Starting phenix.real_space_refine
on Thu Mar 13 07:44:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9faa_50270/03_2025/9faa_50270_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9faa_50270/03_2025/9faa_50270.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9faa_50270/03_2025/9faa_50270.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9faa_50270/03_2025/9faa_50270.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9faa_50270/03_2025/9faa_50270_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9faa_50270/03_2025/9faa_50270_trim.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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    2815      2.51       5
     N     730      2.21       5
     O     905      1.98       5
     H    4235      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8695
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 1725
          Classifications: {'peptide': 118}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 108}
    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
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 4.23, per 1000 atoms: 0.49
  Number of scatterers: 8695
  At special positions: 0
  Unit cell: (88.011, 124.46, 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     905      8.00
     N     730      7.00
     C    2815      6.00
     H    4235      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 C  22 " - pdb=" SG  CYS C  87 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  87 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  87 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  87 " distance=2.02

  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: 2.21
  Conformation dependent library (CDL) restraints added in 840.3 milliseconds
  

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1040

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 37.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 2 through 5
      removed outlier: 6.194A  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: 6.360A  pdb=" N   VAL D  10 " --> pdb=" O   SER B  11 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   SER A   9 " --> pdb=" O   VAL B  10 " (cutoff:3.500A)
      removed outlier: 7.267A  pdb=" N   VAL B  12 " --> pdb=" O   SER A   9 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   SER A  11 " --> pdb=" O   VAL B  12 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 17 through 23
      removed outlier: 6.672A  pdb=" N   THR A  17 " --> pdb=" O   ALA B  18 " (cutoff:3.500A)
      removed outlier: 7.666A  pdb=" N   ILE B  20 " --> pdb=" O   THR A  17 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   ASN A  19 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
      removed outlier: 7.848A  pdb=" N   CYS B  22 " --> pdb=" O   ASN A  19 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   THR A  21 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 26 through 30
      removed outlier: 6.588A  pdb=" N   TYR A  26 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   GLU B  29 " --> pdb=" O   TYR A  26 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   GLY A  28 " --> pdb=" O   GLU B  29 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 36 through 37
      removed outlier: 6.779A  pdb=" N   GLN D  36 " --> pdb=" O   GLN B  37 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   GLN A  36 " --> pdb=" O   GLN C  37 " (cutoff:3.500A)
      removed outlier: 6.847A  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 52
      removed outlier: 6.662A  pdb=" N   VAL A  44 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      removed outlier: 8.183A  pdb=" N   ILE B  47 " --> pdb=" O   VAL A  44 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   VAL A  46 " --> pdb=" O   ILE B  47 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   GLN B  49 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   TYR A  48 " --> pdb=" O   GLN B  49 " (cutoff:3.500A)
      removed outlier: 8.500A  pdb=" N   SER B  51 " --> pdb=" O   TYR A  48 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   SER A  50 " --> pdb=" O   SER B  51 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 64 through 65
      removed outlier: 6.621A  pdb=" N   SER A  62 " --> pdb=" O   GLY B  63 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   ASN B  65 " --> pdb=" O   SER A  62 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   SER A  64 " --> pdb=" O   ASN B  65 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 72 through 75
      removed outlier: 6.788A  pdb=" N   LEU D  72 " --> pdb=" O   THR B  73 " (cutoff:3.500A)
      removed outlier: 8.221A  pdb=" N   SER B  75 " --> pdb=" O   LEU D  72 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ILE D  74 " --> pdb=" O   SER B  75 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   THR A  73 " --> pdb=" O   ILE B  74 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   LEU A  72 " --> pdb=" O   THR C  73 " (cutoff:3.500A)
      removed outlier: 8.237A  pdb=" N   SER C  75 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ILE A  74 " --> pdb=" O   SER C  75 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   LEU C  72 " --> pdb=" O   THR E  73 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   SER E  75 " --> pdb=" O   LEU C  72 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ILE C  74 " --> pdb=" O   SER E  75 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'D' and resid 84 through 86
      removed outlier: 6.542A  pdb=" N   ALA A  83 " --> pdb=" O   ASP B  84 " (cutoff:3.500A)
      removed outlier: 7.814A  pdb=" N   PHE B  86 " --> pdb=" O   ALA A  83 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   TYR A  85 " --> pdb=" O   PHE B  86 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 89 through 97
      removed outlier: 6.457A  pdb=" N   TRP D  90 " --> pdb=" O   ASP B  91 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   THR B  93 " --> pdb=" O   TRP D  90 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   PHE D  92 " --> pdb=" O   THR B  93 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   VAL B  95 " --> pdb=" O   PHE D  92 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   SER D  94 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   PHE B  97 " --> pdb=" O   SER D  94 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   VAL D  96 " --> pdb=" O   PHE B  97 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   PHE A  97 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   TRP A  90 " --> pdb=" O   ASP C  91 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   THR C  93 " --> pdb=" O   TRP A  90 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   PHE A  92 " --> pdb=" O   THR C  93 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   VAL C  95 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   SER A  94 " --> pdb=" O   VAL C  95 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   PHE C  97 " --> pdb=" O   SER A  94 " (cutoff:3.500A)
      removed outlier: 7.682A  pdb=" N   VAL A  96 " --> pdb=" O   PHE C  97 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   TRP C  90 " --> pdb=" O   ASP E  91 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   THR E  93 " --> pdb=" O   TRP C  90 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   PHE C  92 " --> pdb=" O   THR E  93 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   VAL E  95 " --> pdb=" O   PHE C  92 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   SER C  94 " --> pdb=" O   VAL E  95 " (cutoff:3.500A)
      removed outlier: 7.633A  pdb=" N   PHE E  97 " --> pdb=" O   SER C  94 " (cutoff:3.500A)
      removed outlier: 7.684A  pdb=" N   VAL C  96 " --> pdb=" O   PHE E  97 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 102 through 106
      removed outlier: 6.707A  pdb=" N   LEU D 103 " --> pdb=" O   THR B 104 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   LEU B 106 " --> pdb=" O   LEU D 103 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   VAL D 105 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   LEU A 103 " --> pdb=" O   THR C 104 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   LEU C 106 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   VAL A 105 " --> pdb=" O   LEU C 106 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   LEU C 103 " --> pdb=" O   THR E 104 " (cutoff:3.500A)
      removed outlier: 7.600A  pdb=" N   LEU E 106 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   VAL C 105 " --> pdb=" O   LEU E 106 " (cutoff:3.500A)

    93 hydrogen bonds defined for protein.
    270 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.06

  Time building geometry restraints manager: 2.74 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4235
        1.03 -     1.22: 5
        1.22 -     1.42: 1960
        1.42 -     1.61: 2600
        1.61 -     1.81: 10
  Bond restraints: 8810
  Sorted by residual:
  bond pdb=" CB  ILE E  20 "
       pdb=" CG2 ILE E  20 "
    ideal  model  delta    sigma   weight residual
    1.521  1.470  0.051 3.30e-02 9.18e+02 2.41e+00
  bond pdb=" CB  ILE B  20 "
       pdb=" CG2 ILE B  20 "
    ideal  model  delta    sigma   weight residual
    1.521  1.470  0.051 3.30e-02 9.18e+02 2.34e+00
  bond pdb=" CA  GLY C  67 "
       pdb=" C   GLY C  67 "
    ideal  model  delta    sigma   weight residual
    1.516  1.498  0.018 1.18e-02 7.18e+03 2.34e+00
  bond pdb=" CB  ILE C  20 "
       pdb=" CG2 ILE C  20 "
    ideal  model  delta    sigma   weight residual
    1.521  1.471  0.050 3.30e-02 9.18e+02 2.33e+00
  bond pdb=" CB  ILE A  20 "
       pdb=" CG2 ILE A  20 "
    ideal  model  delta    sigma   weight residual
    1.521  1.471  0.050 3.30e-02 9.18e+02 2.29e+00
  ... (remaining 8805 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 14447
        1.41 -     2.82: 1160
        2.82 -     4.23: 173
        4.23 -     5.64: 40
        5.64 -     7.05: 10
  Bond angle restraints: 15830
  Sorted by residual:
  angle pdb=" N   THR A  69 "
        pdb=" CA  THR A  69 "
        pdb=" C   THR A  69 "
      ideal   model   delta    sigma   weight residual
     109.94  102.89    7.05 1.57e+00 4.06e-01 2.02e+01
  angle pdb=" N   THR D  69 "
        pdb=" CA  THR D  69 "
        pdb=" C   THR D  69 "
      ideal   model   delta    sigma   weight residual
     109.94  102.91    7.03 1.57e+00 4.06e-01 2.00e+01
  angle pdb=" N   THR E  69 "
        pdb=" CA  THR E  69 "
        pdb=" C   THR E  69 "
      ideal   model   delta    sigma   weight residual
     109.94  102.93    7.01 1.57e+00 4.06e-01 1.99e+01
  angle pdb=" N   THR B  69 "
        pdb=" CA  THR B  69 "
        pdb=" C   THR B  69 "
      ideal   model   delta    sigma   weight residual
     109.94  102.93    7.01 1.57e+00 4.06e-01 1.99e+01
  angle pdb=" N   THR C  69 "
        pdb=" CA  THR C  69 "
        pdb=" C   THR C  69 "
      ideal   model   delta    sigma   weight residual
     109.94  102.95    6.99 1.57e+00 4.06e-01 1.98e+01
  ... (remaining 15825 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.86: 3772
       14.86 -    29.73: 338
       29.73 -    44.59: 115
       44.59 -    59.45: 95
       59.45 -    74.31: 30
  Dihedral angle restraints: 4350
    sinusoidal: 2390
      harmonic: 1960
  Sorted by residual:
  dihedral pdb=" CA  PHE B  61 "
           pdb=" C   PHE B  61 "
           pdb=" N   SER B  62 "
           pdb=" CA  SER B  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.55   15.45     0      5.00e+00 4.00e-02 9.55e+00
  dihedral pdb=" CA  PHE D  61 "
           pdb=" C   PHE D  61 "
           pdb=" N   SER D  62 "
           pdb=" CA  SER D  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.55   15.45     0      5.00e+00 4.00e-02 9.54e+00
  dihedral pdb=" CA  PHE E  61 "
           pdb=" C   PHE E  61 "
           pdb=" N   SER E  62 "
           pdb=" CA  SER E  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.56   15.44     0      5.00e+00 4.00e-02 9.54e+00
  ... (remaining 4347 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 476
       0.048 -    0.096: 181
       0.096 -    0.144: 43
       0.144 -    0.192: 0
       0.192 -    0.241: 5
  Chirality restraints: 705
  Sorted by residual:
  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   -2.16   -0.24 2.00e-01 2.50e+01 1.45e+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   -2.16   -0.24 2.00e-01 2.50e+01 1.43e+00
  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   -2.16   -0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 702 not shown)

  Planarity restraints: 1350
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN E  49 "    0.029 2.00e-02 2.50e+03   3.69e-02 2.04e+01
        pdb=" CD  GLN E  49 "   -0.022 2.00e-02 2.50e+03
        pdb=" OE1 GLN E  49 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE2 GLN E  49 "   -0.060 2.00e-02 2.50e+03
        pdb="HE21 GLN E  49 "   -0.001 2.00e-02 2.50e+03
        pdb="HE22 GLN E  49 "    0.056 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN D  49 "    0.029 2.00e-02 2.50e+03   3.68e-02 2.03e+01
        pdb=" CD  GLN D  49 "   -0.022 2.00e-02 2.50e+03
        pdb=" OE1 GLN D  49 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE2 GLN D  49 "   -0.060 2.00e-02 2.50e+03
        pdb="HE21 GLN D  49 "   -0.001 2.00e-02 2.50e+03
        pdb="HE22 GLN D  49 "    0.057 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A  49 "    0.029 2.00e-02 2.50e+03   3.68e-02 2.03e+01
        pdb=" CD  GLN A  49 "   -0.022 2.00e-02 2.50e+03
        pdb=" OE1 GLN A  49 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE2 GLN A  49 "   -0.060 2.00e-02 2.50e+03
        pdb="HE21 GLN A  49 "   -0.001 2.00e-02 2.50e+03
        pdb="HE22 GLN A  49 "    0.056 2.00e-02 2.50e+03
  ... (remaining 1347 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.09: 183
        2.09 -     2.72: 14912
        2.72 -     3.34: 22417
        3.34 -     3.97: 31298
        3.97 -     4.60: 46361
  Nonbonded interactions: 115171
  Sorted by model distance:
  nonbonded pdb=" H   ASN A  68 "
            pdb=" OD1 ASN B  68 "
     model   vdw
     1.461 2.450
  nonbonded pdb=" OD1 ASN A  68 "
            pdb=" H   ASN C  68 "
     model   vdw
     1.553 2.450
  nonbonded pdb=" OD1 ASN C  68 "
            pdb=" H   ASN E  68 "
     model   vdw
     1.598 2.450
  nonbonded pdb=" OD1 ASN D  68 "
            pdb=" H   ASN B  68 "
     model   vdw
     1.649 2.450
  nonbonded pdb="HG21 THR E  69 "
            pdb=" H   ALA E  70 "
     model   vdw
     1.788 2.270
  ... (remaining 115166 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.700
  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:             0.150
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.390
  Find NCS groups from input model:        0.140
  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:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
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      :  0.010   0.053   4575  Z= 0.678
  Angle     :  1.099   7.048   6240  Z= 0.623
  Chirality :  0.053   0.241    705
  Planarity :  0.006   0.042    805
  Dihedral  : 11.734  74.313   1690
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.21 (0.24), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.19), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.008   TRP E  90 
 PHE   0.021   0.005   PHE C  61 
 TYR   0.038   0.007   TYR B  85 
 ARG   0.009   0.003   ARG E  53 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 SER cc_start: 0.8275 (t) cc_final: 0.7998 (m)
REVERT: A   91 ASP cc_start: 0.7857 (t0) cc_final: 0.7645 (t0)
REVERT: A  108 GLN cc_start: 0.7845 (pt0) cc_final: 0.7535 (pp30)
REVERT: A  117 LEU cc_start: 0.5983 (mt) cc_final: 0.5694 (mt)
REVERT: D   49 GLN cc_start: 0.7584 (tt0) cc_final: 0.7383 (tt0)
REVERT: D  108 GLN cc_start: 0.7793 (pt0) cc_final: 0.7496 (pp30)
REVERT: C  108 GLN cc_start: 0.7868 (pt0) cc_final: 0.7408 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.3152
  time to fit residues: 31.5968
Evaluate side-chains
  48 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   chunk 22 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0070
   chunk 26 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   overall best weight:    0.7402

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  41 GLN
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  41 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.121745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.102802 restraints weight = 26528.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.106362 restraints weight = 10121.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.108650 restraints weight = 5289.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.4275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.1459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   4575  Z= 0.193
  Angle     :  0.601   4.284   6240  Z= 0.316
  Chirality :  0.051   0.254    705
  Planarity :  0.005   0.046    805
  Dihedral  :  6.096  23.213    730
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  4.90 %
    Favored  : 94.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.84 (0.25), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.19), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  34 
 PHE   0.014   0.001   PHE D   2 
 TYR   0.013   0.002   TYR C  85 
 ARG   0.003   0.000   ARG E  60 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.748 
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    8 SER cc_start: 0.8278 (t) cc_final: 0.7924 (m)
REVERT: A  108 GLN cc_start: 0.7842 (pt0) cc_final: 0.7518 (pp30)
REVERT: A  117 LEU cc_start: 0.6435 (mt) cc_final: 0.6231 (mt)
REVERT: D  108 GLN cc_start: 0.7777 (pt0) cc_final: 0.7337 (pp30)
REVERT: C   91 ASP cc_start: 0.7801 (t0) cc_final: 0.7354 (m-30)
REVERT: C  108 GLN cc_start: 0.7938 (pt0) cc_final: 0.7341 (pp30)
REVERT: E   91 ASP cc_start: 0.8044 (t0) cc_final: 0.7439 (m-30)
  outliers start: 5
  outliers final: 4
  residues processed: 63
  average time/residue: 0.2913
  time to fit residues: 24.8867
Evaluate side-chains
  53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain B residue   17 THR
Chi-restraints excluded: chain E residue   22 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 43 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 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 = 0.4362 r_free = 0.4362 target = 0.120776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.102281 restraints weight = 27113.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.105831 restraints weight = 10472.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.108165 restraints weight = 5500.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.4282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4575  Z= 0.190
  Angle     :  0.555   5.108   6240  Z= 0.287
  Chirality :  0.048   0.222    705
  Planarity :  0.005   0.046    805
  Dihedral  :  5.860  25.483    730
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  5.10 %
    Favored  : 92.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.81 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.89 (0.19), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  34 
 PHE   0.009   0.001   PHE D   2 
 TYR   0.012   0.001   TYR A  85 
 ARG   0.002   0.000   ARG C  60 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.706 
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    8 SER cc_start: 0.8258 (t) cc_final: 0.7839 (m)
REVERT: A  108 GLN cc_start: 0.7864 (pt0) cc_final: 0.7479 (pp30)
REVERT: D  108 GLN cc_start: 0.7907 (pt0) cc_final: 0.7480 (pp30)
REVERT: C  108 GLN cc_start: 0.7935 (pt0) cc_final: 0.7200 (pp30)
REVERT: E   60 ARG cc_start: 0.7825 (mmm160) cc_final: 0.7057 (ttm170)
REVERT: E   91 ASP cc_start: 0.8063 (t0) cc_final: 0.7394 (m-30)
  outliers start: 10
  outliers final: 9
  residues processed: 58
  average time/residue: 0.3849
  time to fit residues: 30.2541
Evaluate side-chains
  56 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   68 ASN
Chi-restraints excluded: chain C residue   17 THR
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain B residue   17 THR
Chi-restraints excluded: chain B residue   68 ASN
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   68 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 43 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 35 optimal weight:    0.7980
   chunk 17 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 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 = 0.4323 r_free = 0.4323 target = 0.118411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.100505 restraints weight = 27490.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.103923 restraints weight = 10672.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.105986 restraints weight = 5604.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.4245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.2482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4575  Z= 0.248
  Angle     :  0.575   3.904   6240  Z= 0.298
  Chirality :  0.048   0.200    705
  Planarity :  0.005   0.046    805
  Dihedral  :  6.348  34.178    730
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  6.12 %
    Favored  : 91.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.96 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.01 (0.20), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  34 
 PHE   0.011   0.001   PHE B  61 
 TYR   0.014   0.002   TYR D  85 
 ARG   0.002   0.000   ARG C  60 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.890 
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    8 SER cc_start: 0.8345 (t) cc_final: 0.7927 (m)
REVERT: A   91 ASP cc_start: 0.7688 (t0) cc_final: 0.7468 (t0)
REVERT: A  108 GLN cc_start: 0.7858 (pt0) cc_final: 0.6911 (pp30)
REVERT: D  108 GLN cc_start: 0.8100 (pt0) cc_final: 0.7533 (pp30)
REVERT: C  108 GLN cc_start: 0.7993 (pt0) cc_final: 0.7143 (pp30)
REVERT: B   69 THR cc_start: 0.7771 (m) cc_final: 0.7226 (p)
REVERT: E   91 ASP cc_start: 0.8011 (t0) cc_final: 0.7297 (m-30)
  outliers start: 10
  outliers final: 8
  residues processed: 65
  average time/residue: 0.2788
  time to fit residues: 24.7243
Evaluate side-chains
  59 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   68 ASN
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain B residue   68 ASN
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   68 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 44 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 25 optimal weight:    0.2980
   chunk 32 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 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 = 0.4347 r_free = 0.4347 target = 0.120259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.102175 restraints weight = 27304.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.105593 restraints weight = 10719.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.107791 restraints weight = 5680.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.4262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   4575  Z= 0.156
  Angle     :  0.534   3.875   6240  Z= 0.275
  Chirality :  0.048   0.221    705
  Planarity :  0.005   0.046    805
  Dihedral  :  5.863  28.954    730
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  :  6.73 %
    Favored  : 91.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.94 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.00 (0.20), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E  34 
 PHE   0.008   0.001   PHE A  61 
 TYR   0.009   0.001   TYR A  85 
 ARG   0.001   0.000   ARG E  60 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.675 
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    8 SER cc_start: 0.8377 (t) cc_final: 0.7960 (m)
REVERT: A  108 GLN cc_start: 0.7869 (pt0) cc_final: 0.6959 (pp30)
REVERT: D    8 SER cc_start: 0.8207 (OUTLIER) cc_final: 0.7867 (p)
REVERT: D  108 GLN cc_start: 0.8099 (pt0) cc_final: 0.7511 (pp30)
REVERT: C  108 GLN cc_start: 0.7969 (pt0) cc_final: 0.7155 (pp30)
REVERT: E   69 THR cc_start: 0.8224 (m) cc_final: 0.7590 (p)
REVERT: E   91 ASP cc_start: 0.8001 (t0) cc_final: 0.7286 (m-30)
  outliers start: 9
  outliers final: 8
  residues processed: 65
  average time/residue: 0.2696
  time to fit residues: 23.6907
Evaluate side-chains
  60 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain D residue    8 SER
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   68 ASN
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain B residue   17 THR
Chi-restraints excluded: chain B residue   68 ASN
Chi-restraints excluded: chain E residue   22 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 33 optimal weight:    8.9990
   chunk 31 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 6 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   chunk 34 optimal weight:    0.4980
   overall best weight:    2.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 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 = 0.4327 r_free = 0.4327 target = 0.118397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.100790 restraints weight = 27736.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.104093 restraints weight = 10831.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.106235 restraints weight = 5740.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.4225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4575  Z= 0.274
  Angle     :  0.588   4.395   6240  Z= 0.307
  Chirality :  0.047   0.193    705
  Planarity :  0.005   0.045    805
  Dihedral  :  6.509  35.881    730
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  7.14 %
    Favored  : 90.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.95 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.01 (0.20), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  34 
 PHE   0.011   0.002   PHE A  61 
 TYR   0.014   0.002   TYR A  85 
 ARG   0.001   0.000   ARG A  60 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.666 
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: A    8 SER cc_start: 0.8367 (t) cc_final: 0.7950 (m)
REVERT: D    8 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.7958 (p)
REVERT: D  108 GLN cc_start: 0.8140 (pt0) cc_final: 0.7528 (pp30)
REVERT: B    8 SER cc_start: 0.7935 (t) cc_final: 0.7588 (m)
REVERT: E   91 ASP cc_start: 0.8066 (t0) cc_final: 0.7310 (m-30)
  outliers start: 10
  outliers final: 9
  residues processed: 62
  average time/residue: 0.2730
  time to fit residues: 22.8677
Evaluate side-chains
  59 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain D residue    8 SER
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   68 ASN
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain B residue   68 ASN
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   68 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 27 optimal weight:    0.0370
   chunk 2 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 17 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0980
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  41 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.120945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.103126 restraints weight = 27334.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.106601 restraints weight = 10706.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.108728 restraints weight = 5631.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.4261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   4575  Z= 0.142
  Angle     :  0.512   3.868   6240  Z= 0.263
  Chirality :  0.048   0.224    705
  Planarity :  0.005   0.046    805
  Dihedral  :  5.679  27.555    730
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  7.76 %
    Favored  : 91.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.94 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.00 (0.20), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  34 
 PHE   0.008   0.001   PHE A  61 
 TYR   0.008   0.001   TYR E  26 
 ARG   0.002   0.000   ARG E  60 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.655 
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: D  108 GLN cc_start: 0.8126 (pt0) cc_final: 0.7515 (pp30)
REVERT: B    8 SER cc_start: 0.7940 (t) cc_final: 0.7670 (m)
REVERT: E   69 THR cc_start: 0.8193 (m) cc_final: 0.7480 (p)
REVERT: E   91 ASP cc_start: 0.7989 (t0) cc_final: 0.7300 (m-30)
  outliers start: 6
  outliers final: 5
  residues processed: 53
  average time/residue: 0.2882
  time to fit residues: 20.5977
Evaluate side-chains
  52 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain E residue   22 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 6 optimal weight:    8.9990
   chunk 53 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
D  41 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.118637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.101108 restraints weight = 27998.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.104453 restraints weight = 10868.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.106568 restraints weight = 5733.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.4228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4575  Z= 0.247
  Angle     :  0.563   4.249   6240  Z= 0.292
  Chirality :  0.047   0.194    705
  Planarity :  0.005   0.045    805
  Dihedral  :  6.293  35.213    730
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  7.14 %
    Favored  : 90.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.94 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.00 (0.20), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  34 
 PHE   0.011   0.001   PHE B  61 
 TYR   0.012   0.002   TYR D  85 
 ARG   0.002   0.000   ARG A  60 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.668 
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: D  108 GLN cc_start: 0.8144 (pt0) cc_final: 0.7542 (pp30)
REVERT: B    8 SER cc_start: 0.7919 (t) cc_final: 0.7655 (m)
  outliers start: 10
  outliers final: 9
  residues processed: 56
  average time/residue: 0.2777
  time to fit residues: 20.9448
Evaluate side-chains
  55 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   68 ASN
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain B residue   68 ASN
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   68 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 44 optimal weight:    8.9990
   chunk 18 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 47 optimal weight:    0.5980
   chunk 12 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 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 = 0.4320 r_free = 0.4320 target = 0.118194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.100573 restraints weight = 28135.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.103835 restraints weight = 10981.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.105891 restraints weight = 5799.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.4217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4575  Z= 0.237
  Angle     :  0.564   4.574   6240  Z= 0.293
  Chirality :  0.048   0.219    705
  Planarity :  0.005   0.048    805
  Dihedral  :  6.320  35.087    730
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  :  7.35 %
    Favored  : 90.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.96 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.01 (0.20), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  34 
 PHE   0.011   0.001   PHE A  61 
 TYR   0.012   0.002   TYR D  85 
 ARG   0.001   0.000   ARG A  53 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.663 
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    8 SER cc_start: 0.8375 (t) cc_final: 0.7939 (m)
REVERT: D    8 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.7916 (p)
REVERT: D  108 GLN cc_start: 0.8160 (pt0) cc_final: 0.7540 (pp30)
REVERT: B    8 SER cc_start: 0.8007 (t) cc_final: 0.7654 (m)
  outliers start: 11
  outliers final: 8
  residues processed: 58
  average time/residue: 0.2735
  time to fit residues: 21.3643
Evaluate side-chains
  55 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain D residue    8 SER
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   68 ASN
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain B residue   68 ASN
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain E residue   22 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 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 = 0.4342 r_free = 0.4342 target = 0.119701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.101914 restraints weight = 27742.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.105393 restraints weight = 10678.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.107571 restraints weight = 5561.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.4243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   4575  Z= 0.158
  Angle     :  0.525   4.511   6240  Z= 0.268
  Chirality :  0.048   0.219    705
  Planarity :  0.005   0.049    805
  Dihedral  :  5.881  30.306    730
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  :  7.55 %
    Favored  : 90.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.96 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.01 (0.20), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A  34 
 PHE   0.009   0.001   PHE D  61 
 TYR   0.008   0.001   TYR C  85 
 ARG   0.001   0.000   ARG A  53 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.648 
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    8 SER cc_start: 0.8373 (t) cc_final: 0.7933 (m)
REVERT: D    8 SER cc_start: 0.8280 (OUTLIER) cc_final: 0.7915 (p)
REVERT: D  108 GLN cc_start: 0.8144 (pt0) cc_final: 0.7556 (pp30)
REVERT: B    8 SER cc_start: 0.7996 (t) cc_final: 0.7645 (m)
  outliers start: 9
  outliers final: 8
  residues processed: 57
  average time/residue: 0.2828
  time to fit residues: 21.7846
Evaluate side-chains
  54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain D residue    8 SER
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain D residue   68 ASN
Chi-restraints excluded: chain C residue   68 ASN
Chi-restraints excluded: chain B residue   68 ASN
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain E residue   22 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 44 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 39 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    2.7986

-------------------------------------------------------------------------------
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 = 0.4282 r_free = 0.4282 target = 0.115732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.098361 restraints weight = 28591.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.101587 restraints weight = 11126.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.103677 restraints weight = 5882.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.4195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.3547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   4575  Z= 0.352
  Angle     :  0.641   4.657   6240  Z= 0.335
  Chirality :  0.048   0.210    705
  Planarity :  0.005   0.048    805
  Dihedral  :  6.976  40.386    730
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.10 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  7.96 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.09 (0.26), residues: 580
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.11 (0.20), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  34 
 PHE   0.013   0.002   PHE A  61 
 TYR   0.017   0.002   TYR E  85 
 ARG   0.002   0.000   ARG B  32 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4311.89 seconds
wall clock time: 76 minutes 8.57 seconds (4568.57 seconds total)