Starting phenix.real_space_refine
on Wed Sep 17 12:23:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fac_50272/09_2025/9fac_50272_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fac_50272/09_2025/9fac_50272.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fac_50272/09_2025/9fac_50272_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fac_50272/09_2025/9fac_50272_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fac_50272/09_2025/9fac_50272.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fac_50272/09_2025/9fac_50272.map"
  }
  resolution = 3.9
  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: 5
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    2770      2.51       5
     N     725      2.21       5
     O     900      1.98       5
     H    4190      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8595
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 1705
          Classifications: {'peptide': 117}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 107}
    Chain: "B"
      Number of atoms: 1705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 1705
          Classifications: {'peptide': 117}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 107}
    Chain: "C"
      Number of atoms: 1705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 1705
          Classifications: {'peptide': 117}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 107}
    Chain: "D"
      Number of atoms: 1705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 1705
          Classifications: {'peptide': 117}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 107}
    Chain: "E"
      Number of atoms: 1705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 1705
          Classifications: {'peptide': 117}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 107}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.88, per 1000 atoms: 0.22
  Number of scatterers: 8595
  At special positions: 0
  Unit cell: (89.789, 120.904, 42.672, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     O     900      8.00
     N     725      7.00
     C    2770      6.00
     H    4190      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  87 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  87 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  87 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  87 " 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
  Links applied
    NAG-ASN
      " NAG A 201 " - " ASN A  19 "
      " NAG B 201 " - " ASN B  19 "
      " NAG C 201 " - " ASN C  19 "
      " NAG D 201 " - " ASN D  19 "
      " NAG E 201 " - " ASN E  19 "
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 344.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1030

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 13 sheets defined
      4.3% alpha, 35.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 69
      removed outlier: 3.789A  pdb=" N   THR A  69 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 69
      removed outlier: 3.785A  pdb=" N   THR B  69 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 65 through 69
      removed outlier: 3.700A  pdb=" N   THR C  69 " --> pdb=" O   SER C  66 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 65 through 69
      removed outlier: 3.765A  pdb=" N   THR D  69 " --> pdb=" O   SER D  66 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 65 through 69
      removed outlier: 3.585A  pdb=" N   THR E  69 " --> pdb=" O   SER E  66 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 2 through 5
      removed outlier: 6.270A  pdb=" N   GLU B   3 " --> pdb=" O   LEU D   4 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   GLU A   3 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 9 through 12
      removed outlier: 6.421A  pdb=" N   VAL A  10 " --> pdb=" O   SER C  11 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   VAL C  10 " --> pdb=" O   SER E  11 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 17 through 23
      removed outlier: 6.771A  pdb=" N   ALA A  18 " --> pdb=" O   ASN C  19 " (cutoff:3.500A)
      removed outlier: 7.792A  pdb=" N   THR C  21 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ILE A  20 " --> pdb=" O   THR C  21 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   SER C  23 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   CYS A  22 " --> pdb=" O   SER C  23 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ALA C  18 " --> pdb=" O   ASN E  19 " (cutoff:3.500A)
      removed outlier: 7.875A  pdb=" N   THR E  21 " --> pdb=" O   ALA C  18 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ILE C  20 " --> pdb=" O   THR E  21 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   SER E  23 " --> pdb=" O   ILE C  20 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   CYS C  22 " --> pdb=" O   SER E  23 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 26 through 30
      removed outlier: 6.817A  pdb=" N   TYR B  26 " --> pdb=" O   LEU D  27 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   GLU D  29 " --> pdb=" O   TYR B  26 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   GLY B  28 " --> pdb=" O   GLU D  29 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   TYR A  26 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
      removed outlier: 7.333A  pdb=" N   GLU B  29 " --> pdb=" O   TYR A  26 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   GLY A  28 " --> pdb=" O   GLU B  29 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   LEU A  27 " --> pdb=" O   GLY C  28 " (cutoff:3.500A)
      removed outlier: 7.463A  pdb=" N   THR C  30 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   GLU A  29 " --> pdb=" O   THR C  30 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 36 through 37
      removed outlier: 6.541A  pdb=" N   GLN A  36 " --> pdb=" O   GLN C  37 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   GLN C  36 " --> pdb=" O   GLN E  37 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 44 through 51
      removed outlier: 6.726A  pdb=" N   VAL B  44 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
      removed outlier: 7.993A  pdb=" N   ILE D  47 " --> pdb=" O   VAL B  44 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   VAL B  46 " --> pdb=" O   ILE D  47 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   GLN D  49 " --> pdb=" O   VAL B  46 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   TYR B  48 " --> pdb=" O   GLN D  49 " (cutoff:3.500A)
      removed outlier: 8.359A  pdb=" N   SER D  51 " --> pdb=" O   TYR B  48 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   SER B  50 " --> pdb=" O   SER D  51 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   VAL A  44 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   ILE B  47 " --> pdb=" O   VAL A  44 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   VAL A  46 " --> pdb=" O   ILE B  47 " (cutoff:3.500A)
      removed outlier: 7.994A  pdb=" N   GLN B  49 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   TYR A  48 " --> pdb=" O   GLN B  49 " (cutoff:3.500A)
      removed outlier: 8.541A  pdb=" N   SER B  51 " --> pdb=" O   TYR A  48 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   SER A  50 " --> pdb=" O   SER B  51 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 72 through 75
      removed outlier: 6.127A  pdb=" N   THR B  73 " --> pdb=" O   ILE D  74 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   THR A  73 " --> pdb=" O   ILE B  74 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   LEU C  72 " --> pdb=" O   THR E  73 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   SER E  75 " --> pdb=" O   LEU C  72 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ILE C  74 " --> pdb=" O   SER E  75 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 83 through 86
      removed outlier: 6.612A  pdb=" N   ALA B  83 " --> pdb=" O   ASP D  84 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   PHE D  86 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   TYR B  85 " --> pdb=" O   PHE D  86 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ALA A  83 " --> pdb=" O   ASP B  84 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   PHE B  86 " --> pdb=" O   ALA A  83 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   TYR A  85 " --> pdb=" O   PHE B  86 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 89 through 92
      removed outlier: 6.831A  pdb=" N   ALA B  89 " --> pdb=" O   TRP D  90 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   PHE D  92 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ASP B  91 " --> pdb=" O   PHE D  92 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   TRP A  90 " --> pdb=" O   ASP C  91 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   TRP C  90 " --> pdb=" O   ASP E  91 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 95 through 97
      removed outlier: 5.482A  pdb=" N   VAL B  96 " --> pdb=" O   PHE D  97 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   VAL A  96 " --> pdb=" O   PHE B  97 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   VAL C  96 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   VAL E  96 " --> pdb=" O   VAL C  95 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 102 through 107
      removed outlier: 6.806A  pdb=" N   LEU A 103 " --> pdb=" O   THR C 104 " (cutoff:3.500A)
      removed outlier: 7.645A  pdb=" N   LEU C 106 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   VAL A 105 " --> pdb=" O   LEU C 106 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   LEU C 103 " --> pdb=" O   THR E 104 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   LEU E 106 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   VAL C 105 " --> pdb=" O   LEU E 106 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 110 through 111
      removed outlier: 6.691A  pdb=" N   LYS B 110 " --> pdb=" O   ALA D 111 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LYS A 110 " --> pdb=" O   ALA B 111 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 114 through 116

    77 hydrogen bonds defined for protein.
    216 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: 1.79

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 4190
        1.03 -     1.23: 28
        1.23 -     1.42: 1902
        1.42 -     1.62: 2575
        1.62 -     1.82: 10
  Bond restraints: 8705
  Sorted by residual:
  bond pdb=" C   THR D  69 "
       pdb=" N   ALA D  70 "
    ideal  model  delta    sigma   weight residual
    1.332  1.354 -0.022 1.40e-02 5.10e+03 2.41e+00
  bond pdb=" C   THR B  69 "
       pdb=" N   ALA B  70 "
    ideal  model  delta    sigma   weight residual
    1.332  1.353 -0.021 1.40e-02 5.10e+03 2.21e+00
  bond pdb=" CB  ASP E  84 "
       pdb=" CG  ASP E  84 "
    ideal  model  delta    sigma   weight residual
    1.516  1.479  0.037 2.50e-02 1.60e+03 2.16e+00
  bond pdb=" N   THR B  69 "
       pdb=" CA  THR B  69 "
    ideal  model  delta    sigma   weight residual
    1.455  1.473 -0.018 1.27e-02 6.20e+03 2.03e+00
  bond pdb=" CB  TRP E  34 "
       pdb=" CG  TRP E  34 "
    ideal  model  delta    sigma   weight residual
    1.498  1.454  0.044 3.10e-02 1.04e+03 2.02e+00
  ... (remaining 8700 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 14692
        1.65 -     3.30: 802
        3.30 -     4.95: 114
        4.95 -     6.60: 36
        6.60 -     8.26: 6
  Bond angle restraints: 15650
  Sorted by residual:
  angle pdb=" C   ARG C  53 "
        pdb=" CA  ARG C  53 "
        pdb=" CB  ARG C  53 "
      ideal   model   delta    sigma   weight residual
     110.81  105.47    5.34 1.27e+00 6.20e-01 1.77e+01
  angle pdb=" C   ARG A  53 "
        pdb=" CA  ARG A  53 "
        pdb=" CB  ARG A  53 "
      ideal   model   delta    sigma   weight residual
     110.81  105.70    5.11 1.27e+00 6.20e-01 1.62e+01
  angle pdb=" C   ARG E  53 "
        pdb=" CA  ARG E  53 "
        pdb=" CB  ARG E  53 "
      ideal   model   delta    sigma   weight residual
     110.81  105.97    4.84 1.27e+00 6.20e-01 1.46e+01
  angle pdb=" N   ALA E  18 "
        pdb=" CA  ALA E  18 "
        pdb=" C   ALA E  18 "
      ideal   model   delta    sigma   weight residual
     108.69  115.08   -6.39 1.77e+00 3.19e-01 1.30e+01
  angle pdb=" N   GLY E  63 "
        pdb=" CA  GLY E  63 "
        pdb=" C   GLY E  63 "
      ideal   model   delta    sigma   weight residual
     113.18  104.92    8.26 2.37e+00 1.78e-01 1.21e+01
  ... (remaining 15645 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.29: 3631
       13.29 -    26.58: 385
       26.58 -    39.86: 114
       39.86 -    53.15: 83
       53.15 -    66.44: 82
  Dihedral angle restraints: 4295
    sinusoidal: 2375
      harmonic: 1920
  Sorted by residual:
  dihedral pdb=" CA  ALA B  70 "
           pdb=" C   ALA B  70 "
           pdb=" N   THR B  71 "
           pdb=" CA  THR B  71 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.19  -15.81     0      5.00e+00 4.00e-02 9.99e+00
  dihedral pdb=" CA  ALA A  70 "
           pdb=" C   ALA A  70 "
           pdb=" N   THR A  71 "
           pdb=" CA  THR A  71 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.34  -15.66     0      5.00e+00 4.00e-02 9.81e+00
  dihedral pdb=" CA  ALA C  70 "
           pdb=" C   ALA C  70 "
           pdb=" N   THR C  71 "
           pdb=" CA  THR C  71 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.60  -15.40     0      5.00e+00 4.00e-02 9.49e+00
  ... (remaining 4292 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 585
       0.082 -    0.165: 107
       0.165 -    0.247: 3
       0.247 -    0.329: 1
       0.329 -    0.411: 4
  Chirality restraints: 700
  Sorted by residual:
  chirality pdb=" C1  NAG D 201 "
            pdb=" ND2 ASN D  19 "
            pdb=" C2  NAG D 201 "
            pdb=" O5  NAG D 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.99   -0.41 2.00e-01 2.50e+01 4.23e+00
  chirality pdb=" C1  NAG A 201 "
            pdb=" ND2 ASN A  19 "
            pdb=" C2  NAG A 201 "
            pdb=" O5  NAG A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.05   -0.35 2.00e-01 2.50e+01 3.05e+00
  chirality pdb=" C1  NAG E 201 "
            pdb=" ND2 ASN E  19 "
            pdb=" C2  NAG E 201 "
            pdb=" O5  NAG E 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.05   -0.35 2.00e-01 2.50e+01 3.01e+00
  ... (remaining 697 not shown)

  Planarity restraints: 1335
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  90 "   -0.007 2.00e-02 2.50e+03   1.30e-02 6.81e+00
        pdb=" CG  TRP B  90 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  90 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  90 "    0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  90 "   -0.030 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  90 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  90 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  90 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  90 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  90 "   -0.009 2.00e-02 2.50e+03
        pdb=" HD1 TRP B  90 "   -0.005 2.00e-02 2.50e+03
        pdb=" HE1 TRP B  90 "    0.022 2.00e-02 2.50e+03
        pdb=" HE3 TRP B  90 "    0.002 2.00e-02 2.50e+03
        pdb=" HZ2 TRP B  90 "    0.010 2.00e-02 2.50e+03
        pdb=" HZ3 TRP B  90 "   -0.016 2.00e-02 2.50e+03
        pdb=" HH2 TRP B  90 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E  90 "   -0.006 2.00e-02 2.50e+03   1.29e-02 6.66e+00
        pdb=" CG  TRP E  90 "    0.015 2.00e-02 2.50e+03
        pdb=" CD1 TRP E  90 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP E  90 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP E  90 "   -0.031 2.00e-02 2.50e+03
        pdb=" CE2 TRP E  90 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP E  90 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E  90 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E  90 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP E  90 "   -0.007 2.00e-02 2.50e+03
        pdb=" HD1 TRP E  90 "   -0.003 2.00e-02 2.50e+03
        pdb=" HE1 TRP E  90 "    0.023 2.00e-02 2.50e+03
        pdb=" HE3 TRP E  90 "    0.002 2.00e-02 2.50e+03
        pdb=" HZ2 TRP E  90 "    0.009 2.00e-02 2.50e+03
        pdb=" HZ3 TRP E  90 "   -0.016 2.00e-02 2.50e+03
        pdb=" HH2 TRP E  90 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C  90 "   -0.004 2.00e-02 2.50e+03   1.28e-02 6.56e+00
        pdb=" CG  TRP C  90 "    0.014 2.00e-02 2.50e+03
        pdb=" CD1 TRP C  90 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP C  90 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP C  90 "   -0.032 2.00e-02 2.50e+03
        pdb=" CE2 TRP C  90 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP C  90 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C  90 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C  90 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP C  90 "   -0.007 2.00e-02 2.50e+03
        pdb=" HD1 TRP C  90 "   -0.003 2.00e-02 2.50e+03
        pdb=" HE1 TRP C  90 "    0.022 2.00e-02 2.50e+03
        pdb=" HE3 TRP C  90 "    0.001 2.00e-02 2.50e+03
        pdb=" HZ2 TRP C  90 "    0.009 2.00e-02 2.50e+03
        pdb=" HZ3 TRP C  90 "   -0.016 2.00e-02 2.50e+03
        pdb=" HH2 TRP C  90 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1332 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 823
        2.21 -     2.81: 17824
        2.81 -     3.41: 21009
        3.41 -     4.00: 30585
        4.00 -     4.60: 43592
  Nonbonded interactions: 113833
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B   3 "
            pdb=" HG1 THR B   5 "
     model   vdw
     1.615 2.450
  nonbonded pdb=" OE2 GLU D   3 "
            pdb=" HG1 THR D   5 "
     model   vdw
     1.626 2.450
  nonbonded pdb=" OE2 GLU C   3 "
            pdb=" HG1 THR C   5 "
     model   vdw
     1.632 2.450
  nonbonded pdb=" HZ2 LYS C  38 "
            pdb=" OD2 ASP C  81 "
     model   vdw
     1.636 2.450
  nonbonded pdb=" OE2 GLU E   3 "
            pdb=" HG1 THR E   5 "
     model   vdw
     1.637 2.450
  ... (remaining 113828 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.530
  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:             0.050
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.100
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6392
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      :  0.007   0.044   4525  Z= 0.330
  Angle     :  1.196   8.255   6185  Z= 0.657
  Chirality :  0.066   0.411    700
  Planarity :  0.009   0.063    795
  Dihedral  : 11.943  66.436   1675
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.35 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.002   ARG D  53 
 TYR   0.020   0.005   TYR D  35 
 PHE   0.035   0.005   PHE C  86 
 TRP   0.017   0.007   TRP B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00689 ( 4515)
  covalent geometry    : angle       1.17134 ( 6160)
  SS BOND              : bond        0.00736 (    5)
  SS BOND              : angle       1.44899 (   10)
  hydrogen bonds       : bond        0.22845 (   77)
  hydrogen bonds       : angle       8.62391 (  216)
  link_NAG-ASN         : bond        0.00866 (    5)
  link_NAG-ASN         : angle       4.95038 (   15)

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 GLN cc_start: 0.6769 (pm20) cc_final: 0.6127 (pp30)
REVERT: A   27 LEU cc_start: 0.7324 (mp) cc_final: 0.6967 (mt)
REVERT: A   75 SER cc_start: 0.7308 (t) cc_final: 0.7057 (m)
REVERT: A   77 THR cc_start: 0.7512 (p) cc_final: 0.7215 (m)
REVERT: B   16 GLN cc_start: 0.6259 (pm20) cc_final: 0.5670 (pp30)
REVERT: D    6 GLN cc_start: 0.7085 (pt0) cc_final: 0.6735 (mp10)
REVERT: D   16 GLN cc_start: 0.6956 (pm20) cc_final: 0.6032 (pp30)
REVERT: D   52 LYS cc_start: 0.6127 (tttt) cc_final: 0.4451 (pttm)
REVERT: E   52 LYS cc_start: 0.5994 (tttt) cc_final: 0.5632 (mtpt)
REVERT: E   75 SER cc_start: 0.7304 (t) cc_final: 0.7000 (m)
REVERT: E   82 GLU cc_start: 0.7323 (mm-30) cc_final: 0.5806 (pp20)
REVERT: E   93 THR cc_start: 0.8219 (m) cc_final: 0.7898 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1499
  time to fit residues: 25.4360
Evaluate side-chains
  94 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0020
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.6388

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
A  49 GLN
A  65 ASN
B   6 GLN
B  49 GLN
B  65 ASN
C   6 GLN
C  65 ASN
D   6 GLN
D  49 GLN
E  49 GLN
E  65 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.161852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.144338 restraints weight = 25982.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.148264 restraints weight = 12021.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.150725 restraints weight = 6962.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.152080 restraints weight = 4761.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.153135 restraints weight = 3760.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.4568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6406
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4525  Z= 0.137
  Angle     :  0.723   6.270   6185  Z= 0.369
  Chirality :  0.055   0.340    700
  Planarity :  0.007   0.043    795
  Dihedral  :  6.348  28.790    725
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 11.55 %
    Favored  : 87.22 %
  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 aren not related in a simple way.
  whole: -3.98 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.03 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  32 
 TYR   0.010   0.001   TYR D  35 
 PHE   0.011   0.001   PHE A   2 
 TRP   0.007   0.001   TRP A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 4515)
  covalent geometry    : angle       0.68667 ( 6160)
  SS BOND              : bond        0.00052 (    5)
  SS BOND              : angle       0.55876 (   10)
  hydrogen bonds       : bond        0.04967 (   77)
  hydrogen bonds       : angle       6.27838 (  216)
  link_NAG-ASN         : bond        0.00412 (    5)
  link_NAG-ASN         : angle       4.66693 (   15)

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   78 GLN cc_start: 0.7662 (tt0) cc_final: 0.7400 (tt0)
REVERT: C   77 THR cc_start: 0.7340 (p) cc_final: 0.7116 (m)
REVERT: D   16 GLN cc_start: 0.6717 (pm20) cc_final: 0.6309 (pp30)
REVERT: D   52 LYS cc_start: 0.6213 (tttt) cc_final: 0.4632 (pttm)
REVERT: E   52 LYS cc_start: 0.5980 (tttt) cc_final: 0.5645 (mtpt)
REVERT: E   75 SER cc_start: 0.7447 (t) cc_final: 0.7214 (m)
REVERT: E   82 GLU cc_start: 0.7221 (mm-30) cc_final: 0.5878 (pp20)
REVERT: E   93 THR cc_start: 0.8188 (m) cc_final: 0.7935 (p)
  outliers start: 6
  outliers final: 4
  residues processed: 103
  average time/residue: 0.1318
  time to fit residues: 18.0697
Evaluate side-chains
  92 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue  104 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
C  37 GLN
E  37 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4651 r_free = 0.4651 target = 0.157935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.142153 restraints weight = 26500.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.145700 restraints weight = 12345.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.147858 restraints weight = 7224.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.149126 restraints weight = 4995.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.149923 restraints weight = 3935.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.4558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6589
moved from start:          0.3022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   4525  Z= 0.240
  Angle     :  0.786   7.046   6185  Z= 0.403
  Chirality :  0.056   0.362    700
  Planarity :  0.008   0.047    795
  Dihedral  :  7.122  31.878    725
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 14.02 %
    Favored  : 83.71 %
  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 aren not related in a simple way.
  whole: -4.13 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.14 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E  53 
 TYR   0.013   0.002   TYR D  35 
 PHE   0.017   0.002   PHE C  86 
 TRP   0.011   0.002   TRP D  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 4515)
  covalent geometry    : angle       0.75940 ( 6160)
  SS BOND              : bond        0.00478 (    5)
  SS BOND              : angle       0.77443 (   10)
  hydrogen bonds       : bond        0.04495 (   77)
  hydrogen bonds       : angle       5.59731 (  216)
  link_NAG-ASN         : bond        0.00379 (    5)
  link_NAG-ASN         : angle       4.15679 (   15)

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ASN cc_start: 0.3209 (OUTLIER) cc_final: 0.2867 (m110)
REVERT: A   80 LEU cc_start: 0.8082 (mp) cc_final: 0.7756 (mp)
REVERT: D   16 GLN cc_start: 0.6820 (pm20) cc_final: 0.6418 (pp30)
REVERT: D   52 LYS cc_start: 0.6591 (tttt) cc_final: 0.4790 (pttm)
REVERT: E   75 SER cc_start: 0.7960 (t) cc_final: 0.7690 (m)
  outliers start: 11
  outliers final: 7
  residues processed: 102
  average time/residue: 0.1235
  time to fit residues: 16.8736
Evaluate side-chains
  99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue  104 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 6 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B  65 ASN
C  49 GLN
** C  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.159640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.143184 restraints weight = 26228.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.146927 restraints weight = 12176.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.149192 restraints weight = 7081.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.150502 restraints weight = 4880.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.151394 restraints weight = 3821.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.4581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6511
moved from start:          0.3435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4525  Z= 0.127
  Angle     :  0.634   5.409   6185  Z= 0.321
  Chirality :  0.053   0.320    700
  Planarity :  0.007   0.044    795
  Dihedral  :  5.941  20.046    725
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.91 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.98 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.02 (0.19), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  32 
 TYR   0.010   0.001   TYR A  26 
 PHE   0.010   0.001   PHE E  92 
 TRP   0.005   0.001   TRP A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 4515)
  covalent geometry    : angle       0.60570 ( 6160)
  SS BOND              : bond        0.00198 (    5)
  SS BOND              : angle       0.48428 (   10)
  hydrogen bonds       : bond        0.03310 (   77)
  hydrogen bonds       : angle       5.32048 (  216)
  link_NAG-ASN         : bond        0.00396 (    5)
  link_NAG-ASN         : angle       3.88033 (   15)

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TYR cc_start: 0.7921 (m-80) cc_final: 0.7711 (m-80)
REVERT: A   65 ASN cc_start: 0.2742 (OUTLIER) cc_final: 0.2415 (m110)
REVERT: D   16 GLN cc_start: 0.6925 (pm20) cc_final: 0.6392 (pp30)
REVERT: D   52 LYS cc_start: 0.6525 (tttt) cc_final: 0.4735 (pttm)
REVERT: E   75 SER cc_start: 0.7981 (t) cc_final: 0.7715 (m)
REVERT: E   82 GLU cc_start: 0.7282 (mm-30) cc_final: 0.5928 (pp20)
  outliers start: 8
  outliers final: 6
  residues processed: 102
  average time/residue: 0.1290
  time to fit residues: 17.5205
Evaluate side-chains
  99 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain B residue   65 ASN
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue  104 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0470
   chunk 15 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.7480

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

Flipped N/Q/H residues before XYZ refinement:
** C  88 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 = 0.4684 r_free = 0.4684 target = 0.160027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.143428 restraints weight = 26009.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.147095 restraints weight = 12204.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.149376 restraints weight = 7181.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.150767 restraints weight = 4933.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.151683 restraints weight = 3854.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.4590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6511
moved from start:          0.3603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4525  Z= 0.120
  Angle     :  0.608   5.140   6185  Z= 0.307
  Chirality :  0.052   0.304    700
  Planarity :  0.007   0.043    795
  Dihedral  :  5.810  20.963    725
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 17.53 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.89 (0.25), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.96 (0.19), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  32 
 TYR   0.009   0.001   TYR A  26 
 PHE   0.012   0.001   PHE A  61 
 TRP   0.004   0.001   TRP D  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 4515)
  covalent geometry    : angle       0.58534 ( 6160)
  SS BOND              : bond        0.00129 (    5)
  SS BOND              : angle       0.62261 (   10)
  hydrogen bonds       : bond        0.03249 (   77)
  hydrogen bonds       : angle       5.21330 (  216)
  link_NAG-ASN         : bond        0.00206 (    5)
  link_NAG-ASN         : angle       3.36485 (   15)

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ASN cc_start: 0.2514 (OUTLIER) cc_final: 0.2186 (m110)
REVERT: D   16 GLN cc_start: 0.6933 (pm20) cc_final: 0.6420 (pp30)
REVERT: D   52 LYS cc_start: 0.6543 (tttt) cc_final: 0.4772 (pttm)
REVERT: E   75 SER cc_start: 0.7990 (t) cc_final: 0.7743 (m)
REVERT: E   82 GLU cc_start: 0.7243 (mm-30) cc_final: 0.5913 (pp20)
  outliers start: 8
  outliers final: 4
  residues processed: 98
  average time/residue: 0.1357
  time to fit residues: 17.6680
Evaluate side-chains
  97 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue  104 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0010
   chunk 30 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.7190

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

Flipped N/Q/H residues before XYZ refinement:
** C  88 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 = 0.4700 r_free = 0.4700 target = 0.161540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.144710 restraints weight = 26096.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.148414 restraints weight = 12453.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4559 r_free = 0.4559 target = 0.150700 restraints weight = 7365.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.152102 restraints weight = 5109.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.152990 restraints weight = 4008.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.4594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6505
moved from start:          0.3817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4525  Z= 0.109
  Angle     :  0.567   5.454   6185  Z= 0.285
  Chirality :  0.051   0.282    700
  Planarity :  0.006   0.042    795
  Dihedral  :  5.475  20.648    725
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 17.94 %
    Favored  : 80.21 %
  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 aren not related in a simple way.
  whole: -3.77 (0.25), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.87 (0.19), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  53 
 TYR   0.012   0.001   TYR A  26 
 PHE   0.017   0.001   PHE B  61 
 TRP   0.004   0.001   TRP D  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 4515)
  covalent geometry    : angle       0.54874 ( 6160)
  SS BOND              : bond        0.00102 (    5)
  SS BOND              : angle       0.78429 (   10)
  hydrogen bonds       : bond        0.02594 (   77)
  hydrogen bonds       : angle       5.05211 (  216)
  link_NAG-ASN         : bond        0.00200 (    5)
  link_NAG-ASN         : angle       2.90993 (   15)

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ASN cc_start: 0.2399 (OUTLIER) cc_final: 0.2083 (m110)
REVERT: D   16 GLN cc_start: 0.6952 (pm20) cc_final: 0.6391 (pp30)
REVERT: D   52 LYS cc_start: 0.6588 (tttt) cc_final: 0.4799 (pttm)
REVERT: E   75 SER cc_start: 0.8001 (t) cc_final: 0.7781 (m)
  outliers start: 9
  outliers final: 8
  residues processed: 97
  average time/residue: 0.1186
  time to fit residues: 15.1397
Evaluate side-chains
  98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue  104 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
C  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.160302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.143512 restraints weight = 26353.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.147281 restraints weight = 12403.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.149576 restraints weight = 7356.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.150989 restraints weight = 5114.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.151871 restraints weight = 4012.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.4592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6541
moved from start:          0.3988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4525  Z= 0.133
  Angle     :  0.574   4.792   6185  Z= 0.288
  Chirality :  0.051   0.283    700
  Planarity :  0.006   0.041    795
  Dihedral  :  5.632  23.471    725
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 17.94 %
    Favored  : 80.00 %
  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 aren not related in a simple way.
  whole: -3.87 (0.25), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.94 (0.19), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  53 
 TYR   0.010   0.001   TYR A  26 
 PHE   0.012   0.001   PHE E  61 
 TRP   0.007   0.001   TRP E  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 4515)
  covalent geometry    : angle       0.55868 ( 6160)
  SS BOND              : bond        0.00281 (    5)
  SS BOND              : angle       0.80662 (   10)
  hydrogen bonds       : bond        0.02666 (   77)
  hydrogen bonds       : angle       4.95962 (  216)
  link_NAG-ASN         : bond        0.00092 (    5)
  link_NAG-ASN         : angle       2.73000 (   15)

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ASN cc_start: 0.2444 (OUTLIER) cc_final: 0.2118 (m110)
REVERT: D   16 GLN cc_start: 0.7053 (pm20) cc_final: 0.6383 (pp30)
REVERT: D   52 LYS cc_start: 0.6624 (tttt) cc_final: 0.4829 (pttm)
REVERT: E   75 SER cc_start: 0.8049 (t) cc_final: 0.7797 (m)
REVERT: E   82 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6017 (pt0)
  outliers start: 10
  outliers final: 8
  residues processed: 96
  average time/residue: 0.1300
  time to fit residues: 16.4735
Evaluate side-chains
  98 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue   88 GLN
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue  104 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** C  88 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 = 0.4671 r_free = 0.4671 target = 0.157251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.140954 restraints weight = 26176.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.144611 restraints weight = 12502.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.146956 restraints weight = 7431.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.148277 restraints weight = 5148.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.149123 restraints weight = 4027.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.4575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6608
moved from start:          0.4144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   4525  Z= 0.217
  Angle     :  0.668   6.006   6185  Z= 0.340
  Chirality :  0.053   0.321    700
  Planarity :  0.007   0.041    795
  Dihedral  :  6.326  30.125    725
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.94 %
    Favored  : 79.59 %
  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 aren not related in a simple way.
  whole: -4.10 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.12 (0.18), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  53 
 TYR   0.024   0.002   TYR C  85 
 PHE   0.014   0.002   PHE E  61 
 TRP   0.008   0.002   TRP E  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 4515)
  covalent geometry    : angle       0.65255 ( 6160)
  SS BOND              : bond        0.00374 (    5)
  SS BOND              : angle       1.01561 (   10)
  hydrogen bonds       : bond        0.03262 (   77)
  hydrogen bonds       : angle       5.03418 (  216)
  link_NAG-ASN         : bond        0.00424 (    5)
  link_NAG-ASN         : angle       2.87897 (   15)

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ASN cc_start: 0.2433 (OUTLIER) cc_final: 0.2033 (m110)
REVERT: D   16 GLN cc_start: 0.7259 (pm20) cc_final: 0.6409 (pp30)
REVERT: D   52 LYS cc_start: 0.6714 (tttt) cc_final: 0.4883 (pttm)
REVERT: E   75 SER cc_start: 0.8255 (t) cc_final: 0.7941 (m)
  outliers start: 12
  outliers final: 11
  residues processed: 100
  average time/residue: 0.1302
  time to fit residues: 17.3765
Evaluate side-chains
  104 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain A residue   85 TYR
Chi-restraints excluded: chain B residue   61 PHE
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue   17 THR
Chi-restraints excluded: chain E residue   65 ASN
Chi-restraints excluded: chain E residue  104 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   chunk 36 optimal weight:    0.1980
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** C  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  37 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.160690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.144487 restraints weight = 26198.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.148248 restraints weight = 12312.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4559 r_free = 0.4559 target = 0.150603 restraints weight = 7194.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.152080 restraints weight = 4888.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.152978 restraints weight = 3683.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.4610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6554
moved from start:          0.4313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4525  Z= 0.126
  Angle     :  0.577   4.683   6185  Z= 0.289
  Chirality :  0.052   0.299    700
  Planarity :  0.006   0.041    795
  Dihedral  :  5.609  22.436    725
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 18.56 %
    Favored  : 78.56 %
  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 aren not related in a simple way.
  whole: -4.04 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.07 (0.19), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  53 
 TYR   0.014   0.001   TYR A  26 
 PHE   0.010   0.001   PHE E  61 
 TRP   0.004   0.001   TRP A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4515)
  covalent geometry    : angle       0.55846 ( 6160)
  SS BOND              : bond        0.00123 (    5)
  SS BOND              : angle       0.76766 (   10)
  hydrogen bonds       : bond        0.02623 (   77)
  hydrogen bonds       : angle       4.95236 (  216)
  link_NAG-ASN         : bond        0.00229 (    5)
  link_NAG-ASN         : angle       2.97057 (   15)

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ASN cc_start: 0.2281 (OUTLIER) cc_final: 0.1901 (m110)
REVERT: D   16 GLN cc_start: 0.7234 (pm20) cc_final: 0.6425 (pp30)
REVERT: D   52 LYS cc_start: 0.6667 (tttt) cc_final: 0.4873 (pttm)
REVERT: E   75 SER cc_start: 0.8199 (t) cc_final: 0.7805 (m)
REVERT: E   82 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6015 (pt0)
  outliers start: 14
  outliers final: 13
  residues processed: 101
  average time/residue: 0.1231
  time to fit residues: 16.6540
Evaluate side-chains
  105 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   61 PHE
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue   16 GLN
Chi-restraints excluded: chain E residue   17 THR
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   65 ASN
Chi-restraints excluded: chain E residue  104 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 13 optimal weight:    0.4980
   chunk 42 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.161722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.145195 restraints weight = 26297.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.149053 restraints weight = 12352.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.151371 restraints weight = 7191.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.152817 restraints weight = 4956.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.153741 restraints weight = 3796.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.4599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6535
moved from start:          0.4381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4525  Z= 0.111
  Angle     :  0.556   4.640   6185  Z= 0.278
  Chirality :  0.051   0.278    700
  Planarity :  0.006   0.042    795
  Dihedral  :  5.470  21.603    725
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 18.35 %
    Favored  : 78.76 %
  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 aren not related in a simple way.
  whole: -4.02 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.06 (0.19), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  32 
 TYR   0.015   0.001   TYR A  26 
 PHE   0.011   0.001   PHE B  61 
 TRP   0.004   0.001   TRP D  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 4515)
  covalent geometry    : angle       0.54112 ( 6160)
  SS BOND              : bond        0.00093 (    5)
  SS BOND              : angle       0.61499 (   10)
  hydrogen bonds       : bond        0.02474 (   77)
  hydrogen bonds       : angle       4.89896 (  216)
  link_NAG-ASN         : bond        0.00164 (    5)
  link_NAG-ASN         : angle       2.60174 (   15)

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

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

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1150 Ramachandran restraints generated.
    575 Oldfield, 0 Emsley, 575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 ASN cc_start: 0.2251 (OUTLIER) cc_final: 0.1845 (m110)
REVERT: D   16 GLN cc_start: 0.7251 (pm20) cc_final: 0.6362 (pp30)
REVERT: D   52 LYS cc_start: 0.6751 (tttt) cc_final: 0.4888 (pttm)
REVERT: E   75 SER cc_start: 0.8143 (t) cc_final: 0.7829 (m)
REVERT: E   82 GLU cc_start: 0.7221 (mm-30) cc_final: 0.5874 (pt0)
  outliers start: 14
  outliers final: 12
  residues processed: 102
  average time/residue: 0.1165
  time to fit residues: 15.9710
Evaluate side-chains
  106 residues out of total 485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ASN
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   61 PHE
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   51 SER
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue   17 THR
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   65 ASN
Chi-restraints excluded: chain E residue  104 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4697 r_free = 0.4697 target = 0.161948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.145565 restraints weight = 26948.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.149432 restraints weight = 12509.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.151820 restraints weight = 7283.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.153190 restraints weight = 4976.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.154110 restraints weight = 3836.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.4605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6544
moved from start:          0.4515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4525  Z= 0.127
  Angle     :  0.568   4.664   6185  Z= 0.285
  Chirality :  0.051   0.274    700
  Planarity :  0.006   0.042    795
  Dihedral  :  5.603  24.308    725
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 18.14 %
    Favored  : 78.76 %
  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 aren not related in a simple way.
  whole: -4.12 (0.24), residues: 575
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.13 (0.19), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  53 
 TYR   0.014   0.001   TYR A  26 
 PHE   0.013   0.001   PHE E  61 
 TRP   0.006   0.001   TRP D  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 4515)
  covalent geometry    : angle       0.55475 ( 6160)
  SS BOND              : bond        0.00125 (    5)
  SS BOND              : angle       0.74705 (   10)
  hydrogen bonds       : bond        0.02522 (   77)
  hydrogen bonds       : angle       4.83388 (  216)
  link_NAG-ASN         : bond        0.00149 (    5)
  link_NAG-ASN         : angle       2.50266 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1997.08 seconds
wall clock time: 34 minutes 41.04 seconds (2081.04 seconds total)