Starting phenix.real_space_refine
on Wed Mar  4 20:09:19 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pkg_13471/03_2026/7pkg_13471.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pkg_13471/03_2026/7pkg_13471.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pkg_13471/03_2026/7pkg_13471.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pkg_13471/03_2026/7pkg_13471.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pkg_13471/03_2026/7pkg_13471.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pkg_13471/03_2026/7pkg_13471.map"
  }
  resolution = 3.3
  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    7980      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 75 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: 16155
  Number of models: 1
  Model: ""
    Number of chains: 15
    Chain: "E"
      Number of atoms: 3226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3226
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "D"
      Number of atoms: 3226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3226
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "C"
      Number of atoms: 3226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3226
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "B"
      Number of atoms: 3226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3226
          Classifications: {'peptide': 206}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 194}
    Chain: "A"
      Number of atoms: 3226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3226
          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: 3.31, per 1000 atoms: 0.20
  Number of scatterers: 16155
  At special positions: 0
  Unit cell: (114.532, 112.86, 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    7980      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=2.03
    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=2.03
    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: 1.36
  Conformation dependent library (CDL) restraints added in 439.0 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 16 sheets defined
      12.4% alpha, 38.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'E' and resid 42 through 46
      removed outlier: 3.852A  pdb=" N   SER E  45 " --> pdb=" O   GLU E  42 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 148 through 151
    Processing helix  chain 'E' and resid 167 through 176
    Processing helix  chain 'E' and resid 186 through 190
      removed outlier: 3.990A  pdb=" N   LEU E 190 " --> pdb=" O   TRP E 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 42 through 46
      removed outlier: 3.989A  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 177
    Processing helix  chain 'D' and resid 186 through 190
      removed outlier: 4.095A  pdb=" N   LEU D 190 " --> pdb=" O   TRP D 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 46
      removed outlier: 3.791A  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 177
    Processing helix  chain 'C' and resid 186 through 190
      removed outlier: 4.070A  pdb=" N   LEU C 190 " --> pdb=" O   TRP C 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 46
      removed outlier: 3.824A  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 177
    Processing helix  chain 'B' and resid 186 through 190
      removed outlier: 4.009A  pdb=" N   LEU B 190 " --> pdb=" O   TRP B 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 46
      removed outlier: 3.773A  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 177
    Processing helix  chain 'A' and resid 186 through 190
      removed outlier: 3.958A  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: 3.787A  pdb=" N   ILE E 106 " --> pdb=" O   GLU E 101 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   THR E  34 " --> pdb=" O   MET E 161 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   MET E 161 " --> pdb=" O   THR E  34 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   CYS E  36 " --> pdb=" O   VAL E 159 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   VAL E 159 " --> pdb=" O   CYS E  36 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   ASN E 158 " --> pdb=" O   LYS E   7 " (cutoff:3.500A)
      removed outlier: 10.193A  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: 3.739A  pdb=" N   TYR E  73 " --> pdb=" O   PHE E  84 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   ASN E  61 " --> pdb=" O   THR E  56 " (cutoff:3.500A)
      removed outlier: 7.129A  pdb=" N   THR E  56 " --> pdb=" O   ASN E  61 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   TRP E  67 " --> pdb=" O   SER E  50 " (cutoff:3.500A)
      removed outlier: 5.542A  pdb=" N   SER E  50 " --> pdb=" O   TRP E  67 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ILE E 133 " --> pdb=" O   LEU E  22 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 139 through 141
      removed outlier: 7.066A  pdb=" N   GLN E 139 " --> pdb=" O   PHE E 146 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   PHE E 146 " --> pdb=" O   GLN E 139 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 114 through 115
    Processing sheet with id=AA6, first strand: chain 'D' and resid 114 through 115
      removed outlier: 3.749A  pdb=" N   ILE D 106 " --> pdb=" O   GLU D 101 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   THR D  34 " --> pdb=" O   MET D 161 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   MET D 161 " --> pdb=" O   THR D  34 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   CYS D  36 " --> pdb=" O   VAL D 159 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   VAL D 159 " --> pdb=" O   CYS D  36 " (cutoff:3.500A)
      removed outlier: 4.916A  pdb=" N   ASN D 158 " --> pdb=" O   LYS D   7 " (cutoff:3.500A)
      removed outlier: 10.173A  pdb=" N   LYS D   7 " --> pdb=" O   ASN D 158 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 80 through 85
      removed outlier: 3.639A  pdb=" N   TYR D  73 " --> pdb=" O   PHE D  84 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   ASN D  61 " --> pdb=" O   THR D  56 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   THR D  56 " --> pdb=" O   ASN D  61 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   TRP D  67 " --> pdb=" O   SER D  50 " (cutoff:3.500A)
      removed outlier: 5.581A  pdb=" N   SER D  50 " --> pdb=" O   TRP D  67 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ILE D 133 " --> pdb=" O   LEU D  22 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 115
    Processing sheet with id=AA9, first strand: chain 'C' and resid 114 through 115
      removed outlier: 3.915A  pdb=" N   ILE C 106 " --> pdb=" O   GLU C 101 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLU C 101 " --> pdb=" O   ILE C 106 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   THR C  34 " --> pdb=" O   MET C 161 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   MET C 161 " --> pdb=" O   THR C  34 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   CYS C  36 " --> pdb=" O   VAL C 159 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   VAL C 159 " --> pdb=" O   CYS C  36 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   ASN C 158 " --> pdb=" O   LYS C   7 " (cutoff:3.500A)
      removed outlier: 10.258A  pdb=" N   LYS C   7 " --> pdb=" O   ASN C 158 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 80 through 85
      removed outlier: 3.769A  pdb=" N   TYR C  73 " --> pdb=" O   PHE C  84 " (cutoff:3.500A)
      removed outlier: 5.875A  pdb=" N   ASN C  61 " --> pdb=" O   THR C  56 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   THR C  56 " --> pdb=" O   ASN C  61 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   TRP C  67 " --> pdb=" O   SER C  50 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   SER C  50 " --> pdb=" O   TRP C  67 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ILE C 133 " --> pdb=" O   LEU C  22 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 114 through 115
    Processing sheet with id=AB3, first strand: chain 'B' and resid 114 through 115
      removed outlier: 3.776A  pdb=" N   ILE B 106 " --> pdb=" O   GLU B 101 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   THR B  34 " --> pdb=" O   MET B 161 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   MET B 161 " --> pdb=" O   THR B  34 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   CYS B  36 " --> pdb=" O   VAL B 159 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL B 159 " --> pdb=" O   CYS B  36 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   ASN B 158 " --> pdb=" O   LYS B   7 " (cutoff:3.500A)
      removed outlier: 9.997A  pdb=" N   LYS B   7 " --> pdb=" O   ASN B 158 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 80 through 85
      removed outlier: 3.605A  pdb=" N   TYR B  73 " --> pdb=" O   PHE B  84 " (cutoff:3.500A)
      removed outlier: 5.943A  pdb=" N   ASN B  61 " --> pdb=" O   THR B  56 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   THR B  56 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   TRP B  67 " --> pdb=" O   SER B  50 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   SER B  50 " --> pdb=" O   TRP B  67 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ILE B 133 " --> pdb=" O   LEU B  22 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 114 through 115
    Processing sheet with id=AB6, first strand: chain 'A' and resid 114 through 115
      removed outlier: 3.840A  pdb=" N   ILE A 106 " --> pdb=" O   GLU A 101 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLU A 101 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   THR A  34 " --> pdb=" O   MET A 161 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   MET A 161 " --> pdb=" O   THR A  34 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   CYS A  36 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   VAL A 159 " --> pdb=" O   CYS A  36 " (cutoff:3.500A)
      removed outlier: 4.901A  pdb=" N   ASN A 158 " --> pdb=" O   LYS A   7 " (cutoff:3.500A)
      removed outlier: 10.141A  pdb=" N   LYS A   7 " --> pdb=" O   ASN A 158 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 80 through 85
      removed outlier: 3.610A  pdb=" N   TYR A  73 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
      removed outlier: 5.849A  pdb=" N   ASN A  61 " --> pdb=" O   THR A  56 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   THR A  56 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   TRP A  67 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
      removed outlier: 5.805A  pdb=" N   SER A  50 " --> pdb=" O   TRP A  67 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE A 133 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)

    338 hydrogen bonds defined for protein.
    819 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: 3.71

  Time building geometry restraints manager: 1.89 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: 7980
        1.03 -     1.22: 3
        1.22 -     1.42: 3615
        1.42 -     1.61: 4742
        1.61 -     1.80: 30
  Bond restraints: 16370
  Sorted by residual:
  bond pdb=" CA  PHE B  84 "
       pdb=" CB  PHE B  84 "
    ideal  model  delta    sigma   weight residual
    1.528  1.499  0.029 2.61e-02 1.47e+03 1.26e+00
  bond pdb=" CB  ASN D 186 "
       pdb=" CG  ASN D 186 "
    ideal  model  delta    sigma   weight residual
    1.516  1.489  0.027 2.50e-02 1.60e+03 1.20e+00
  bond pdb=" CG  PRO D  87 "
       pdb=" CD  PRO D  87 "
    ideal  model  delta    sigma   weight residual
    1.503  1.540 -0.037 3.40e-02 8.65e+02 1.16e+00
  bond pdb=" CB  VAL C  91 "
       pdb=" CG1 VAL C  91 "
    ideal  model  delta    sigma   weight residual
    1.521  1.552 -0.031 3.30e-02 9.18e+02 8.72e-01
  bond pdb=" CG1 ILE A  82 "
       pdb=" CD1 ILE A  82 "
    ideal  model  delta    sigma   weight residual
    1.513  1.477  0.036 3.90e-02 6.57e+02 8.50e-01
  ... (remaining 16365 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.64: 29475
        5.64 -    11.29: 36
       11.29 -    16.93: 2
       16.93 -    22.58: 1
       22.58 -    28.22: 41
  Bond angle restraints: 29555
  Sorted by residual:
  angle pdb=" CG2 THR A  46 "
        pdb=" CB  THR A  46 "
        pdb=" HB  THR A  46 "
      ideal   model   delta    sigma   weight residual
     108.00   79.78   28.22 3.00e+00 1.11e-01 8.85e+01
  angle pdb=" CG2 THR B  46 "
        pdb=" CB  THR B  46 "
        pdb=" HB  THR B  46 "
      ideal   model   delta    sigma   weight residual
     108.00   80.12   27.88 3.00e+00 1.11e-01 8.64e+01
  angle pdb=" OG1 THR A  46 "
        pdb=" CB  THR A  46 "
        pdb=" HB  THR A  46 "
      ideal   model   delta    sigma   weight residual
     109.00   81.49   27.51 3.00e+00 1.11e-01 8.41e+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   80.56   27.44 3.00e+00 1.11e-01 8.37e+01
  angle pdb=" CG2 THR E 126 "
        pdb=" CB  THR E 126 "
        pdb=" HB  THR E 126 "
      ideal   model   delta    sigma   weight residual
     108.00   80.97   27.03 3.00e+00 1.11e-01 8.12e+01
  ... (remaining 29550 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.49: 7007
       17.49 -    34.98: 494
       34.98 -    52.46: 163
       52.46 -    69.95: 105
       69.95 -    87.44: 16
  Dihedral angle restraints: 7785
    sinusoidal: 4100
      harmonic: 3685
  Sorted by residual:
  dihedral pdb=" CA  TYR E  73 "
           pdb=" C   TYR E  73 "
           pdb=" N   SER E  74 "
           pdb=" CA  SER E  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.15   28.85     0      5.00e+00 4.00e-02 3.33e+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  152.50   27.50     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  TYR C  73 "
           pdb=" C   TYR C  73 "
           pdb=" N   SER C  74 "
           pdb=" CA  SER C  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.57   27.43     0      5.00e+00 4.00e-02 3.01e+01
  ... (remaining 7782 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.348: 1221
       0.348 -    0.696: 0
       0.696 -    1.043: 0
       1.043 -    1.391: 4
       1.391 -    1.739: 10
  Chirality restraints: 1235
  Sorted by residual:
  chirality pdb=" CG  LEU A  83 "
            pdb=" CB  LEU A  83 "
            pdb=" CD1 LEU A  83 "
            pdb=" CD2 LEU A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.85   -1.74 2.00e-01 2.50e+01 7.56e+01
  chirality pdb=" CG  LEU D  43 "
            pdb=" CB  LEU D  43 "
            pdb=" CD1 LEU D  43 "
            pdb=" CD2 LEU D  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.92   -1.67 2.00e-01 2.50e+01 6.98e+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   -0.93   -1.66 2.00e-01 2.50e+01 6.90e+01
  ... (remaining 1232 not shown)

  Planarity restraints: 2420
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  58 "   -0.050 9.50e-02 1.11e+02   4.15e-02 3.27e+01
        pdb=" NE  ARG B  58 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  58 "   -0.025 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  58 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  58 "    0.079 2.00e-02 2.50e+03
        pdb="HH11 ARG B  58 "   -0.007 2.00e-02 2.50e+03
        pdb="HH12 ARG B  58 "    0.034 2.00e-02 2.50e+03
        pdb="HH21 ARG B  58 "    0.002 2.00e-02 2.50e+03
        pdb="HH22 ARG B  58 "   -0.069 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 188 "   -0.083 9.50e-02 1.11e+02   4.07e-02 2.09e+01
        pdb=" NE  ARG C 188 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 188 "   -0.058 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 188 "    0.056 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 188 "    0.027 2.00e-02 2.50e+03
        pdb="HH11 ARG C 188 "   -0.012 2.00e-02 2.50e+03
        pdb="HH12 ARG C 188 "   -0.017 2.00e-02 2.50e+03
        pdb="HH21 ARG C 188 "   -0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG C 188 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS E  38 "   -0.005 2.00e-02 2.50e+03   2.73e-02 1.86e+01
        pdb=" CG  HIS E  38 "    0.020 2.00e-02 2.50e+03
        pdb=" ND1 HIS E  38 "    0.047 2.00e-02 2.50e+03
        pdb=" CD2 HIS E  38 "    0.014 2.00e-02 2.50e+03
        pdb=" CE1 HIS E  38 "    0.018 2.00e-02 2.50e+03
        pdb=" NE2 HIS E  38 "    0.019 2.00e-02 2.50e+03
        pdb=" HD1 HIS E  38 "   -0.050 2.00e-02 2.50e+03
        pdb=" HD2 HIS E  38 "   -0.031 2.00e-02 2.50e+03
        pdb=" HE1 HIS E  38 "   -0.015 2.00e-02 2.50e+03
        pdb=" HE2 HIS E  38 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 2417 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 752
        2.15 -     2.77: 31109
        2.77 -     3.38: 46031
        3.38 -     3.99: 63656
        3.99 -     4.60: 97925
  Nonbonded interactions: 239473
  Sorted by model distance:
  nonbonded pdb=" H   SER A 167 "
            pdb=" OE1 GLU A 170 "
     model   vdw
     1.543 2.450
  nonbonded pdb=" H   SER B 167 "
            pdb=" OE1 GLU B 170 "
     model   vdw
     1.565 2.450
  nonbonded pdb=" O   GLU E  85 "
            pdb="HH22 ARG E 116 "
     model   vdw
     1.565 2.450
  nonbonded pdb=" OD1 ASP E   3 "
            pdb=" HG  SER E   5 "
     model   vdw
     1.569 2.450
  nonbonded pdb=" H   SER D 167 "
            pdb=" OE1 GLU D 170 "
     model   vdw
     1.577 2.450
  ... (remaining 239468 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:             3.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.090
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     16.610
  Find NCS groups from input model:        0.240
  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:             0.010
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
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      :  0.005   0.037   8395  Z= 0.216
  Angle     :  0.856  15.383  11415  Z= 0.459
  Chirality :  0.166   1.739   1235
  Planarity :  0.006   0.080   1450
  Dihedral  : 13.676  87.441   2990
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  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: -1.10 (0.24), residues: 1020
  helix: -1.53 (0.44), residues: 55
  sheet: -0.38 (0.26), residues: 360
  loop : -0.82 (0.24), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.069   0.013   ARG C 188 
 TYR   0.023   0.005   TYR E 125 
 PHE   0.018   0.003   PHE C  84 
 TRP   0.026   0.006   TRP E 187 
 HIS   0.011   0.004   HIS C  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 8390)
  covalent geometry    : angle       0.85492 (11405)
  SS BOND              : bond        0.00312 (    5)
  SS BOND              : angle       1.93062 (   10)
  hydrogen bonds       : bond        0.19264 (  328)
  hydrogen bonds       : angle       8.03881 (  819)

*********************** 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
  95 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
REVERT: E  161 MET cc_start: 0.8031 (ttt) cc_final: 0.7746 (ttt)
REVERT: A   83 LEU cc_start: 0.8808 (mt) cc_final: 0.8591 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.2795
  time to fit residues: 33.6386
Evaluate side-chains
  67 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0050
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
C  61 ASN
B  61 ASN
A  61 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.086736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.070894 restraints weight = 37250.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.2791 rms_B_bonded: 2.58
r_work: 0.2678 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2528 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.1269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8395  Z= 0.157
  Angle     :  0.785  15.704  11415  Z= 0.409
  Chirality :  0.167   1.701   1235
  Planarity :  0.004   0.048   1450
  Dihedral  :  6.403  21.697   1100
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  3.00 %
    Favored  : 96.67 %
  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: -0.77 (0.24), residues: 1020
  helix:  1.22 (0.53), residues: 55
  sheet: -0.40 (0.23), residues: 420
  loop : -0.70 (0.26), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 188 
 TYR   0.023   0.002   TYR E  54 
 PHE   0.014   0.002   PHE E  52 
 TRP   0.010   0.001   TRP D 110 
 HIS   0.007   0.002   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8390)
  covalent geometry    : angle       0.78525 (11405)
  SS BOND              : bond        0.00098 (    5)
  SS BOND              : angle       0.38982 (   10)
  hydrogen bonds       : bond        0.04970 (  328)
  hydrogen bonds       : angle       6.25603 (  819)

*********************** 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
  79 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.465 
Fit side-chains
REVERT: E  161 MET cc_start: 0.8605 (ttt) cc_final: 0.8391 (ttt)
REVERT: E  186 ASN cc_start: 0.8596 (t0) cc_final: 0.8132 (t0)
REVERT: D   18 SER cc_start: 0.9066 (m) cc_final: 0.8613 (p)
REVERT: C  197 GLU cc_start: 0.7935 (tt0) cc_final: 0.7225 (pp20)
REVERT: B  163 ASP cc_start: 0.8600 (p0) cc_final: 0.8391 (p0)
REVERT: A   18 SER cc_start: 0.9007 (m) cc_final: 0.8590 (p)
  outliers start: 3
  outliers final: 2
  residues processed: 79
  average time/residue: 0.2624
  time to fit residues: 26.7192
Evaluate side-chains
  70 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain C residue   46 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 158 ASN
A  95 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.093262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.077762 restraints weight = 35699.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 2.53
r_work: 0.2726 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2576 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8395  Z= 0.169
  Angle     :  0.755  15.338  11415  Z= 0.390
  Chirality :  0.167   1.723   1235
  Planarity :  0.004   0.060   1450
  Dihedral  :  5.764  19.366   1100
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  4.56 %
    Favored  : 94.89 %
  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: -0.75 (0.25), residues: 1020
  helix:  2.06 (0.61), residues: 55
  sheet: -0.56 (0.22), residues: 445
  loop : -0.62 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  58 
 TYR   0.024   0.001   TYR E  54 
 PHE   0.011   0.001   PHE A  52 
 TRP   0.010   0.001   TRP A 162 
 HIS   0.007   0.002   HIS A  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 8390)
  covalent geometry    : angle       0.75494 (11405)
  SS BOND              : bond        0.00080 (    5)
  SS BOND              : angle       0.39264 (   10)
  hydrogen bonds       : bond        0.04409 (  328)
  hydrogen bonds       : angle       5.95438 (  819)

*********************** 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
  83 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.437 
Fit side-chains
REVERT: E  161 MET cc_start: 0.8656 (ttt) cc_final: 0.8442 (ttt)
REVERT: D   18 SER cc_start: 0.9083 (m) cc_final: 0.8666 (p)
REVERT: C  197 GLU cc_start: 0.7940 (tt0) cc_final: 0.7202 (pp20)
REVERT: A  197 GLU cc_start: 0.8300 (pt0) cc_final: 0.7951 (pp20)
  outliers start: 5
  outliers final: 2
  residues processed: 82
  average time/residue: 0.2324
  time to fit residues: 25.3284
Evaluate side-chains
  73 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain A residue  166 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 31 optimal weight:    0.0970
   chunk 16 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 89 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.093259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.077440 restraints weight = 35365.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 2.54
r_work: 0.2738 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2587 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.2039

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= 0.131
  Angle     :  0.729  15.714  11415  Z= 0.375
  Chirality :  0.165   1.711   1235
  Planarity :  0.003   0.034   1450
  Dihedral  :  5.409  18.013   1100
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  6.44 %
    Favored  : 93.22 %
  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: -0.68 (0.25), residues: 1020
  helix:  2.46 (0.63), residues: 55
  sheet: -0.57 (0.22), residues: 445
  loop : -0.55 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  58 
 TYR   0.019   0.001   TYR E  54 
 PHE   0.010   0.001   PHE B  52 
 TRP   0.009   0.001   TRP A 162 
 HIS   0.005   0.002   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8390)
  covalent geometry    : angle       0.72944 (11405)
  SS BOND              : bond        0.00117 (    5)
  SS BOND              : angle       0.42088 (   10)
  hydrogen bonds       : bond        0.03897 (  328)
  hydrogen bonds       : angle       5.73305 (  819)

*********************** 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
  84 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.451 
Fit side-chains
REVERT: E  161 MET cc_start: 0.8667 (ttt) cc_final: 0.8443 (ttt)
REVERT: D   18 SER cc_start: 0.9069 (m) cc_final: 0.8613 (p)
REVERT: C  197 GLU cc_start: 0.7834 (tt0) cc_final: 0.7113 (pp20)
REVERT: A   28 LYS cc_start: 0.8047 (mmmt) cc_final: 0.7670 (pttp)
REVERT: A  180 PHE cc_start: 0.8597 (p90) cc_final: 0.8362 (p90)
REVERT: A  197 GLU cc_start: 0.8365 (pt0) cc_final: 0.7904 (pp20)
  outliers start: 3
  outliers final: 2
  residues processed: 83
  average time/residue: 0.2429
  time to fit residues: 26.4351
Evaluate side-chains
  72 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain B residue   82 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.092457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.076771 restraints weight = 35649.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.2826 rms_B_bonded: 2.53
r_work: 0.2711 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2562 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8395  Z= 0.181
  Angle     :  0.737  16.077  11415  Z= 0.378
  Chirality :  0.166   1.712   1235
  Planarity :  0.003   0.037   1450
  Dihedral  :  5.340  18.067   1100
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  8.11 %
    Favored  : 91.33 %
  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: -0.76 (0.25), residues: 1020
  helix:  2.55 (0.65), residues: 55
  sheet: -0.60 (0.22), residues: 445
  loop : -0.64 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 188 
 TYR   0.020   0.001   TYR E  54 
 PHE   0.013   0.002   PHE A  52 
 TRP   0.010   0.001   TRP A 162 
 HIS   0.006   0.002   HIS A  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 8390)
  covalent geometry    : angle       0.73673 (11405)
  SS BOND              : bond        0.00099 (    5)
  SS BOND              : angle       0.40497 (   10)
  hydrogen bonds       : bond        0.03967 (  328)
  hydrogen bonds       : angle       5.65279 (  819)

*********************** 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
  80 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.437 
Fit side-chains
REVERT: D   18 SER cc_start: 0.9057 (m) cc_final: 0.8667 (p)
REVERT: C  197 GLU cc_start: 0.7855 (tt0) cc_final: 0.7150 (pp20)
REVERT: A   28 LYS cc_start: 0.8117 (mmmt) cc_final: 0.7750 (pttp)
REVERT: A  180 PHE cc_start: 0.8637 (p90) cc_final: 0.8363 (p90)
  outliers start: 5
  outliers final: 3
  residues processed: 80
  average time/residue: 0.2568
  time to fit residues: 26.4654
Evaluate side-chains
  73 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 70
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain D residue   80 SER
Chi-restraints excluded: chain A residue  166 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 81 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.092286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.076500 restraints weight = 35423.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.2823 rms_B_bonded: 2.54
r_work: 0.2710 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2559 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8395  Z= 0.177
  Angle     :  0.735  16.544  11415  Z= 0.377
  Chirality :  0.166   1.735   1235
  Planarity :  0.003   0.036   1450
  Dihedral  :  5.288  17.188   1100
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  9.33 %
    Favored  : 90.22 %
  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: -0.82 (0.25), residues: 1020
  helix:  2.51 (0.65), residues: 55
  sheet: -0.63 (0.22), residues: 445
  loop : -0.71 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 188 
 TYR   0.018   0.001   TYR E  54 
 PHE   0.013   0.002   PHE B  52 
 TRP   0.010   0.001   TRP A 162 
 HIS   0.005   0.002   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 8390)
  covalent geometry    : angle       0.73503 (11405)
  SS BOND              : bond        0.00097 (    5)
  SS BOND              : angle       0.37602 (   10)
  hydrogen bonds       : bond        0.03855 (  328)
  hydrogen bonds       : angle       5.59709 (  819)

*********************** 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
  75 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.428 
Fit side-chains
REVERT: E  161 MET cc_start: 0.8738 (ttt) cc_final: 0.8442 (ttt)
REVERT: D   18 SER cc_start: 0.9056 (m) cc_final: 0.8694 (p)
REVERT: C  197 GLU cc_start: 0.7835 (tt0) cc_final: 0.7131 (pp20)
REVERT: A   28 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7740 (pttp)
REVERT: A  180 PHE cc_start: 0.8635 (p90) cc_final: 0.8318 (p90)
  outliers start: 4
  outliers final: 3
  residues processed: 75
  average time/residue: 0.2846
  time to fit residues: 27.5320
Evaluate side-chains
  71 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain D residue   80 SER
Chi-restraints excluded: chain A residue  166 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 81 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 80 optimal weight:    0.5980
   chunk 70 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0060
   chunk 21 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.093661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.077961 restraints weight = 35350.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 2.53
r_work: 0.2734 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2584 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.2524

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= 0.125
  Angle     :  0.715  16.223  11415  Z= 0.366
  Chirality :  0.162   1.695   1235
  Planarity :  0.003   0.033   1450
  Dihedral  :  5.092  15.408   1100
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  9.56 %
    Favored  : 90.11 %
  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: -0.76 (0.25), residues: 1020
  helix:  2.75 (0.65), residues: 55
  sheet: -0.61 (0.23), residues: 445
  loop : -0.67 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 188 
 TYR   0.014   0.001   TYR E  54 
 PHE   0.010   0.001   PHE B 180 
 TRP   0.010   0.001   TRP A 162 
 HIS   0.005   0.002   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8390)
  covalent geometry    : angle       0.71474 (11405)
  SS BOND              : bond        0.00148 (    5)
  SS BOND              : angle       0.40588 (   10)
  hydrogen bonds       : bond        0.03598 (  328)
  hydrogen bonds       : angle       5.50326 (  819)

*********************** 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
  75 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
REVERT: E  161 MET cc_start: 0.8682 (ttt) cc_final: 0.8381 (ttt)
REVERT: D   18 SER cc_start: 0.9027 (m) cc_final: 0.8699 (p)
REVERT: D   40 TYR cc_start: 0.9247 (t80) cc_final: 0.8976 (t80)
REVERT: A   28 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7706 (pttp)
REVERT: A   80 SER cc_start: 0.7913 (t) cc_final: 0.7614 (m)
REVERT: A  180 PHE cc_start: 0.8610 (p90) cc_final: 0.8261 (p90)
  outliers start: 3
  outliers final: 2
  residues processed: 75
  average time/residue: 0.2688
  time to fit residues: 25.9637
Evaluate side-chains
  73 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain D residue   80 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 77 optimal weight:    0.0670
   chunk 82 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.9920

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.092320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.076665 restraints weight = 35829.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.2823 rms_B_bonded: 2.54
r_work: 0.2710 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2561 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.2548

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= 0.184
  Angle     :  0.730  16.489  11415  Z= 0.375
  Chirality :  0.164   1.699   1235
  Planarity :  0.003   0.032   1450
  Dihedral  :  5.129  16.372   1100
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  9.67 %
    Favored  : 89.89 %
  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: -0.89 (0.25), residues: 1020
  helix:  2.49 (0.65), residues: 55
  sheet: -0.62 (0.23), residues: 445
  loop : -0.81 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 188 
 TYR   0.018   0.001   TYR E  54 
 PHE   0.013   0.002   PHE A  52 
 TRP   0.011   0.001   TRP D 162 
 HIS   0.005   0.002   HIS A  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 8390)
  covalent geometry    : angle       0.72992 (11405)
  SS BOND              : bond        0.00086 (    5)
  SS BOND              : angle       0.36330 (   10)
  hydrogen bonds       : bond        0.03814 (  328)
  hydrogen bonds       : angle       5.51351 (  819)

*********************** 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: 4
    poor density    : 75
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  161 MET cc_start: 0.8720 (ttt) cc_final: 0.8371 (ttt)
REVERT: D   18 SER cc_start: 0.9063 (m) cc_final: 0.8736 (p)
REVERT: C  197 GLU cc_start: 0.8053 (pt0) cc_final: 0.7188 (pp20)
REVERT: A   28 LYS cc_start: 0.8169 (mmmt) cc_final: 0.7806 (pttp)
REVERT: A  180 PHE cc_start: 0.8647 (p90) cc_final: 0.8311 (p90)
  outliers start: 4
  outliers final: 2
  residues processed: 79
  average time/residue: 0.2572
  time to fit residues: 26.6162
Evaluate side-chains
  74 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain D residue   80 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.091548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.076160 restraints weight = 35768.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.2805 rms_B_bonded: 2.46
r_work: 0.2690 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2540 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   8395  Z= 0.226
  Angle     :  0.743  16.474  11415  Z= 0.384
  Chirality :  0.163   1.703   1235
  Planarity :  0.004   0.033   1450
  Dihedral  :  5.264  17.768   1100
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  9.56 %
    Favored  : 90.00 %
  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: -1.08 (0.24), residues: 1020
  helix:  2.28 (0.66), residues: 55
  sheet: -0.68 (0.23), residues: 420
  loop : -1.01 (0.25), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 188 
 TYR   0.020   0.001   TYR E  54 
 PHE   0.017   0.002   PHE E  52 
 TRP   0.011   0.001   TRP D 162 
 HIS   0.005   0.002   HIS A  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 ( 8390)
  covalent geometry    : angle       0.74313 (11405)
  SS BOND              : bond        0.00055 (    5)
  SS BOND              : angle       0.34778 (   10)
  hydrogen bonds       : bond        0.03967 (  328)
  hydrogen bonds       : angle       5.58243 (  819)

*********************** 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
  76 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: E  161 MET cc_start: 0.8757 (ttt) cc_final: 0.8395 (ttt)
REVERT: D   18 SER cc_start: 0.9060 (m) cc_final: 0.8747 (p)
REVERT: C  197 GLU cc_start: 0.8214 (pt0) cc_final: 0.7390 (pp20)
REVERT: A   28 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7797 (pttp)
REVERT: A  180 PHE cc_start: 0.8668 (p90) cc_final: 0.8392 (p90)
  outliers start: 4
  outliers final: 3
  residues processed: 76
  average time/residue: 0.2644
  time to fit residues: 25.8889
Evaluate side-chains
  74 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain D residue   80 SER
Chi-restraints excluded: chain C residue   83 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0980
   chunk 16 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.093608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.078596 restraints weight = 35359.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.2837 rms_B_bonded: 2.35
r_work: 0.2725 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2576 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8395  Z= 0.142
  Angle     :  0.718  16.353  11415  Z= 0.368
  Chirality :  0.163   1.684   1235
  Planarity :  0.003   0.033   1450
  Dihedral  :  5.074  16.504   1100
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  9.89 %
    Favored  : 89.78 %
  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: -0.95 (0.25), residues: 1020
  helix:  2.62 (0.65), residues: 55
  sheet: -0.65 (0.23), residues: 445
  loop : -0.89 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 116 
 TYR   0.014   0.001   TYR E  54 
 PHE   0.010   0.001   PHE B  52 
 TRP   0.010   0.001   TRP D 162 
 HIS   0.005   0.002   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 8390)
  covalent geometry    : angle       0.71809 (11405)
  SS BOND              : bond        0.00135 (    5)
  SS BOND              : angle       0.35788 (   10)
  hydrogen bonds       : bond        0.03611 (  328)
  hydrogen bonds       : angle       5.48453 (  819)

********************** 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: 3
    poor density    : 79
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  161 MET cc_start: 0.8699 (ttt) cc_final: 0.8306 (ttt)
REVERT: D   18 SER cc_start: 0.9078 (m) cc_final: 0.8770 (p)
REVERT: D   40 TYR cc_start: 0.9279 (t80) cc_final: 0.9032 (t80)
REVERT: C  197 GLU cc_start: 0.8188 (pt0) cc_final: 0.7445 (pp20)
REVERT: B  180 PHE cc_start: 0.8423 (p90) cc_final: 0.8197 (p90)
REVERT: A   28 LYS cc_start: 0.8144 (mmmt) cc_final: 0.7778 (pttp)
REVERT: A   80 SER cc_start: 0.7939 (t) cc_final: 0.7632 (m)
REVERT: A  180 PHE cc_start: 0.8640 (p90) cc_final: 0.8320 (p90)
  outliers start: 3
  outliers final: 3
  residues processed: 82
  average time/residue: 0.2687
  time to fit residues: 28.2730
Evaluate side-chains
  81 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   46 THR
Chi-restraints excluded: chain D residue   80 SER
Chi-restraints excluded: chain C residue   83 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0980
   chunk 27 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.093673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.078739 restraints weight = 35305.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.2850 rms_B_bonded: 2.33
r_work: 0.2739 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2589 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.2757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8395  Z= 0.145
  Angle     :  0.716  16.347  11415  Z= 0.367
  Chirality :  0.164   1.693   1235
  Planarity :  0.004   0.033   1450
  Dihedral  :  4.985  16.101   1100
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  9.89 %
    Favored  : 89.78 %
  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: -0.95 (0.25), residues: 1020
  helix:  2.66 (0.65), residues: 55
  sheet: -0.65 (0.23), residues: 445
  loop : -0.89 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 188 
 TYR   0.015   0.001   TYR E  54 
 PHE   0.011   0.001   PHE E  52 
 TRP   0.011   0.001   TRP D 162 
 HIS   0.005   0.002   HIS E  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 8390)
  covalent geometry    : angle       0.71625 (11405)
  SS BOND              : bond        0.00117 (    5)
  SS BOND              : angle       0.35087 (   10)
  hydrogen bonds       : bond        0.03623 (  328)
  hydrogen bonds       : angle       5.44704 (  819)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3554.96 seconds
wall clock time: 60 minutes 57.06 seconds (3657.06 seconds total)