdb=" N   TYR C  73 " --> pdb=" O   PHE C  84 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ASN C  61 " --> pdb=" O   THR C  56 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   THR C  56 " --> pdb=" O   ASN C  61 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   TRP C  67 " --> pdb=" O   SER C  50 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   SER C  50 " --> pdb=" O   TRP C  67 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ILE C 133 " --> pdb=" O   LEU C  22 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 114 through 115
    Processing sheet with id=AB2, first strand: chain 'B' and resid 114 through 115
      removed outlier: 6.539A  pdb=" N   THR B  34 " --> pdb=" O   MET B 161 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   MET B 161 " --> pdb=" O   THR B  34 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   CYS B  36 " --> pdb=" O   VAL B 159 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   VAL B 159 " --> pdb=" O   CYS B  36 " (cutoff:3.500A)
      removed outlier: 4.870A  pdb=" N   ASN B 158 " --> pdb=" O   LYS B   7 " (cutoff:3.500A)
      removed outlier: 9.995A  pdb=" N   LYS B   7 " --> pdb=" O   ASN B 158 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 80 through 85
      removed outlier: 3.520A  pdb=" N   TYR B  73 " --> pdb=" O   PHE B  84 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   ASN B  61 " --> pdb=" O   THR B  56 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   THR B  56 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   TRP B  67 " --> pdb=" O   SER B  50 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   SER B  50 " --> pdb=" O   TRP B  67 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ILE B 133 " --> pdb=" O   LEU B  22 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 114 through 115
    Processing sheet with id=AB5, first strand: chain 'A' and resid 114 through 115
      removed outlier: 3.551A  pdb=" N   ILE A 106 " --> pdb=" O   GLU A 101 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   THR A  34 " --> pdb=" O   MET A 161 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   MET A 161 " --> pdb=" O   THR A  34 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   CYS A  36 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   VAL A 159 " --> pdb=" O   CYS A  36 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   ASN A 158 " --> pdb=" O   LYS A   7 " (cutoff:3.500A)
      removed outlier: 10.127A  pdb=" N   LYS A   7 " --> pdb=" O   ASN A 158 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 80 through 85
      removed outlier: 6.176A  pdb=" N   ASN A  61 " --> pdb=" O   THR A  56 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   THR A  56 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   TRP A  67 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
      removed outlier: 5.785A  pdb=" N   SER A  50 " --> pdb=" O   TRP A  67 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ILE A 133 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)

    338 hydrogen bonds defined for protein.
    810 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.05

  Time building geometry restraints manager: 1.78 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 7970
        1.03 -     1.22: 0
        1.22 -     1.41: 3613
        1.41 -     1.61: 4747
        1.61 -     1.80: 30
  Bond restraints: 16360
  Sorted by residual:
  bond pdb=" CB  THR D  98 "
       pdb=" CG2 THR D  98 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.87e+00
  bond pdb=" CB  VAL D  94 "
       pdb=" CG1 VAL D  94 "
    ideal  model  delta    sigma   weight residual
    1.521  1.470  0.051 3.30e-02 9.18e+02 2.36e+00
  bond pdb=" CB  VAL E  94 "
       pdb=" CG1 VAL E  94 "
    ideal  model  delta    sigma   weight residual
    1.521  1.471  0.050 3.30e-02 9.18e+02 2.27e+00
  bond pdb=" CB  THR B  76 "
       pdb=" CG2 THR B  76 "
    ideal  model  delta    sigma   weight residual
    1.521  1.472  0.049 3.30e-02 9.18e+02 2.16e+00
  bond pdb=" CB  VAL C  94 "
       pdb=" CG1 VAL C  94 "
    ideal  model  delta    sigma   weight residual
    1.521  1.475  0.046 3.30e-02 9.18e+02 1.98e+00
  ... (remaining 16355 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.63: 29479
        5.63 -    11.27: 25
       11.27 -    16.90: 1
       16.90 -    22.53: 0
       22.53 -    28.17: 30
  Bond angle restraints: 29535
  Sorted by residual:
  angle pdb=" CG1 VAL A  77 "
        pdb=" CB  VAL A  77 "
        pdb=" HB  VAL A  77 "
      ideal   model   delta    sigma   weight residual
     108.00   79.83   28.17 3.00e+00 1.11e-01 8.81e+01
  angle pdb=" CG2 VAL A  77 "
        pdb=" CB  VAL A  77 "
        pdb=" HB  VAL A  77 "
      ideal   model   delta    sigma   weight residual
     108.00   80.17   27.83 3.00e+00 1.11e-01 8.61e+01
  angle pdb=" CG2 ILE A  82 "
        pdb=" CB  ILE A  82 "
        pdb=" HB  ILE A  82 "
      ideal   model   delta    sigma   weight residual
     109.00   81.65   27.35 3.00e+00 1.11e-01 8.31e+01
  angle pdb=" CG1 VAL E  77 "
        pdb=" CB  VAL E  77 "
        pdb=" HB  VAL E  77 "
      ideal   model   delta    sigma   weight residual
     108.00   80.70   27.30 3.00e+00 1.11e-01 8.28e+01
  angle pdb=" CG2 THR A 173 "
        pdb=" CB  THR A 173 "
        pdb=" HB  THR A 173 "
      ideal   model   delta    sigma   weight residual
     108.00   80.75   27.25 3.00e+00 1.11e-01 8.25e+01
  ... (remaining 29530 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 7037
       17.99 -    35.98: 453
       35.98 -    53.97: 179
       53.97 -    71.96: 99
       71.96 -    89.95: 7
  Dihedral angle restraints: 7775
    sinusoidal: 4100
      harmonic: 3675
  Sorted by residual:
  dihedral pdb=" CA  GLU C  62 "
           pdb=" C   GLU C  62 "
           pdb=" N   ILE C  63 "
           pdb=" CA  ILE C  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.00   27.00     0      5.00e+00 4.00e-02 2.92e+01
  dihedral pdb=" CA  GLU B  62 "
           pdb=" C   GLU B  62 "
           pdb=" N   ILE B  63 "
           pdb=" CA  ILE B  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.26   26.74     0      5.00e+00 4.00e-02 2.86e+01
  dihedral pdb=" CA  GLU E  62 "
           pdb=" C   GLU E  62 "
           pdb=" N   ILE E  63 "
           pdb=" CA  ILE E  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.43   26.57     0      5.00e+00 4.00e-02 2.82e+01
  ... (remaining 7772 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.349: 1225
       0.349 -    0.698: 0
       0.698 -    1.047: 0
       1.047 -    1.395: 5
       1.395 -    1.744: 5
  Chirality restraints: 1235
  Sorted by residual:
  chirality pdb=" CG  LEU D  83 "
            pdb=" CB  LEU D  83 "
            pdb=" CD1 LEU D  83 "
            pdb=" CD2 LEU D  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.85   -1.74 2.00e-01 2.50e+01 7.61e+01
  chirality pdb=" CG  LEU C  83 "
            pdb=" CB  LEU C  83 "
            pdb=" CD1 LEU C  83 "
            pdb=" CD2 LEU C  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.90   -1.69 2.00e-01 2.50e+01 7.16e+01
  chirality pdb=" CB  VAL B  89 "
            pdb=" CA  VAL B  89 "
            pdb=" CG1 VAL B  89 "
            pdb=" CG2 VAL B  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.08   -1.55 2.00e-01 2.50e+01 5.98e+01
  ... (remaining 1232 not shown)

  Planarity restraints: 2420
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN E 183 "   -0.032 2.00e-02 2.50e+03   4.02e-02 2.42e+01
        pdb=" CG  ASN E 183 "    0.025 2.00e-02 2.50e+03
        pdb=" OD1 ASN E 183 "    0.002 2.00e-02 2.50e+03
        pdb=" ND2 ASN E 183 "    0.065 2.00e-02 2.50e+03
        pdb="HD21 ASN E 183 "    0.001 2.00e-02 2.50e+03
        pdb="HD22 ASN E 183 "   -0.061 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  86 "    0.073 5.00e-02 4.00e+02   1.10e-01 1.93e+01
        pdb=" N   PRO B  87 "   -0.190 5.00e-02 4.00e+02
        pdb=" CA  PRO B  87 "    0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO B  87 "    0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D 183 "    0.028 2.00e-02 2.50e+03   3.49e-02 1.82e+01
        pdb=" CG  ASN D 183 "   -0.022 2.00e-02 2.50e+03
        pdb=" OD1 ASN D 183 "   -0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN D 183 "   -0.057 2.00e-02 2.50e+03
        pdb="HD21 ASN D 183 "   -0.001 2.00e-02 2.50e+03
        pdb="HD22 ASN D 183 "    0.053 2.00e-02 2.50e+03
  ... (remaining 2417 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.14: 625
        2.14 -     2.76: 30525
        2.76 -     3.37: 45052
        3.37 -     3.99: 63257
        3.99 -     4.60: 96940
  Nonbonded interactions: 236399
  Sorted by model distance:
  nonbonded pdb=" HG1 THR B  41 "
            pdb=" O   VAL B 153 "
     model   vdw
     1.531 2.450
  nonbonded pdb=" HG1 THR C  41 "
            pdb=" O   VAL C 153 "
     model   vdw
     1.541 2.450
  nonbonded pdb=" OE1 GLU A 101 "
            pdb=" HG  SER A 104 "
     model   vdw
     1.545 2.450
  nonbonded pdb="HH22 ARG E  47 "
            pdb=" O   SER E 151 "
     model   vdw
     1.556 2.450
  nonbonded pdb=" HG1 THR A  41 "
            pdb=" O   VAL A 153 "
     model   vdw
     1.557 2.450
  ... (remaining 236394 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.300
  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:             0.080
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.400
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.020
  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:1.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
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   0.056   8395  Z= 0.330
  Angle     :  0.904  14.543  11415  Z= 0.500
  Chirality :  0.142   1.744   1235
  Planarity :  0.006   0.110   1450
  Dihedral  : 13.281  89.946   2990
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.10 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.24), residues: 1020
  helix: -1.59 (0.49), residues: 55
  sheet: -0.19 (0.23), residues: 425
  loop : -0.86 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.063   0.012   ARG E   6 
 TYR   0.025   0.005   TYR D  54 
 PHE   0.018   0.003   PHE D 109 
 TRP   0.028   0.006   TRP A  67 
 HIS   0.007   0.003   HIS D  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00793 ( 8390)
  covalent geometry    : angle       0.90323 (11405)
  SS BOND              : bond        0.00365 (    5)
  SS BOND              : angle       1.79525 (   10)
  hydrogen bonds       : bond        0.19116 (  328)
  hydrogen bonds       : angle       7.68697 (  810)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.368 
Fit side-chains
REVERT: D   60 ASP cc_start: 0.7358 (p0) cc_final: 0.7086 (p0)
REVERT: C   81 GLU cc_start: 0.7682 (tt0) cc_final: 0.7373 (tt0)
REVERT: C  163 ASP cc_start: 0.7947 (p0) cc_final: 0.7715 (p0)
REVERT: A   60 ASP cc_start: 0.7556 (p0) cc_final: 0.7051 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.3100
  time to fit residues: 36.0750
Evaluate side-chains
  76 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.0070
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
E   1 GLN
C  95 HIS
B  95 HIS
A  95 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.084231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.069262 restraints weight = 37771.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.2579 rms_B_bonded: 2.49
r_work: 0.2461 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2316 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8395  Z= 0.143
  Angle     :  0.720  15.156  11415  Z= 0.377
  Chirality :  0.141   1.705   1235
  Planarity :  0.004   0.059   1450
  Dihedral  :  6.129  21.536   1100
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  2.11 %
    Favored  : 97.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.25), residues: 1020
  helix:  1.41 (0.59), residues: 55
  sheet:  0.29 (0.24), residues: 415
  loop : -0.62 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 188 
 TYR   0.021   0.001   TYR C  54 
 PHE   0.016   0.001   PHE E  66 
 TRP   0.009   0.001   TRP D 162 
 HIS   0.004   0.002   HIS D  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8390)
  covalent geometry    : angle       0.71961 (11405)
  SS BOND              : bond        0.00087 (    5)
  SS BOND              : angle       0.95440 (   10)
  hydrogen bonds       : bond        0.04994 (  328)
  hydrogen bonds       : angle       6.09987 (  810)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.395 
Fit side-chains
REVERT: D   60 ASP cc_start: 0.7453 (p0) cc_final: 0.7063 (p0)
REVERT: C  163 ASP cc_start: 0.8182 (p0) cc_final: 0.7941 (p0)
REVERT: B  101 GLU cc_start: 0.7928 (tt0) cc_final: 0.7706 (tt0)
REVERT: A   28 LYS cc_start: 0.7197 (ttpt) cc_final: 0.6877 (mptt)
REVERT: A   60 ASP cc_start: 0.7499 (p0) cc_final: 0.6956 (p0)
REVERT: A  188 ARG cc_start: 0.8191 (mtt90) cc_final: 0.7963 (mtp85)
  outliers start: 3
  outliers final: 3
  residues processed: 102
  average time/residue: 0.3148
  time to fit residues: 40.0054
Evaluate side-chains
  82 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  134 ILE
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain A residue  134 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
E  38 HIS
E  95 HIS
D  59 GLN
D  95 HIS
A  59 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.082356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.067157 restraints weight = 38283.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.2566 rms_B_bonded: 2.51
r_work: 0.2447 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2302 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8395  Z= 0.173
  Angle     :  0.691  15.706  11415  Z= 0.362
  Chirality :  0.141   1.702   1235
  Planarity :  0.004   0.040   1450
  Dihedral  :  5.602  22.023   1100
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  4.22 %
    Favored  : 95.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.25), residues: 1020
  helix:  1.55 (0.56), residues: 55
  sheet:  0.12 (0.24), residues: 415
  loop : -0.60 (0.27), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 188 
 TYR   0.021   0.001   TYR C  54 
 PHE   0.012   0.001   PHE A 109 
 TRP   0.010   0.001   TRP D 162 
 HIS   0.004   0.002   HIS D  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 8390)
  covalent geometry    : angle       0.69120 (11405)
  SS BOND              : bond        0.00124 (    5)
  SS BOND              : angle       0.71508 (   10)
  hydrogen bonds       : bond        0.04684 (  328)
  hydrogen bonds       : angle       5.76800 (  810)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.437 
Fit side-chains
REVERT: E  147 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6889 (mt-10)
REVERT: D   81 GLU cc_start: 0.8340 (tt0) cc_final: 0.7903 (tt0)
REVERT: C   59 GLN cc_start: 0.8558 (tp40) cc_final: 0.8346 (tp40)
REVERT: A   60 ASP cc_start: 0.7621 (p0) cc_final: 0.7170 (p0)
  outliers start: 3
  outliers final: 3
  residues processed: 86
  average time/residue: 0.3195
  time to fit residues: 34.1519
Evaluate side-chains
  80 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  134 ILE
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain A residue  134 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 78 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.2823 r_free = 0.2823 target = 0.078847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2548 r_free = 0.2548 target = 0.063527 restraints weight = 38940.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.2557 rms_B_bonded: 2.54
r_work: 0.2439 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2293 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8395  Z= 0.165
  Angle     :  0.677  15.567  11415  Z= 0.353
  Chirality :  0.141   1.699   1235
  Planarity :  0.004   0.061   1450
  Dihedral  :  5.392  22.050   1100
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  5.22 %
    Favored  : 94.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.26), residues: 1020
  helix:  1.54 (0.57), residues: 55
  sheet:  0.01 (0.24), residues: 415
  loop : -0.65 (0.27), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 188 
 TYR   0.019   0.001   TYR E  54 
 PHE   0.010   0.001   PHE A 109 
 TRP   0.010   0.001   TRP D 162 
 HIS   0.007   0.002   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 8390)
  covalent geometry    : angle       0.67693 (11405)
  SS BOND              : bond        0.00158 (    5)
  SS BOND              : angle       0.49423 (   10)
  hydrogen bonds       : bond        0.04210 (  328)
  hydrogen bonds       : angle       5.61583 (  810)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.428 
Fit side-chains
REVERT: E  147 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7033 (mt-10)
REVERT: C   59 GLN cc_start: 0.8543 (tp40) cc_final: 0.8331 (tp40)
REVERT: A   59 GLN cc_start: 0.8541 (tp40) cc_final: 0.8333 (tp-100)
REVERT: A   60 ASP cc_start: 0.7640 (p0) cc_final: 0.7179 (p0)
REVERT: A   76 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8868 (m)
REVERT: A  188 ARG cc_start: 0.8353 (mtt90) cc_final: 0.8060 (mtp85)
  outliers start: 4
  outliers final: 3
  residues processed: 83
  average time/residue: 0.3303
  time to fit residues: 34.1151
Evaluate side-chains
  82 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  134 ILE
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  134 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 15 optimal weight:    0.0980
   chunk 68 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 81 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
B  59 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.085158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.069651 restraints weight = 37748.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.2587 rms_B_bonded: 2.55
r_work: 0.2468 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2322 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8395  Z= 0.132
  Angle     :  0.654  15.452  11415  Z= 0.339
  Chirality :  0.141   1.679   1235
  Planarity :  0.004   0.045   1450
  Dihedral  :  5.073  19.842   1100
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  5.56 %
    Favored  : 93.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.26), residues: 1020
  helix:  1.70 (0.58), residues: 55
  sheet:  0.02 (0.24), residues: 415
  loop : -0.63 (0.27), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 188 
 TYR   0.016   0.001   TYR E  54 
 PHE   0.009   0.001   PHE D  39 
 TRP   0.010   0.001   TRP D 162 
 HIS   0.005   0.001   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8390)
  covalent geometry    : angle       0.65437 (11405)
  SS BOND              : bond        0.00142 (    5)
  SS BOND              : angle       0.42801 (   10)
  hydrogen bonds       : bond        0.03837 (  328)
  hydrogen bonds       : angle       5.49838 (  810)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.445 
Fit side-chains
REVERT: E  147 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7074 (mt-10)
REVERT: C   59 GLN cc_start: 0.8572 (tp40) cc_final: 0.8348 (tp-100)
REVERT: B   59 GLN cc_start: 0.8537 (tp40) cc_final: 0.8285 (tp40)
REVERT: A   59 GLN cc_start: 0.8616 (tp40) cc_final: 0.8405 (tp-100)
REVERT: A   60 ASP cc_start: 0.7661 (p0) cc_final: 0.7176 (p0)
  outliers start: 6
  outliers final: 2
  residues processed: 91
  average time/residue: 0.3149
  time to fit residues: 35.9103
Evaluate side-chains
  79 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  134 ILE
Chi-restraints excluded: chain A residue  134 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0980
   chunk 15 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.2824 r_free = 0.2824 target = 0.078919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2549 r_free = 0.2549 target = 0.063587 restraints weight = 38594.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.2601 rms_B_bonded: 2.53
r_work: 0.2481 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2333 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8395  Z= 0.140
  Angle     :  0.652  15.412  11415  Z= 0.337
  Chirality :  0.141   1.679   1235
  Planarity :  0.004   0.067   1450
  Dihedral  :  5.023  19.674   1100
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  6.33 %
    Favored  : 93.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.26), residues: 1020
  helix:  1.60 (0.58), residues: 55
  sheet:  0.03 (0.25), residues: 415
  loop : -0.63 (0.27), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 188 
 TYR   0.015   0.001   TYR E  54 
 PHE   0.010   0.001   PHE D  39 
 TRP   0.010   0.001   TRP D 162 
 HIS   0.005   0.002   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 8390)
  covalent geometry    : angle       0.65221 (11405)
  SS BOND              : bond        0.00162 (    5)
  SS BOND              : angle       0.38257 (   10)
  hydrogen bonds       : bond        0.03785 (  328)
  hydrogen bonds       : angle       5.43555 (  810)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.460 
Fit side-chains
REVERT: E  147 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7129 (mt-10)
REVERT: D   16 ASP cc_start: 0.8123 (m-30) cc_final: 0.7700 (m-30)
REVERT: C   59 GLN cc_start: 0.8595 (tp40) cc_final: 0.8387 (tp-100)
REVERT: A   60 ASP cc_start: 0.7623 (p0) cc_final: 0.7178 (p0)
  outliers start: 3
  outliers final: 2
  residues processed: 82
  average time/residue: 0.3145
  time to fit residues: 32.4640
Evaluate side-chains
  76 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  134 ILE
Chi-restraints excluded: chain A residue  134 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0870
   chunk 93 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 68 optimal weight:    0.0170
   chunk 90 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.4996

-------------------------------------------------------------------------------
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 = 0.2863 r_free = 0.2863 target = 0.081142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2584 r_free = 0.2584 target = 0.065350 restraints weight = 38300.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.2574 rms_B_bonded: 2.65
r_work: 0.2454 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2309 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8395  Z= 0.111
  Angle     :  0.636  15.411  11415  Z= 0.327
  Chirality :  0.140   1.674   1235
  Planarity :  0.003   0.057   1450
  Dihedral  :  4.788  17.475   1100
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  6.56 %
    Favored  : 93.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.26), residues: 1020
  helix:  1.79 (0.59), residues: 55
  sheet:  0.09 (0.25), residues: 415
  loop : -0.56 (0.28), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 188 
 TYR   0.012   0.001   TYR E  54 
 PHE   0.011   0.001   PHE D  39 
 TRP   0.010   0.001   TRP D 162 
 HIS   0.005   0.001   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 8390)
  covalent geometry    : angle       0.63589 (11405)
  SS BOND              : bond        0.00150 (    5)
  SS BOND              : angle       0.36564 (   10)
  hydrogen bonds       : bond        0.03485 (  328)
  hydrogen bonds       : angle       5.32328 (  810)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.467 
Fit side-chains
REVERT: E  147 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7041 (mt-10)
REVERT: D   16 ASP cc_start: 0.8115 (m-30) cc_final: 0.7681 (m-30)
REVERT: C   59 GLN cc_start: 0.8553 (tp40) cc_final: 0.8328 (tp-100)
REVERT: C   81 GLU cc_start: 0.8175 (tt0) cc_final: 0.7842 (tt0)
REVERT: A   60 ASP cc_start: 0.7636 (p0) cc_final: 0.7140 (p0)
REVERT: A  112 ASP cc_start: 0.8946 (m-30) cc_final: 0.8703 (m-30)
  outliers start: 1
  outliers final: 1
  residues processed: 89
  average time/residue: 0.2931
  time to fit residues: 33.0002
Evaluate side-chains
  82 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.2830 r_free = 0.2830 target = 0.079245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2553 r_free = 0.2553 target = 0.063726 restraints weight = 39034.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.2565 rms_B_bonded: 2.56
r_work: 0.2447 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2302 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8395  Z= 0.155
  Angle     :  0.651  15.624  11415  Z= 0.337
  Chirality :  0.141   1.681   1235
  Planarity :  0.004   0.052   1450
  Dihedral  :  4.906  19.001   1100
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 1.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  6.78 %
    Favored  : 93.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.41 (0.26), residues: 1020
  helix:  1.55 (0.59), residues: 55
  sheet:  0.01 (0.25), residues: 415
  loop : -0.63 (0.28), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 188 
 TYR   0.015   0.001   TYR E  54 
 PHE   0.010   0.001   PHE D  39 
 TRP   0.010   0.001   TRP D 162 
 HIS   0.005   0.002   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 8390)
  covalent geometry    : angle       0.65141 (11405)
  SS BOND              : bond        0.00165 (    5)
  SS BOND              : angle       0.33634 (   10)
  hydrogen bonds       : bond        0.03747 (  328)
  hydrogen bonds       : angle       5.35671 (  810)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.436 
Fit side-chains
REVERT: E  147 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7030 (mt-10)
REVERT: D   16 ASP cc_start: 0.8122 (m-30) cc_final: 0.7746 (m-30)
REVERT: C   59 GLN cc_start: 0.8565 (tp40) cc_final: 0.8328 (tp-100)
REVERT: C   81 GLU cc_start: 0.8175 (tt0) cc_final: 0.7814 (tt0)
REVERT: A   60 ASP cc_start: 0.7550 (p0) cc_final: 0.7065 (p0)
REVERT: A  112 ASP cc_start: 0.8943 (m-30) cc_final: 0.8736 (m-30)
REVERT: A  188 ARG cc_start: 0.8309 (mtt90) cc_final: 0.8053 (mtp85)
  outliers start: 1
  outliers final: 1
  residues processed: 79
  average time/residue: 0.3342
  time to fit residues: 32.6571
Evaluate side-chains
  79 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 96 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 90 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   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 = 0.2929 r_free = 0.2929 target = 0.084998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.069228 restraints weight = 37445.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.2586 rms_B_bonded: 2.56
r_work: 0.2468 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2320 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.2608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8395  Z= 0.149
  Angle     :  0.648  15.492  11415  Z= 0.335
  Chirality :  0.141   1.668   1235
  Planarity :  0.003   0.050   1450
  Dihedral  :  4.919  19.977   1100
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  6.89 %
    Favored  : 92.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.26), residues: 1020
  helix:  1.55 (0.59), residues: 55
  sheet: -0.01 (0.25), residues: 415
  loop : -0.70 (0.27), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 188 
 TYR   0.014   0.001   TYR E  54 
 PHE   0.010   0.001   PHE D  39 
 TRP   0.010   0.001   TRP D 162 
 HIS   0.005   0.002   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 8390)
  covalent geometry    : angle       0.64781 (11405)
  SS BOND              : bond        0.00151 (    5)
  SS BOND              : angle       0.31318 (   10)
  hydrogen bonds       : bond        0.03703 (  328)
  hydrogen bonds       : angle       5.36173 (  810)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.454 
Fit side-chains
REVERT: E  147 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7080 (mt-10)
REVERT: D   16 ASP cc_start: 0.8121 (m-30) cc_final: 0.7753 (m-30)
REVERT: C   59 GLN cc_start: 0.8578 (tp40) cc_final: 0.8361 (tp-100)
REVERT: C   81 GLU cc_start: 0.8139 (tt0) cc_final: 0.7783 (tt0)
REVERT: A   60 ASP cc_start: 0.7624 (p0) cc_final: 0.7146 (p0)
REVERT: A  112 ASP cc_start: 0.8970 (m-30) cc_final: 0.8762 (m-30)
REVERT: A  188 ARG cc_start: 0.8346 (mtt90) cc_final: 0.8085 (mtp85)
  outliers start: 2
  outliers final: 2
  residues processed: 82
  average time/residue: 0.3223
  time to fit residues: 32.6605
Evaluate side-chains
  83 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 81
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  134 ILE
Chi-restraints excluded: chain A residue  134 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 99 optimal weight:    0.4980
   chunk 40 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   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 = 0.2831 r_free = 0.2831 target = 0.079298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2553 r_free = 0.2553 target = 0.063752 restraints weight = 38608.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.2559 rms_B_bonded: 2.54
r_work: 0.2441 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2295 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8395  Z= 0.154
  Angle     :  0.650  15.549  11415  Z= 0.336
  Chirality :  0.141   1.676   1235
  Planarity :  0.004   0.049   1450
  Dihedral  :  4.924  20.222   1100
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  6.89 %
    Favored  : 92.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.26), residues: 1020
  helix:  1.52 (0.59), residues: 55
  sheet: -0.01 (0.25), residues: 415
  loop : -0.74 (0.27), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 188 
 TYR   0.015   0.001   TYR E  54 
 PHE   0.010   0.001   PHE D  39 
 TRP   0.010   0.001   TRP D 162 
 HIS   0.005   0.002   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 8390)
  covalent geometry    : angle       0.64998 (11405)
  SS BOND              : bond        0.00157 (    5)
  SS BOND              : angle       0.32002 (   10)
  hydrogen bonds       : bond        0.03745 (  328)
  hydrogen bonds       : angle       5.37545 (  810)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.457 
Fit side-chains
REVERT: E  147 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7030 (mt-10)
REVERT: D   16 ASP cc_start: 0.8108 (m-30) cc_final: 0.7729 (m-30)
REVERT: C   59 GLN cc_start: 0.8544 (tp40) cc_final: 0.8310 (tp-100)
REVERT: C   81 GLU cc_start: 0.8170 (tt0) cc_final: 0.7792 (tt0)
REVERT: A   60 ASP cc_start: 0.7540 (p0) cc_final: 0.7082 (p0)
REVERT: A  101 GLU cc_start: 0.8290 (tt0) cc_final: 0.8032 (tt0)
REVERT: A  112 ASP cc_start: 0.8945 (m-30) cc_final: 0.8734 (m-30)
REVERT: A  188 ARG cc_start: 0.8316 (mtt90) cc_final: 0.8042 (mtp85)
  outliers start: 2
  outliers final: 2
  residues processed: 82
  average time/residue: 0.3379
  time to fit residues: 34.3233
Evaluate side-chains
  82 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  134 ILE
Chi-restraints excluded: chain A residue  134 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 28 optimal weight:    0.3980
   chunk 79 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 92 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 86 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 = 0.2822 r_free = 0.2822 target = 0.078636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2540 r_free = 0.2540 target = 0.063014 restraints weight = 38652.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.2573 rms_B_bonded: 2.58
r_work: 0.2453 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2306 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8395  Z= 0.153
  Angle     :  0.648  15.558  11415  Z= 0.335
  Chirality :  0.141   1.672   1235
  Planarity :  0.004   0.048   1450
  Dihedral  :  4.928  20.377   1100
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  7.11 %
    Favored  : 92.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.26), residues: 1020
  helix:  1.51 (0.59), residues: 55
  sheet: -0.02 (0.25), residues: 415
  loop : -0.79 (0.27), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 188 
 TYR   0.014   0.001   TYR E  54 
 PHE   0.010   0.001   PHE D  39 
 TRP   0.010   0.001   TRP E 162 
 HIS   0.005   0.002   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 8390)
  covalent geometry    : angle       0.64849 (11405)
  SS BOND              : bond        0.00153 (    5)
  SS BOND              : angle       0.31656 (   10)
  hydrogen bonds       : bond        0.03725 (  328)
  hydrogen bonds       : angle       5.36745 (  810)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3883.11 seconds
wall clock time: 66 minutes 30.44 seconds (3990.44 seconds total)