Starting phenix.real_space_refine
on Fri Dec  8 02:15:43 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oh0_3809/12_2023/5oh0_3809_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oh0_3809/12_2023/5oh0_3809.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oh0_3809/12_2023/5oh0_3809.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oh0_3809/12_2023/5oh0_3809.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oh0_3809/12_2023/5oh0_3809_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oh0_3809/12_2023/5oh0_3809_neut.pdb"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    4032      2.51       5
     N    1158      2.21       5
     O    1386      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG  136": "NH1" <-> "NH2"
    Residue "B ARG  136": "NH1" <-> "NH2"
    Residue "C ARG  136": "NH1" <-> "NH2"
    Residue "D ARG  136": "NH1" <-> "NH2"
    Residue "E ARG  136": "NH1" <-> "NH2"
    Residue "F ARG  136": "NH1" <-> "NH2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 6588
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1098
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1098
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 2, 'TRANS': 154}
    Chain: "B"
      Number of atoms: 1098
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1098
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 2, 'TRANS': 154}
    Chain: "C"
      Number of atoms: 1098
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1098
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 2, 'TRANS': 154}
    Chain: "D"
      Number of atoms: 1098
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1098
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 2, 'TRANS': 154}
    Chain: "E"
      Number of atoms: 1098
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1098
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 2, 'TRANS': 154}
    Chain: "F"
      Number of atoms: 1098
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1098
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 2, 'TRANS': 154}
  Time building chain proxies: 3.97, per 1000 atoms: 0.60
  Number of scatterers: 6588
  At special positions: 0
  Unit cell: (87.01, 84.75, 84.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      12     16.00
     O    1386      8.00
     N    1158      7.00
     C    4032      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  21 " - pdb=" SG  CYS A  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  21 " - pdb=" SG  CYS B  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  21 " - pdb=" SG  CYS C  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  21 " - pdb=" SG  CYS D  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  21 " - pdb=" SG  CYS E  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  21 " - pdb=" SG  CYS F  61 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.38
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1692

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 17 sheets defined
      5.2% alpha, 40.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 27
      No H-bonds generated for 'chain 'A' and resid 25 through 27'
    Processing helix  chain 'A' and resid 38 through 42
    Processing helix  chain 'B' and resid 25 through 27
      No H-bonds generated for 'chain 'B' and resid 25 through 27'
    Processing helix  chain 'B' and resid 38 through 42
    Processing helix  chain 'C' and resid 25 through 27
      No H-bonds generated for 'chain 'C' and resid 25 through 27'
    Processing helix  chain 'C' and resid 38 through 42
    Processing helix  chain 'D' and resid 25 through 27
      No H-bonds generated for 'chain 'D' and resid 25 through 27'
    Processing helix  chain 'D' and resid 38 through 42
    Processing helix  chain 'E' and resid 25 through 27
      No H-bonds generated for 'chain 'E' and resid 25 through 27'
    Processing helix  chain 'E' and resid 38 through 42
    Processing helix  chain 'F' and resid 25 through 28
      removed outlier: 4.033A  pdb=" N   VAL F  28 " --> pdb=" O   ALA F  25 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 25 through 28'
    Processing helix  chain 'F' and resid 38 through 42
    Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23
      removed outlier: 6.519A  pdb=" N   THR A  48 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   ALA A 139 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   SER A  50 " --> pdb=" O   TYR A 137 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   TYR A 137 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33
      removed outlier: 6.967A  pdb=" N   GLN A  30 " --> pdb=" O   HIS B  11 " (cutoff:3.500A)
      removed outlier: 8.208A  pdb=" N   LYS B  13 " --> pdb=" O   GLN A  30 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   VAL A  32 " --> pdb=" O   LYS B  13 " (cutoff:3.500A)
      removed outlier: 9.262A  pdb=" N   GLU B  15 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   PHE A 154 " --> pdb=" O   GLY B   7 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   THR B   9 " --> pdb=" O   ALA A 152 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   ALA A 152 " --> pdb=" O   THR B   9 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 33
      removed outlier: 6.967A  pdb=" N   GLN A  30 " --> pdb=" O   HIS B  11 " (cutoff:3.500A)
      removed outlier: 8.208A  pdb=" N   LYS B  13 " --> pdb=" O   GLN A  30 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   VAL A  32 " --> pdb=" O   LYS B  13 " (cutoff:3.500A)
      removed outlier: 9.262A  pdb=" N   GLU B  15 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA A 148 " --> pdb=" O   GLY B  14 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   VAL B  16 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 23
      removed outlier: 6.519A  pdb=" N   THR B  48 " --> pdb=" O   ALA B 139 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   ALA B 139 " --> pdb=" O   THR B  48 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   SER B  50 " --> pdb=" O   TYR B 137 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   TYR B 137 " --> pdb=" O   SER B  50 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 33
      removed outlier: 6.970A  pdb=" N   GLN B  30 " --> pdb=" O   HIS C  11 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   LYS C  13 " --> pdb=" O   GLN B  30 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   VAL B  32 " --> pdb=" O   LYS C  13 " (cutoff:3.500A)
      removed outlier: 9.204A  pdb=" N   GLU C  15 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   PHE B 154 " --> pdb=" O   GLY C   7 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   THR C   9 " --> pdb=" O   ALA B 152 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   ALA B 152 " --> pdb=" O   THR C   9 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 33
      removed outlier: 6.970A  pdb=" N   GLN B  30 " --> pdb=" O   HIS C  11 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   LYS C  13 " --> pdb=" O   GLN B  30 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   VAL B  32 " --> pdb=" O   LYS C  13 " (cutoff:3.500A)
      removed outlier: 9.204A  pdb=" N   GLU C  15 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA B 148 " --> pdb=" O   GLY C  14 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   VAL C  16 " --> pdb=" O   GLY B 146 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 22 through 23
      removed outlier: 6.519A  pdb=" N   THR C  48 " --> pdb=" O   ALA C 139 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   ALA C 139 " --> pdb=" O   THR C  48 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   SER C  50 " --> pdb=" O   TYR C 137 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   TYR C 137 " --> pdb=" O   SER C  50 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 35
      removed outlier: 3.788A  pdb=" N   GLN C  30 " --> pdb=" O   THR D   9 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   VAL C  32 " --> pdb=" O   HIS D  11 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   GLU D  15 " --> pdb=" O   LEU C  34 " (cutoff:3.500A)
      removed outlier: 5.695A  pdb=" N   PHE C 154 " --> pdb=" O   GLY D   7 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   THR D   9 " --> pdb=" O   ALA C 152 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ALA C 152 " --> pdb=" O   THR D   9 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 35
      removed outlier: 3.788A  pdb=" N   GLN C  30 " --> pdb=" O   THR D   9 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   VAL C  32 " --> pdb=" O   HIS D  11 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   GLU D  15 " --> pdb=" O   LEU C  34 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ALA C 148 " --> pdb=" O   GLY D  14 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   VAL D  16 " --> pdb=" O   GLY C 146 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 22 through 23
      removed outlier: 6.518A  pdb=" N   THR D  48 " --> pdb=" O   ALA D 139 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   ALA D 139 " --> pdb=" O   THR D  48 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   SER D  50 " --> pdb=" O   TYR D 137 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   TYR D 137 " --> pdb=" O   SER D  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 29 through 33
      removed outlier: 6.940A  pdb=" N   GLN D  30 " --> pdb=" O   HIS E  11 " (cutoff:3.500A)
      removed outlier: 8.187A  pdb=" N   LYS E  13 " --> pdb=" O   GLN D  30 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   VAL D  32 " --> pdb=" O   LYS E  13 " (cutoff:3.500A)
      removed outlier: 9.248A  pdb=" N   GLU E  15 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 5.852A  pdb=" N   PHE D 154 " --> pdb=" O   GLY E   7 " (cutoff:3.500A)
      removed outlier: 5.025A  pdb=" N   THR E   9 " --> pdb=" O   ALA D 152 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ALA D 152 " --> pdb=" O   THR E   9 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 29 through 33
      removed outlier: 6.940A  pdb=" N   GLN D  30 " --> pdb=" O   HIS E  11 " (cutoff:3.500A)
      removed outlier: 8.187A  pdb=" N   LYS E  13 " --> pdb=" O   GLN D  30 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   VAL D  32 " --> pdb=" O   LYS E  13 " (cutoff:3.500A)
      removed outlier: 9.248A  pdb=" N   GLU E  15 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA D 148 " --> pdb=" O   GLY E  14 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   VAL E  16 " --> pdb=" O   GLY D 146 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 22 through 23
      removed outlier: 6.518A  pdb=" N   THR E  48 " --> pdb=" O   ALA E 139 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   ALA E 139 " --> pdb=" O   THR E  48 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   SER E  50 " --> pdb=" O   TYR E 137 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   TYR E 137 " --> pdb=" O   SER E  50 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 29 through 35
      removed outlier: 3.720A  pdb=" N   GLN E  30 " --> pdb=" O   THR F   9 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   VAL E  32 " --> pdb=" O   HIS F  11 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   GLU F  15 " --> pdb=" O   LEU E  34 " (cutoff:3.500A)
      removed outlier: 5.801A  pdb=" N   PHE E 154 " --> pdb=" O   GLY F   7 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   THR F   9 " --> pdb=" O   ALA E 152 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   ALA E 152 " --> pdb=" O   THR F   9 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 29 through 35
      removed outlier: 3.720A  pdb=" N   GLN E  30 " --> pdb=" O   THR F   9 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   VAL E  32 " --> pdb=" O   HIS F  11 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   GLU F  15 " --> pdb=" O   LEU E  34 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ALA E 148 " --> pdb=" O   GLY F  14 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL F  16 " --> pdb=" O   GLY E 146 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 22 through 23
      removed outlier: 6.519A  pdb=" N   THR F  48 " --> pdb=" O   ALA F 139 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   ALA F 139 " --> pdb=" O   THR F  48 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   SER F  50 " --> pdb=" O   TYR F 137 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   TYR F 137 " --> pdb=" O   SER F  50 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 70 through 74

    145 hydrogen bonds defined for protein.
    312 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: 1.37

  Time building geometry restraints manager: 2.60 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2328
        1.34 -     1.46: 1473
        1.46 -     1.58: 2847
        1.58 -     1.70: 0
        1.70 -     1.82: 12
  Bond restraints: 6660
  Sorted by residual:
  bond pdb=" N   GLY A  53 "
       pdb=" CA  GLY A  53 "
    ideal  model  delta    sigma   weight residual
    1.444  1.455 -0.011 1.02e-02 9.61e+03 1.24e+00
  bond pdb=" N   GLY F  53 "
       pdb=" CA  GLY F  53 "
    ideal  model  delta    sigma   weight residual
    1.444  1.455 -0.011 1.02e-02 9.61e+03 1.18e+00
  bond pdb=" N   GLY E  53 "
       pdb=" CA  GLY E  53 "
    ideal  model  delta    sigma   weight residual
    1.444  1.455 -0.011 1.02e-02 9.61e+03 1.16e+00
  bond pdb=" N   GLY D  53 "
       pdb=" CA  GLY D  53 "
    ideal  model  delta    sigma   weight residual
    1.444  1.455 -0.011 1.02e-02 9.61e+03 1.14e+00
  bond pdb=" N   GLY B  53 "
       pdb=" CA  GLY B  53 "
    ideal  model  delta    sigma   weight residual
    1.444  1.455 -0.011 1.02e-02 9.61e+03 1.11e+00
  ... (remaining 6655 not shown)

  Histogram of bond angle deviations from ideal:
      102.56 -   108.30: 211
      108.30 -   114.04: 3831
      114.04 -   119.79: 1535
      119.79 -   125.53: 3489
      125.53 -   131.27: 36
  Bond angle restraints: 9102
  Sorted by residual:
  angle pdb=" N   ASP A 114 "
        pdb=" CA  ASP A 114 "
        pdb=" C   ASP A 114 "
      ideal   model   delta    sigma   weight residual
     114.56  110.82    3.74 1.27e+00 6.20e-01 8.70e+00
  angle pdb=" N   ASP D 114 "
        pdb=" CA  ASP D 114 "
        pdb=" C   ASP D 114 "
      ideal   model   delta    sigma   weight residual
     114.56  110.84    3.72 1.27e+00 6.20e-01 8.59e+00
  angle pdb=" N   ASP C 114 "
        pdb=" CA  ASP C 114 "
        pdb=" C   ASP C 114 "
      ideal   model   delta    sigma   weight residual
     114.56  110.84    3.72 1.27e+00 6.20e-01 8.58e+00
  angle pdb=" N   ASP F 114 "
        pdb=" CA  ASP F 114 "
        pdb=" C   ASP F 114 "
      ideal   model   delta    sigma   weight residual
     114.56  110.86    3.70 1.27e+00 6.20e-01 8.48e+00
  angle pdb=" N   ASP B 114 "
        pdb=" CA  ASP B 114 "
        pdb=" C   ASP B 114 "
      ideal   model   delta    sigma   weight residual
     114.56  110.86    3.70 1.27e+00 6.20e-01 8.47e+00
  ... (remaining 9097 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.28: 3710
       14.28 -    28.57: 136
       28.57 -    42.85: 30
       42.85 -    57.13: 0
       57.13 -    71.42: 6
  Dihedral angle restraints: 3882
    sinusoidal: 1242
      harmonic: 2640
  Sorted by residual:
  dihedral pdb=" CA  PHE E 154 "
           pdb=" C   PHE E 154 "
           pdb=" N   LYS E 155 "
           pdb=" CA  LYS E 155 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.13  -15.87     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CA  PHE D 154 "
           pdb=" C   PHE D 154 "
           pdb=" N   LYS D 155 "
           pdb=" CA  LYS D 155 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.14  -15.86     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CA  PHE C 154 "
           pdb=" C   PHE C 154 "
           pdb=" N   LYS C 155 "
           pdb=" CA  LYS C 155 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.15  -15.85     0      5.00e+00 4.00e-02 1.00e+01
  ... (remaining 3879 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 614
       0.030 -    0.059: 322
       0.059 -    0.089: 113
       0.089 -    0.119: 60
       0.119 -    0.148: 31
  Chirality restraints: 1140
  Sorted by residual:
  chirality pdb=" CA  VAL E   5 "
            pdb=" N   VAL E   5 "
            pdb=" C   VAL E   5 "
            pdb=" CB  VAL E   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.50e-01
  chirality pdb=" CA  VAL C   5 "
            pdb=" N   VAL C   5 "
            pdb=" C   VAL C   5 "
            pdb=" CB  VAL C   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.49e-01
  chirality pdb=" CA  VAL F   5 "
            pdb=" N   VAL F   5 "
            pdb=" C   VAL F   5 "
            pdb=" CB  VAL F   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.44e-01
  ... (remaining 1137 not shown)

  Planarity restraints: 1218
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 131 "    0.026 5.00e-02 4.00e+02   3.95e-02 2.49e+00
        pdb=" N   PRO D 132 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D 132 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO D 132 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 131 "   -0.026 5.00e-02 4.00e+02   3.94e-02 2.49e+00
        pdb=" N   PRO B 132 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B 132 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 132 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 131 "    0.026 5.00e-02 4.00e+02   3.94e-02 2.49e+00
        pdb=" N   PRO C 132 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO C 132 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C 132 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1215 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2071
        2.82 -     3.34: 4982
        3.34 -     3.86: 10156
        3.86 -     4.38: 10347
        4.38 -     4.90: 19483
  Nonbonded interactions: 47039
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A  98 "
            pdb=" OG1 THR A 140 "
     model   vdw
     2.295 2.440
  nonbonded pdb=" OD1 ASN D  98 "
            pdb=" OG1 THR D 140 "
     model   vdw
     2.296 2.440
  nonbonded pdb=" OD1 ASN E  98 "
            pdb=" OG1 THR E 140 "
     model   vdw
     2.296 2.440
  nonbonded pdb=" OD1 ASN B  98 "
            pdb=" OG1 THR B 140 "
     model   vdw
     2.296 2.440
  nonbonded pdb=" OD1 ASN C  98 "
            pdb=" OG1 THR C 140 "
     model   vdw
     2.296 2.440
  ... (remaining 47034 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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 group one per residue
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:             0.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          3.120
  Check model and map are aligned:         0.100
  Set scattering table:                    0.070
  Process input model:                     20.840
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.030
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
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      :  0.003   0.023   6660  Z= 0.212
  Angle     :  0.750   5.312   9102  Z= 0.463
  Chirality :  0.047   0.148   1140
  Planarity :  0.004   0.039   1218
  Dihedral  :  8.942  71.416   2172
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.74 (0.24), residues: 930
  helix:  None (None), residues: 0
  sheet: -1.38 (0.38), residues: 216
  loop : -3.13 (0.19), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS B  11 
   PHE   0.020   0.002   PHE E 154 
   TYR   0.002   0.001   TYR F 158 
   ARG   0.001   0.000   ARG A 106 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.706 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.2102
  time to fit residues: 22.6323
Evaluate side-chains
  22 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.754 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9130
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    9.9990
   chunk 68 optimal weight:    0.0870
   chunk 37 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 46 optimal weight:    8.9990
   chunk 36 optimal weight:    2.9990
   chunk 70 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9990
   chunk 42 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   chunk 81 optimal weight:   20.0000
   overall best weight:    1.2164

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 134 GLN
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 125 ASN
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  33 GLN
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   6660  Z= 0.138
  Angle     :  0.437   3.690   9102  Z= 0.243
  Chirality :  0.038   0.121   1140
  Planarity :  0.003   0.032   1218
  Dihedral  :  3.820  12.621    966
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.03 (0.25), residues: 930
  helix:  None (None), residues: 0
  sheet: -1.00 (0.35), residues: 240
  loop : -2.61 (0.20), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A  11 
   PHE   0.007   0.001   PHE F 118 
   TYR   0.002   0.000   TYR F 158 
   ARG   0.002   0.000   ARG C  38 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.784 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1434
  time to fit residues: 8.4133
Evaluate side-chains
  19 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.664 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8556
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 55 optimal weight:    9.9990
   chunk 22 optimal weight:    7.9990
   chunk 81 optimal weight:   20.0000
   chunk 88 optimal weight:   10.0000
   chunk 72 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 134 GLN
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.2861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.024   6660  Z= 0.309
  Angle     :  0.538   7.052   9102  Z= 0.291
  Chirality :  0.038   0.115   1140
  Planarity :  0.003   0.027   1218
  Dihedral  :  4.454  13.800    966
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.72 (0.26), residues: 930
  helix:  None (None), residues: 0
  sheet: -0.42 (0.37), residues: 240
  loop : -2.54 (0.21), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  11 
   PHE   0.009   0.001   PHE A 133 
   TYR   0.005   0.001   TYR F 158 
   ARG   0.003   0.001   ARG A 136 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.679 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.1227
  time to fit residues: 5.8685
Evaluate side-chains
  15 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.659 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8394
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0170
   chunk 54 optimal weight:   10.0000
   chunk 82 optimal weight:    2.9990
   chunk 86 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 49 optimal weight:    0.0370
   overall best weight:    1.4100

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   6660  Z= 0.139
  Angle     :  0.425   4.117   9102  Z= 0.233
  Chirality :  0.037   0.121   1140
  Planarity :  0.002   0.023   1218
  Dihedral  :  3.688  12.278    966
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.42 (0.26), residues: 930
  helix:  None (None), residues: 0
  sheet: -0.16 (0.36), residues: 240
  loop : -2.35 (0.21), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A  11 
   PHE   0.006   0.001   PHE E 154 
   TYR   0.002   0.000   TYR E 158 
   ARG   0.001   0.000   ARG A 136 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.855 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.1975
  time to fit residues: 8.2742
Evaluate side-chains
  16 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.727 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9271
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 74 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 44 optimal weight:   10.0000
   chunk 78 optimal weight:    0.6980
   chunk 21 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    1.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   6660  Z= 0.163
  Angle     :  0.425   4.435   9102  Z= 0.232
  Chirality :  0.037   0.119   1140
  Planarity :  0.002   0.022   1218
  Dihedral  :  3.586  11.861    966
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.26), residues: 930
  helix:  None (None), residues: 0
  sheet:  0.18 (0.37), residues: 216
  loop : -2.35 (0.21), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A  11 
   PHE   0.006   0.001   PHE C 133 
   TYR   0.002   0.000   TYR F 158 
   ARG   0.002   0.000   ARG A 136 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.728 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.1267
  time to fit residues: 5.3581
Evaluate side-chains
  17 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.709 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9476
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 87 optimal weight:    9.9990
   chunk 72 optimal weight:    0.6980
   chunk 40 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 45 optimal weight:   10.0000
   chunk 83 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   chunk 49 optimal weight:    0.0170
   overall best weight:    4.7424

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 125 ASN
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  64 ASN
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.3688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   6660  Z= 0.422
  Angle     :  0.612   7.875   9102  Z= 0.326
  Chirality :  0.039   0.116   1140
  Planarity :  0.003   0.025   1218
  Dihedral  :  4.844  17.138    966
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.26), residues: 930
  helix:  None (None), residues: 0
  sheet: -0.06 (0.36), residues: 216
  loop : -2.39 (0.21), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  11 
   PHE   0.009   0.002   PHE C 133 
   TYR   0.009   0.001   TYR F 158 
   ARG   0.004   0.001   ARG A 136 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.676 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.1287
  time to fit residues: 5.3265
Evaluate side-chains
  16 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.890 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9133
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   chunk 73 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 86 optimal weight:   10.0000
   chunk 54 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 40 optimal weight:    8.9990
   chunk 53 optimal weight:    0.8980
   chunk 34 optimal weight:    9.9990
   chunk 51 optimal weight:    8.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.3749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   6660  Z= 0.280
  Angle     :  0.507   6.127   9102  Z= 0.275
  Chirality :  0.038   0.120   1140
  Planarity :  0.002   0.020   1218
  Dihedral  :  4.393  15.092    966
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.40 (0.26), residues: 930
  helix:  None (None), residues: 0
  sheet: -0.00 (0.35), residues: 216
  loop : -2.33 (0.21), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A  11 
   PHE   0.008   0.001   PHE C 133 
   TYR   0.004   0.001   TYR E 158 
   ARG   0.003   0.000   ARG A 136 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 1.343 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.1439
  time to fit residues: 5.5985
Evaluate side-chains
  16 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.743 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9226
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 55 optimal weight:    6.9990
   chunk 59 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 68 optimal weight:    9.9990
   chunk 78 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9980
   chunk 75 optimal weight:   10.0000
   overall best weight:    3.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  64 ASN
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.3893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   6660  Z= 0.317
  Angle     :  0.539   6.342   9102  Z= 0.289
  Chirality :  0.038   0.120   1140
  Planarity :  0.002   0.021   1218
  Dihedral  :  4.572  16.039    966
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.44 (0.26), residues: 930
  helix:  None (None), residues: 0
  sheet: -0.07 (0.35), residues: 216
  loop : -2.33 (0.21), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.001   HIS F  82 
   PHE   0.007   0.001   PHE C 133 
   TYR   0.005   0.001   TYR C 158 
   ARG   0.003   0.001   ARG A 136 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.707 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.1198
  time to fit residues: 5.0470
Evaluate side-chains
  17 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.731 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9165
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 80 optimal weight:    4.9990
   chunk 83 optimal weight:    9.9990
   chunk 48 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 63 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 73 optimal weight:    5.9990
   chunk 76 optimal weight:    3.9990
   chunk 53 optimal weight:   10.0000
   chunk 85 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.3917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6660  Z= 0.250
  Angle     :  0.495   5.469   9102  Z= 0.268
  Chirality :  0.038   0.120   1140
  Planarity :  0.002   0.020   1218
  Dihedral  :  4.314  15.739    966
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.26), residues: 930
  helix:  None (None), residues: 0
  sheet: -0.01 (0.35), residues: 216
  loop : -2.27 (0.22), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A  11 
   PHE   0.007   0.001   PHE B 133 
   TYR   0.003   0.001   TYR C 158 
   ARG   0.002   0.000   ARG A 136 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.785 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.1314
  time to fit residues: 5.5772
Evaluate side-chains
  17 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.726 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9351
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 40 optimal weight:    7.9990
   chunk 59 optimal weight:   10.0000
   chunk 89 optimal weight:    0.2980
   chunk 82 optimal weight:    4.9990
   chunk 71 optimal weight:    7.9990
   chunk 7 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 56 optimal weight:    7.9990
   chunk 76 optimal weight:    4.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    2.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.3958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6660  Z= 0.198
  Angle     :  0.456   5.008   9102  Z= 0.248
  Chirality :  0.038   0.119   1140
  Planarity :  0.002   0.018   1218
  Dihedral  :  3.951  13.274    966
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.26 (0.26), residues: 930
  helix:  None (None), residues: 0
  sheet:  0.07 (0.35), residues: 216
  loop : -2.22 (0.22), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A  11 
   PHE   0.006   0.001   PHE B 133 
   TYR   0.003   0.001   TYR E 158 
   ARG   0.002   0.000   ARG A 136 

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.689 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.1272
  time to fit residues: 5.1712
Evaluate side-chains
  19 residues out of total 666 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.700 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.9041
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 71 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   chunk 73 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  64 ASN
** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.043239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2549 r_free = 0.2549 target = 0.037763 restraints weight = 39603.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.038838 restraints weight = 23071.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.039583 restraints weight = 15499.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.2606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start:          0.4038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6660  Z= 0.246
  Angle     :  0.484   5.414   9102  Z= 0.261
  Chirality :  0.038   0.119   1140
  Planarity :  0.002   0.019   1218
  Dihedral  :  4.146  13.622    966
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.26 (0.26), residues: 930
  helix:  None (None), residues: 0
  sheet:  0.01 (0.34), residues: 216
  loop : -2.19 (0.22), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS E  11 
   PHE   0.007   0.001   PHE B 133 
   TYR   0.004   0.001   TYR C 158 
   ARG   0.002   0.000   ARG A 136 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1180.40 seconds
wall clock time: 22 minutes 30.19 seconds (1350.19 seconds total)