Starting phenix.real_space_refine
on Mon Jan 20 07:29:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x7i_38099/01_2025/8x7i_38099.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x7i_38099/01_2025/8x7i_38099.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x7i_38099/01_2025/8x7i_38099.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x7i_38099/01_2025/8x7i_38099.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x7i_38099/01_2025/8x7i_38099.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x7i_38099/01_2025/8x7i_38099.cif"
  }
  resolution = 3.27
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1119 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      28      5.16       5
     C    8076      2.51       5
     N    2655      2.21       5
     O    3245      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 14300
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 810
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 668
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 668
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 845
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 105}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "G"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "I"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "D"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "H"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "K"
      Number of atoms: 1125
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1125
          Classifications: {'peptide': 147}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131}
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 40
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 34
    Chain: "L"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 641
          Classifications: {'peptide': 83}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 73}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "M"
      Number of atoms: 413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 413
          Classifications: {'peptide': 62}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 56}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 86
          Unresolved non-hydrogen angles: 106
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 45
    Chain: "L"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  13447  SG  CYS L  31      56.643  71.877  28.876  1.00218.04           S
  ATOM  13589  SG  CYS L  51      58.205  75.289  28.905  1.00210.14           S
  ATOM  13613  SG  CYS L  54      54.564  75.086  28.068  1.00213.50           S
  ATOM  13338  SG  CYS L  16      67.989  71.834  23.293  1.00283.03           S
  ATOM  13356  SG  CYS L  19      71.632  71.909  22.328  1.00282.47           S
  ATOM  13486  SG  CYS L  36      70.625  69.933  25.344  1.00253.66           S
  ATOM  13504  SG  CYS L  39      70.429  73.629  25.607  1.00248.31           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   GLY M  75 " occ=0.45
      ... (2 atoms not shown)
      pdb=" O   GLY M  75 " occ=0.45
  Time building chain proxies: 8.53, per 1000 atoms: 0.60
  Number of scatterers: 14300
  At special positions: 0
  Unit cell: (118.14, 128.88, 112.77, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      28     16.00
     P     294     15.00
     O    3245      8.00
     N    2655      7.00
     C    8076      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.76
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN L 201 "
        pdb="ZN    ZN L 201 " - pdb=" ND1 HIS L  33 "
        pdb="ZN    ZN L 201 " - pdb=" SG  CYS L  51 "
        pdb="ZN    ZN L 201 " - pdb=" SG  CYS L  31 "
        pdb="ZN    ZN L 201 " - pdb=" SG  CYS L  54 "
      pdb="  ZN L 202 "
        pdb="ZN    ZN L 202 " - pdb=" SG  CYS L  36 "
        pdb="ZN    ZN L 202 " - pdb=" SG  CYS L  16 "
        pdb="ZN    ZN L 202 " - pdb=" SG  CYS L  39 "
        pdb="ZN    ZN L 202 " - pdb=" SG  CYS L  19 "
      Number of angles added : 9


  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2002

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 13 sheets defined
      62.3% alpha, 4.2% beta
      143 base pairs and 243 stacking pairs defined.
    Time for finding SS restraints: 6.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.594A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.816A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.399A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.627A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 23 through 29
      removed outlier: 3.667A  pdb=" N   ILE F  26 " --> pdb=" O   ARG F  23 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.548A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ARG F  55 " --> pdb=" O   TYR F  51 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LYS F  59 " --> pdb=" O   ARG F  55 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   THR F  71 " --> pdb=" O   ARG F  67 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.523A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.514A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.587A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 3.512A  pdb=" N   ALA D 124 " --> pdb=" O   LYS D 120 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.548A  pdb=" N   THR H  96 " --> pdb=" O   ARG H  92 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 104 through 124
    Processing helix  chain 'K' and resid 2 through 16
    Processing helix  chain 'K' and resid 86 through 91
    Processing helix  chain 'K' and resid 98 through 112
    Processing helix  chain 'K' and resid 120 through 130
    Processing helix  chain 'K' and resid 130 through 145
    Processing helix  chain 'L' and resid 10 through 15
    Processing helix  chain 'L' and resid 36 through 47
      removed outlier: 4.833A  pdb=" N   GLU L  45 " --> pdb=" O   GLN L  41 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ALA L  47 " --> pdb=" O   THR L  43 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 58 through 69
      removed outlier: 3.757A  pdb=" N   ARG L  67 " --> pdb=" O   ARG L  63 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   ARG L  68 " --> pdb=" O   TYR L  64 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 73 through 84
    Processing helix  chain 'M' and resid 22 through 35
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.869A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.469A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
      removed outlier: 6.817A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.062A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.292A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 32 through 38
    Processing sheet with id=AB3, first strand: chain 'L' and resid 27 through 28
      removed outlier: 3.552A  pdb=" N   LEU L  35 " --> pdb=" O   VAL L  27 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'M' and resid 3 through 6

    484 hydrogen bonds defined for protein.
    1431 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      343 hydrogen bonds
      598 hydrogen bond angles
      0 basepair planarities
      143 basepair parallelities
      243 stacking parallelities
  Total time for adding SS restraints: 5.16

  Time building geometry restraints manager: 4.25 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3279
        1.33 -     1.45: 4408
        1.45 -     1.57: 6848
        1.57 -     1.69: 586
        1.69 -     1.81: 44
  Bond restraints: 15165
  Sorted by residual:
  bond pdb=" CA  ILE C  79 "
       pdb=" CB  ILE C  79 "
    ideal  model  delta    sigma   weight residual
    1.546  1.534  0.012 8.80e-03 1.29e+04 2.01e+00
  bond pdb=" CA  ILE G  79 "
       pdb=" CB  ILE G  79 "
    ideal  model  delta    sigma   weight residual
    1.546  1.534  0.012 8.80e-03 1.29e+04 1.97e+00
  bond pdb=" C3'  DG I  20 "
       pdb=" O3'  DG I  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.66e+00
  bond pdb=" C3'  DT I -59 "
       pdb=" O3'  DT I -59 "
    ideal  model  delta    sigma   weight residual
    1.422  1.456 -0.034 3.00e-02 1.11e+03 1.29e+00
  bond pdb=" C4'  DA J  32 "
       pdb=" C3'  DA J  32 "
    ideal  model  delta    sigma   weight residual
    1.523  1.502  0.021 2.00e-02 2.50e+03 1.14e+00
  ... (remaining 15160 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 20960
        1.44 -     2.88: 761
        2.88 -     4.32: 45
        4.32 -     5.76: 14
        5.76 -     7.20: 1
  Bond angle restraints: 21781
  Sorted by residual:
  angle pdb=" N   VAL E 117 "
        pdb=" CA  VAL E 117 "
        pdb=" C   VAL E 117 "
      ideal   model   delta    sigma   weight residual
     113.47  109.08    4.39 1.01e+00 9.80e-01 1.89e+01
  angle pdb=" C   PRO L   4 "
        pdb=" N   LYS L   5 "
        pdb=" CA  LYS L   5 "
      ideal   model   delta    sigma   weight residual
     121.70  128.90   -7.20 1.80e+00 3.09e-01 1.60e+01
  angle pdb=" N   VAL L  58 "
        pdb=" CA  VAL L  58 "
        pdb=" C   VAL L  58 "
      ideal   model   delta    sigma   weight residual
     113.20  109.66    3.54 9.60e-01 1.09e+00 1.36e+01
  angle pdb=" N   GLN C  24 "
        pdb=" CA  GLN C  24 "
        pdb=" C   GLN C  24 "
      ideal   model   delta    sigma   weight residual
     114.04  109.54    4.50 1.24e+00 6.50e-01 1.32e+01
  angle pdb=" C   ASP K  59 "
        pdb=" N   TYR K  60 "
        pdb=" CA  TYR K  60 "
      ideal   model   delta    sigma   weight residual
     120.39  124.50   -4.11 1.39e+00 5.18e-01 8.73e+00
  ... (remaining 21776 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.16: 7056
       35.16 -    70.32: 1302
       70.32 -   105.48: 11
      105.48 -   140.64: 1
      140.64 -   175.80: 2
  Dihedral angle restraints: 8372
    sinusoidal: 5285
      harmonic: 3087
  Sorted by residual:
  dihedral pdb=" C4'  DT I -59 "
           pdb=" C3'  DT I -59 "
           pdb=" O3'  DT I -59 "
           pdb=" P    DC I -58 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   44.20  175.80     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG I  20 "
           pdb=" C3'  DG I  20 "
           pdb=" O3'  DG I  20 "
           pdb=" P    DG I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   58.69  161.31     1      3.50e+01 8.16e-04 1.53e+01
  dihedral pdb=" C4'  DC I  52 "
           pdb=" C3'  DC I  52 "
           pdb=" O3'  DC I  52 "
           pdb=" P    DC I  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   84.74  135.26     1      3.50e+01 8.16e-04 1.34e+01
  ... (remaining 8369 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1584
       0.032 -    0.064: 688
       0.064 -    0.095: 164
       0.095 -    0.127: 49
       0.127 -    0.159: 4
  Chirality restraints: 2489
  Sorted by residual:
  chirality pdb=" CA  PRO L   4 "
            pdb=" N   PRO L   4 "
            pdb=" C   PRO L   4 "
            pdb=" CB  PRO L   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.30e-01
  chirality pdb=" CA  ILE M  36 "
            pdb=" N   ILE M  36 "
            pdb=" C   ILE M  36 "
            pdb=" CB  ILE M  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.76e-01
  chirality pdb=" C3'  DT I -59 "
            pdb=" C4'  DT I -59 "
            pdb=" O3'  DT I -59 "
            pdb=" C2'  DT I -59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.53   -0.13 2.00e-01 2.50e+01 4.20e-01
  ... (remaining 2486 not shown)

  Planarity restraints: 1746
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU L   3 "    0.035 5.00e-02 4.00e+02   5.32e-02 4.53e+00
        pdb=" N   PRO L   4 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO L   4 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO L   4 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  47 "    0.024 2.00e-02 2.50e+03   9.90e-03 2.69e+00
        pdb=" N9   DA I  47 "   -0.017 2.00e-02 2.50e+03
        pdb=" C8   DA I  47 "   -0.007 2.00e-02 2.50e+03
        pdb=" N7   DA I  47 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5   DA I  47 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  47 "    0.009 2.00e-02 2.50e+03
        pdb=" N1   DA I  47 "    0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DA I  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DA I  47 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I -35 "   -0.024 2.00e-02 2.50e+03   9.41e-03 2.66e+00
        pdb=" N9   DG I -35 "    0.019 2.00e-02 2.50e+03
        pdb=" C8   DG I -35 "    0.005 2.00e-02 2.50e+03
        pdb=" N7   DG I -35 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DG I -35 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DG I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" O6   DG I -35 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DG I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DG I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" N2   DG I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DG I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DG I -35 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1743 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 425
        2.65 -     3.22: 12761
        3.22 -     3.78: 27171
        3.78 -     4.34: 34185
        4.34 -     4.90: 49782
  Nonbonded interactions: 124324
  Sorted by model distance:
  nonbonded pdb=" N2   DG I  51 "
            pdb=" O2   DC J -51 "
     model   vdw
     2.093 2.496
  nonbonded pdb=" N2   DG I  46 "
            pdb=" O2   DC J -46 "
     model   vdw
     2.094 2.496
  nonbonded pdb=" O2   DC I  52 "
            pdb=" N2   DG J -52 "
     model   vdw
     2.109 2.496
  nonbonded pdb=" O2   DC I  40 "
            pdb=" N2   DG J -40 "
     model   vdw
     2.115 2.496
  nonbonded pdb=" O2   DC I -52 "
            pdb=" N2   DG J  52 "
     model   vdw
     2.122 2.496
  ... (remaining 124319 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 38 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and (resid 19 through 22 or (resid 23 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 24 through 101))
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and (resid 10 through 14 or resid 16 through 118))
  selection = (chain 'G' and (resid 10 through 14 or resid 16 through 118))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.100
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     40.390
  Find NCS groups from input model:        0.390
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
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      :  0.006   0.046  15165  Z= 0.317
  Angle     :  0.603   7.198  21781  Z= 0.372
  Chirality :  0.037   0.159   2489
  Planarity :  0.004   0.053   1746
  Dihedral  : 25.488 175.796   6370
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.87 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  4.61 %
    Favored  : 93.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    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:  1.53 (0.27), residues: 1033
  helix:  1.99 (0.21), residues: 656
  sheet: -0.84 (1.01), residues: 24
  loop : -0.72 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP K  93 
 HIS   0.003   0.001   HIS H  49 
 PHE   0.011   0.001   PHE E  67 
 TYR   0.008   0.001   TYR B  51 
 ARG   0.003   0.000   ARG C  88 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 273
  time to evaluate  : 1.234 
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: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8664 (tm-30)
REVERT: C   38 ASN cc_start: 0.8754 (m-40) cc_final: 0.7563 (m-40)
REVERT: C   68 ASN cc_start: 0.8990 (m-40) cc_final: 0.8672 (m-40)
REVERT: E   73 GLU cc_start: 0.8063 (tt0) cc_final: 0.7672 (tt0)
REVERT: E   94 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8308 (mm-30)
REVERT: E  115 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8944 (mppt)
REVERT: F   88 TYR cc_start: 0.8862 (m-10) cc_final: 0.6969 (m-10)
REVERT: F   91 LYS cc_start: 0.9298 (ttmt) cc_final: 0.8971 (ttpt)
REVERT: G   61 GLU cc_start: 0.8624 (tp30) cc_final: 0.8342 (mm-30)
REVERT: D   93 GLU cc_start: 0.8250 (mp0) cc_final: 0.7960 (mp0)
REVERT: D  116 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8617 (mtpt)
REVERT: H   68 ASP cc_start: 0.8790 (t70) cc_final: 0.8487 (t0)
REVERT: H   72 ARG cc_start: 0.9054 (mtt180) cc_final: 0.8848 (mtt180)
REVERT: K   38 MET cc_start: 0.8957 (mtt) cc_final: 0.8534 (tpt)
REVERT: K   62 PHE cc_start: 0.9102 (m-80) cc_final: 0.8871 (m-80)
REVERT: K   87 ASP cc_start: 0.8780 (p0) cc_final: 0.8481 (p0)
REVERT: K   92 GLN cc_start: 0.8971 (tp-100) cc_final: 0.8579 (tp-100)
REVERT: K  120 VAL cc_start: 0.7361 (t) cc_final: 0.7125 (t)
REVERT: L   20 MET cc_start: 0.7447 (mmt) cc_final: 0.7150 (mmt)
REVERT: L   45 GLU cc_start: 0.8965 (pm20) cc_final: 0.8601 (pm20)
REVERT: L   60 SER cc_start: 0.8715 (m) cc_final: 0.8424 (m)
REVERT: L   73 ASN cc_start: 0.7355 (OUTLIER) cc_final: 0.7141 (t0)
  outliers start: 16
  outliers final: 5
  residues processed: 285
  average time/residue: 0.3662
  time to fit residues: 137.9475
Evaluate side-chains
  207 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 199
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain D residue  116 LYS
Chi-restraints excluded: chain L residue   14 CYS
Chi-restraints excluded: chain L residue   73 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 97 optimal weight:    6.9990
   chunk 54 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   chunk 101 optimal weight:    6.9990
   chunk 39 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 117 optimal weight:    0.5980
   overall best weight:    3.0786

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  24 GLN
E  68 GLN
F  27 GLN
G  38 ASN
G  84 GLN
D  47 GLN
D  95 GLN
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 109 HIS
L  41 GLN
L  73 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.049044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.032711 restraints weight = 81542.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.2718 rms_B_bonded: 3.00
r_work: 0.2538 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.2538
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2531
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2531 r_free = 0.2531    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2529 r_free = 0.2529    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2529
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8885
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  15165  Z= 0.315
  Angle     :  0.627   9.492  21781  Z= 0.365
  Chirality :  0.038   0.148   2489
  Planarity :  0.004   0.055   1746
  Dihedral  : 29.417 175.134   4396
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.29 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 13.61 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    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:  1.76 (0.27), residues: 1033
  helix:  2.20 (0.21), residues: 656
  sheet: -0.69 (1.00), residues: 24
  loop : -0.70 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP K 141 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.014   0.002   PHE K  51 
 TYR   0.013   0.002   TYR D  83 
 ARG   0.006   0.000   ARG K 136 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 222
  time to evaluate  : 1.228 
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   59 GLU cc_start: 0.9119 (pm20) cc_final: 0.8820 (pm20)
REVERT: A   73 GLU cc_start: 0.9458 (tm-30) cc_final: 0.9219 (tm-30)
REVERT: A   94 GLU cc_start: 0.8946 (tp30) cc_final: 0.8703 (tp30)
REVERT: A  125 GLN cc_start: 0.9241 (mt0) cc_final: 0.8092 (mt0)
REVERT: C   24 GLN cc_start: 0.9395 (mm-40) cc_final: 0.8801 (mp10)
REVERT: C   56 GLU cc_start: 0.9282 (tt0) cc_final: 0.8774 (tt0)
REVERT: C   68 ASN cc_start: 0.9093 (m-40) cc_final: 0.8699 (m-40)
REVERT: E   94 GLU cc_start: 0.9233 (mm-30) cc_final: 0.9017 (mm-30)
REVERT: E  115 LYS cc_start: 0.9462 (OUTLIER) cc_final: 0.9250 (mppt)
REVERT: F   91 LYS cc_start: 0.9432 (ttmt) cc_final: 0.9098 (ttpt)
REVERT: G   61 GLU cc_start: 0.9106 (tp30) cc_final: 0.8873 (tp30)
REVERT: D   83 TYR cc_start: 0.8388 (m-10) cc_final: 0.8137 (m-10)
REVERT: D   93 GLU cc_start: 0.8918 (mp0) cc_final: 0.8592 (mp0)
REVERT: H   33 ARG cc_start: 0.8447 (mtp85) cc_final: 0.7693 (ttt180)
REVERT: H   68 ASP cc_start: 0.9271 (t70) cc_final: 0.9060 (t0)
REVERT: H   88 THR cc_start: 0.9296 (m) cc_final: 0.9075 (m)
REVERT: H  105 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7801 (tm-30)
REVERT: H  106 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9112 (mt)
REVERT: K    1 MET cc_start: 0.7490 (tmm) cc_final: 0.7180 (tmm)
REVERT: K   16 ASP cc_start: 0.9284 (m-30) cc_final: 0.9001 (p0)
REVERT: K   38 MET cc_start: 0.9068 (mtt) cc_final: 0.8690 (tpt)
REVERT: K   69 PHE cc_start: 0.8700 (m-80) cc_final: 0.8490 (t80)
REVERT: K   87 ASP cc_start: 0.9023 (p0) cc_final: 0.8790 (p0)
REVERT: K   92 GLN cc_start: 0.9054 (tp-100) cc_final: 0.8674 (tp-100)
REVERT: K  120 VAL cc_start: 0.7612 (t) cc_final: 0.7276 (t)
REVERT: L   20 MET cc_start: 0.7508 (mmt) cc_final: 0.7133 (mmt)
  outliers start: 24
  outliers final: 15
  residues processed: 237
  average time/residue: 0.3410
  time to fit residues: 109.8547
Evaluate side-chains
  221 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 204
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  120 THR
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain H residue  106 LEU
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue   98 THR
Chi-restraints excluded: chain L residue   40 PHE
Chi-restraints excluded: chain L residue   74 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 102 optimal weight:    8.9990
   chunk 96 optimal weight:    2.9990
   chunk 70 optimal weight:    8.9990
   chunk 61 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.049738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.033367 restraints weight = 80566.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.2742 rms_B_bonded: 3.00
r_work: 0.2564 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2564
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2559
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2559 r_free = 0.2559    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2559 r_free = 0.2559    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2559
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8856
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15165  Z= 0.196
  Angle     :  0.588   7.982  21781  Z= 0.345
  Chirality :  0.036   0.149   2489
  Planarity :  0.004   0.056   1746
  Dihedral  : 29.321 173.941   4389
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.10 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 15.46 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    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:  1.76 (0.27), residues: 1033
  helix:  2.24 (0.21), residues: 655
  sheet: -0.76 (0.92), residues: 24
  loop : -0.76 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP K 141 
 HIS   0.002   0.001   HIS G  31 
 PHE   0.013   0.001   PHE A  67 
 TYR   0.015   0.001   TYR H 121 
 ARG   0.007   0.000   ARG K 125 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 226
  time to evaluate  : 1.190 
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   59 GLU cc_start: 0.9133 (pm20) cc_final: 0.8815 (pm20)
REVERT: A   73 GLU cc_start: 0.9446 (tm-30) cc_final: 0.9188 (tm-30)
REVERT: A   94 GLU cc_start: 0.8847 (tp30) cc_final: 0.8544 (tt0)
REVERT: B   23 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8296 (ptp90)
REVERT: C   24 GLN cc_start: 0.9289 (mm-40) cc_final: 0.8793 (mp10)
REVERT: C   56 GLU cc_start: 0.9233 (tt0) cc_final: 0.8932 (tt0)
REVERT: E   73 GLU cc_start: 0.8629 (tt0) cc_final: 0.8420 (tt0)
REVERT: E   94 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8924 (mm-30)
REVERT: F   91 LYS cc_start: 0.9434 (ttmt) cc_final: 0.9081 (ttpt)
REVERT: G   61 GLU cc_start: 0.9042 (tp30) cc_final: 0.8728 (tp30)
REVERT: D   93 GLU cc_start: 0.8859 (mp0) cc_final: 0.8575 (mp0)
REVERT: H   33 ARG cc_start: 0.8446 (mtp85) cc_final: 0.7611 (ttt180)
REVERT: H  105 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7768 (tm-30)
REVERT: H  106 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9113 (mt)
REVERT: H  113 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8931 (mm-30)
REVERT: K    1 MET cc_start: 0.7492 (tmm) cc_final: 0.7161 (tmm)
REVERT: K   38 MET cc_start: 0.9050 (mtt) cc_final: 0.8703 (tpt)
REVERT: K   87 ASP cc_start: 0.9030 (p0) cc_final: 0.8816 (p0)
REVERT: K   92 GLN cc_start: 0.9083 (tp-100) cc_final: 0.8761 (tp-100)
REVERT: K  120 VAL cc_start: 0.7456 (t) cc_final: 0.6876 (m)
REVERT: K  125 ARG cc_start: 0.8875 (mtm110) cc_final: 0.8562 (ptp-170)
REVERT: K  147 MET cc_start: 0.8576 (mtt) cc_final: 0.8111 (mpp)
REVERT: L   20 MET cc_start: 0.7486 (mmt) cc_final: 0.7090 (mmt)
REVERT: L   55 ARG cc_start: 0.7712 (mmp80) cc_final: 0.7460 (tpt90)
  outliers start: 18
  outliers final: 11
  residues processed: 231
  average time/residue: 0.3255
  time to fit residues: 103.6993
Evaluate side-chains
  220 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 207
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   23 ARG
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain H residue  106 LEU
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue   45 TYR
Chi-restraints excluded: chain L residue   74 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 96 optimal weight:    0.7980
   chunk 9 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 116 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 91 optimal weight:    6.9990
   chunk 43 optimal weight:    3.9990
   chunk 108 optimal weight:    0.8980
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  41 ASN ** 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 = 0.3376 r_free = 0.3376 target = 0.049048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.032655 restraints weight = 81773.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.2715 rms_B_bonded: 3.01
r_work: 0.2538 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.2538
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2532
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2532 r_free = 0.2532    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2532 r_free = 0.2532    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2532
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8884
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  15165  Z= 0.311
  Angle     :  0.614  11.159  21781  Z= 0.356
  Chirality :  0.038   0.147   2489
  Planarity :  0.004   0.059   1746
  Dihedral  : 29.416 174.097   4381
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.48 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.46 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    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:  1.90 (0.27), residues: 1033
  helix:  2.37 (0.21), residues: 650
  sheet: -0.60 (0.94), residues: 24
  loop : -0.72 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP L  61 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.012   0.002   PHE E  67 
 TYR   0.032   0.002   TYR D  83 
 ARG   0.010   0.000   ARG A 128 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 209
  time to evaluate  : 1.295 
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   59 GLU cc_start: 0.9129 (pm20) cc_final: 0.8767 (pm20)
REVERT: A   73 GLU cc_start: 0.9469 (tm-30) cc_final: 0.9230 (tm-30)
REVERT: A   94 GLU cc_start: 0.8893 (tp30) cc_final: 0.8587 (tt0)
REVERT: B   23 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8211 (ptp90)
REVERT: C   24 GLN cc_start: 0.9410 (mm-40) cc_final: 0.9070 (mm110)
REVERT: E   73 GLU cc_start: 0.8572 (tt0) cc_final: 0.8366 (tt0)
REVERT: E   94 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8984 (mm-30)
REVERT: F   91 LYS cc_start: 0.9447 (ttmt) cc_final: 0.9125 (ttpt)
REVERT: G   38 ASN cc_start: 0.8283 (t0) cc_final: 0.8051 (t0)
REVERT: G   61 GLU cc_start: 0.9056 (tp30) cc_final: 0.8758 (tp30)
REVERT: G   64 GLU cc_start: 0.9260 (OUTLIER) cc_final: 0.9047 (pp20)
REVERT: D   93 GLU cc_start: 0.8914 (mp0) cc_final: 0.8657 (mp0)
REVERT: H   33 ARG cc_start: 0.8399 (mtp85) cc_final: 0.7667 (ttt90)
REVERT: H   83 TYR cc_start: 0.8574 (m-10) cc_final: 0.8251 (m-10)
REVERT: H  113 GLU cc_start: 0.9314 (mm-30) cc_final: 0.8974 (mm-30)
REVERT: K    1 MET cc_start: 0.7509 (tmm) cc_final: 0.7169 (tmm)
REVERT: K   38 MET cc_start: 0.9123 (mtt) cc_final: 0.8770 (tpt)
REVERT: K   92 GLN cc_start: 0.9135 (tp-100) cc_final: 0.8831 (tp-100)
REVERT: L   20 MET cc_start: 0.7515 (mmt) cc_final: 0.7176 (mmt)
  outliers start: 22
  outliers final: 16
  residues processed: 218
  average time/residue: 0.2972
  time to fit residues: 91.7556
Evaluate side-chains
  213 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 195
  time to evaluate  : 1.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   23 ARG
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue   45 TYR
Chi-restraints excluded: chain K residue   69 PHE
Chi-restraints excluded: chain K residue  132 ASP
Chi-restraints excluded: chain L residue   40 PHE
Chi-restraints excluded: chain L residue   74 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 113 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 66 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 72 optimal weight:    6.9990
   chunk 127 optimal weight:   40.0000
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  41 ASN
L  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.049648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.033507 restraints weight = 82198.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.2744 rms_B_bonded: 2.99
r_work: 0.2575 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.2575
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2567
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2567 r_free = 0.2567    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2567 r_free = 0.2567    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2567
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8846
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15165  Z= 0.191
  Angle     :  0.588   8.597  21781  Z= 0.342
  Chirality :  0.036   0.182   2489
  Planarity :  0.004   0.059   1746
  Dihedral  : 29.365 173.210   4381
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.61 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.27), residues: 1033
  helix:  2.45 (0.21), residues: 648
  sheet: -0.34 (0.97), residues: 24
  loop : -0.66 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP K 141 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.012   0.001   PHE A  67 
 TYR   0.047   0.002   TYR D  83 
 ARG   0.005   0.000   ARG A 128 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 216
  time to evaluate  : 1.243 
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   59 GLU cc_start: 0.9116 (pm20) cc_final: 0.8779 (pm20)
REVERT: A   62 ILE cc_start: 0.9478 (mt) cc_final: 0.9145 (mt)
REVERT: A   73 GLU cc_start: 0.9468 (tm-30) cc_final: 0.9194 (tm-30)
REVERT: A   94 GLU cc_start: 0.8862 (tp30) cc_final: 0.8532 (tt0)
REVERT: A   97 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8597 (mm-30)
REVERT: B   88 TYR cc_start: 0.8881 (m-80) cc_final: 0.8536 (m-80)
REVERT: C   24 GLN cc_start: 0.9263 (mm-40) cc_final: 0.8792 (mp10)
REVERT: C   56 GLU cc_start: 0.9273 (tt0) cc_final: 0.9027 (tt0)
REVERT: F   91 LYS cc_start: 0.9426 (ttmt) cc_final: 0.9092 (ttpt)
REVERT: G   38 ASN cc_start: 0.8281 (t0) cc_final: 0.8044 (t0)
REVERT: G   61 GLU cc_start: 0.8959 (tp30) cc_final: 0.8719 (tp30)
REVERT: G   64 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.9059 (pp20)
REVERT: D   83 TYR cc_start: 0.8305 (m-10) cc_final: 0.8006 (m-80)
REVERT: D   93 GLU cc_start: 0.8848 (mp0) cc_final: 0.8627 (mp0)
REVERT: H   33 ARG cc_start: 0.8395 (mtp85) cc_final: 0.7735 (ttt90)
REVERT: H   51 ASP cc_start: 0.8603 (p0) cc_final: 0.8389 (p0)
REVERT: H   83 TYR cc_start: 0.8559 (m-10) cc_final: 0.8204 (m-10)
REVERT: H  106 LEU cc_start: 0.9383 (mt) cc_final: 0.9084 (mt)
REVERT: H  113 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8886 (mt-10)
REVERT: K    1 MET cc_start: 0.7498 (tmm) cc_final: 0.7170 (tmm)
REVERT: K   38 MET cc_start: 0.9112 (mtt) cc_final: 0.8789 (tpt)
REVERT: K   87 ASP cc_start: 0.8703 (p0) cc_final: 0.8490 (t0)
REVERT: K  120 VAL cc_start: 0.6652 (m) cc_final: 0.5770 (p)
REVERT: K  125 ARG cc_start: 0.8853 (mtm110) cc_final: 0.8627 (ptp-170)
REVERT: K  136 ARG cc_start: 0.9296 (ptt90) cc_final: 0.8972 (ttp-110)
REVERT: L   50 CYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7385 (t)
  outliers start: 20
  outliers final: 13
  residues processed: 227
  average time/residue: 0.3207
  time to fit residues: 101.2652
Evaluate side-chains
  219 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 204
  time to evaluate  : 1.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain C residue  120 THR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue   45 TYR
Chi-restraints excluded: chain K residue   98 THR
Chi-restraints excluded: chain K residue  132 ASP
Chi-restraints excluded: chain L residue   50 CYS
Chi-restraints excluded: chain L residue   74 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 27 optimal weight:    0.1980
   chunk 67 optimal weight:    8.9990
   chunk 66 optimal weight:    7.9990
   chunk 59 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   chunk 9 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 128 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 46 optimal weight:    7.9990
   overall best weight:    3.2388

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
D  95 GLN
K  92 GLN
** L  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  81 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.048917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.032533 restraints weight = 82752.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.2712 rms_B_bonded: 3.01
r_work: 0.2537 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2537
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2531
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2531 r_free = 0.2531    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2531 r_free = 0.2531    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2531
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8884
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      :  0.006   0.049  15165  Z= 0.326
  Angle     :  0.621   8.824  21781  Z= 0.360
  Chirality :  0.038   0.157   2489
  Planarity :  0.004   0.056   1746
  Dihedral  : 29.452 173.788   4381
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.49 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    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:  1.96 (0.27), residues: 1033
  helix:  2.39 (0.21), residues: 655
  sheet: -0.71 (0.91), residues: 24
  loop : -0.68 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP K 141 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.013   0.002   PHE E  67 
 TYR   0.042   0.002   TYR D  83 
 ARG   0.005   0.000   ARG D  99 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 203
  time to evaluate  : 1.140 
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: A   59 GLU cc_start: 0.9137 (pm20) cc_final: 0.8801 (pm20)
REVERT: A   73 GLU cc_start: 0.9480 (tm-30) cc_final: 0.9186 (tm-30)
REVERT: A   94 GLU cc_start: 0.8899 (tp30) cc_final: 0.8600 (tt0)
REVERT: C   24 GLN cc_start: 0.9410 (mm-40) cc_final: 0.8818 (mp10)
REVERT: C   56 GLU cc_start: 0.9308 (tt0) cc_final: 0.8906 (tt0)
REVERT: E   73 GLU cc_start: 0.8638 (tt0) cc_final: 0.8383 (tt0)
REVERT: E   94 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8935 (mm-30)
REVERT: F   91 LYS cc_start: 0.9452 (ttmt) cc_final: 0.9118 (ttpt)
REVERT: G   38 ASN cc_start: 0.8410 (t0) cc_final: 0.8171 (t0)
REVERT: G   61 GLU cc_start: 0.9059 (tp30) cc_final: 0.8779 (tp30)
REVERT: D   83 TYR cc_start: 0.8282 (m-10) cc_final: 0.8009 (m-80)
REVERT: D   93 GLU cc_start: 0.8966 (mp0) cc_final: 0.8755 (mp0)
REVERT: H   33 ARG cc_start: 0.8373 (mtp85) cc_final: 0.7641 (ttt90)
REVERT: H   83 TYR cc_start: 0.8595 (m-10) cc_final: 0.8261 (m-10)
REVERT: H  106 LEU cc_start: 0.9419 (mt) cc_final: 0.9107 (mt)
REVERT: H  113 GLU cc_start: 0.9334 (mm-30) cc_final: 0.9051 (mm-30)
REVERT: K    1 MET cc_start: 0.7501 (tmm) cc_final: 0.7150 (tmm)
REVERT: K   38 MET cc_start: 0.9081 (mtt) cc_final: 0.8680 (tpt)
REVERT: K   87 ASP cc_start: 0.8815 (p0) cc_final: 0.8530 (t0)
REVERT: K  120 VAL cc_start: 0.6810 (m) cc_final: 0.6397 (p)
REVERT: K  136 ARG cc_start: 0.9303 (ptt90) cc_final: 0.8947 (ttp-110)
REVERT: L   50 CYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7552 (t)
  outliers start: 25
  outliers final: 16
  residues processed: 216
  average time/residue: 0.3030
  time to fit residues: 91.3804
Evaluate side-chains
  214 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 197
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue   45 TYR
Chi-restraints excluded: chain K residue  132 ASP
Chi-restraints excluded: chain L residue   40 PHE
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   50 CYS
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain M residue   36 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 82 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 76 optimal weight:    5.9990
   chunk 80 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 67 optimal weight:    7.9990
   chunk 119 optimal weight:   40.0000
   chunk 24 optimal weight:    0.0980
   chunk 12 optimal weight:    1.9990
   overall best weight:    2.2188

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  15 GLN
L  81 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.049333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.032979 restraints weight = 81816.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.2728 rms_B_bonded: 3.00
r_work: 0.2552 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2552
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2545
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2545 r_free = 0.2545    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2545 r_free = 0.2545    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2545
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8872
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15165  Z= 0.252
  Angle     :  0.602   8.459  21781  Z= 0.349
  Chirality :  0.036   0.150   2489
  Planarity :  0.004   0.058   1746
  Dihedral  : 29.470 173.292   4381
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 18.34 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.27), residues: 1033
  helix:  2.50 (0.21), residues: 649
  sheet: -0.93 (0.89), residues: 24
  loop : -0.63 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K 141 
 HIS   0.004   0.001   HIS F  75 
 PHE   0.012   0.001   PHE E  67 
 TYR   0.034   0.002   TYR D  83 
 ARG   0.006   0.000   ARG K 125 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 203
  time to evaluate  : 1.288 
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   59 GLU cc_start: 0.9123 (pm20) cc_final: 0.8800 (pm20)
REVERT: A   73 GLU cc_start: 0.9468 (tm-30) cc_final: 0.9215 (tm-30)
REVERT: A   94 GLU cc_start: 0.8869 (tp30) cc_final: 0.8658 (tt0)
REVERT: C   24 GLN cc_start: 0.9374 (mm-40) cc_final: 0.8785 (mp10)
REVERT: C   56 GLU cc_start: 0.9309 (tt0) cc_final: 0.8863 (tt0)
REVERT: E   73 GLU cc_start: 0.8601 (tt0) cc_final: 0.8322 (tt0)
REVERT: F   91 LYS cc_start: 0.9456 (ttmt) cc_final: 0.9117 (ttpt)
REVERT: G   61 GLU cc_start: 0.9093 (tp30) cc_final: 0.8813 (tp30)
REVERT: D   42 TYR cc_start: 0.8690 (t80) cc_final: 0.8487 (t80)
REVERT: D   93 GLU cc_start: 0.8970 (mp0) cc_final: 0.8767 (mp0)
REVERT: H   33 ARG cc_start: 0.8336 (mtp85) cc_final: 0.7677 (ttt90)
REVERT: H   83 TYR cc_start: 0.8583 (m-10) cc_final: 0.8287 (m-10)
REVERT: H  106 LEU cc_start: 0.9392 (mt) cc_final: 0.9088 (mt)
REVERT: H  113 GLU cc_start: 0.9326 (mm-30) cc_final: 0.8901 (mt-10)
REVERT: K    1 MET cc_start: 0.7475 (tmm) cc_final: 0.7148 (tmm)
REVERT: K   38 MET cc_start: 0.9097 (mtt) cc_final: 0.8680 (tpt)
REVERT: K   87 ASP cc_start: 0.8854 (p0) cc_final: 0.8549 (t0)
REVERT: K  120 VAL cc_start: 0.6842 (m) cc_final: 0.6482 (p)
REVERT: K  136 ARG cc_start: 0.9279 (ptt90) cc_final: 0.8948 (ttp-110)
REVERT: L   50 CYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7536 (t)
  outliers start: 20
  outliers final: 15
  residues processed: 214
  average time/residue: 0.2920
  time to fit residues: 88.2389
Evaluate side-chains
  211 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 195
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue   45 TYR
Chi-restraints excluded: chain K residue   98 THR
Chi-restraints excluded: chain K residue  132 ASP
Chi-restraints excluded: chain L residue   50 CYS
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain M residue   36 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 47 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 59 optimal weight:    6.9990
   chunk 103 optimal weight:   30.0000
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.049591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.033255 restraints weight = 81624.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.2739 rms_B_bonded: 2.98
r_work: 0.2563 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.2563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2558
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2558 r_free = 0.2558    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2558 r_free = 0.2558    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2558
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.2721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15165  Z= 0.229
  Angle     :  0.604   9.285  21781  Z= 0.350
  Chirality :  0.036   0.153   2489
  Planarity :  0.004   0.058   1746
  Dihedral  : 29.430 173.204   4381
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 18.34 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.27), residues: 1033
  helix:  2.50 (0.21), residues: 648
  sheet: -0.94 (0.89), residues: 24
  loop : -0.64 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K 141 
 HIS   0.004   0.001   HIS K  75 
 PHE   0.013   0.001   PHE E  67 
 TYR   0.055   0.002   TYR D  83 
 ARG   0.006   0.000   ARG K 125 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 205
  time to evaluate  : 1.131 
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   59 GLU cc_start: 0.9098 (pm20) cc_final: 0.8787 (pm20)
REVERT: A   73 GLU cc_start: 0.9463 (tm-30) cc_final: 0.9174 (tm-30)
REVERT: A   79 LYS cc_start: 0.9140 (tptm) cc_final: 0.8707 (tptp)
REVERT: A   94 GLU cc_start: 0.8841 (tp30) cc_final: 0.8615 (tt0)
REVERT: C   24 GLN cc_start: 0.9370 (mm-40) cc_final: 0.8790 (mp10)
REVERT: C   56 GLU cc_start: 0.9303 (tt0) cc_final: 0.8865 (tt0)
REVERT: E   73 GLU cc_start: 0.8619 (tt0) cc_final: 0.8336 (tt0)
REVERT: F   91 LYS cc_start: 0.9449 (ttmt) cc_final: 0.9106 (ttpt)
REVERT: G   61 GLU cc_start: 0.9068 (tp30) cc_final: 0.8779 (tp30)
REVERT: D   42 TYR cc_start: 0.8665 (t80) cc_final: 0.8464 (t80)
REVERT: D   93 GLU cc_start: 0.8966 (mp0) cc_final: 0.8760 (mp0)
REVERT: H   33 ARG cc_start: 0.8299 (mtp85) cc_final: 0.7663 (ttt90)
REVERT: H   83 TYR cc_start: 0.8567 (m-10) cc_final: 0.8328 (m-10)
REVERT: H  106 LEU cc_start: 0.9385 (mt) cc_final: 0.9081 (mt)
REVERT: H  113 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8894 (mt-10)
REVERT: K    1 MET cc_start: 0.7513 (tmm) cc_final: 0.7182 (tmm)
REVERT: K   38 MET cc_start: 0.9074 (mtt) cc_final: 0.8664 (tpt)
REVERT: K   87 ASP cc_start: 0.8853 (p0) cc_final: 0.8549 (t0)
REVERT: K  120 VAL cc_start: 0.6922 (m) cc_final: 0.6492 (p)
REVERT: K  125 ARG cc_start: 0.8857 (mtm110) cc_final: 0.8600 (ptp-170)
REVERT: L   50 CYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7639 (t)
  outliers start: 23
  outliers final: 17
  residues processed: 219
  average time/residue: 0.2985
  time to fit residues: 91.4913
Evaluate side-chains
  214 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 196
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   13 LYS
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue   45 TYR
Chi-restraints excluded: chain K residue   98 THR
Chi-restraints excluded: chain K residue  132 ASP
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   50 CYS
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain M residue   36 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 111 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9980
   chunk 118 optimal weight:    7.9990
   chunk 92 optimal weight:    6.9990
   chunk 86 optimal weight:    0.6980
   chunk 48 optimal weight:    5.9990
   chunk 119 optimal weight:    9.9990
   chunk 58 optimal weight:    7.9990
   chunk 114 optimal weight:    5.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.049198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.032776 restraints weight = 81583.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.2721 rms_B_bonded: 2.98
r_work: 0.2543 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.2543
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2538
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2538 r_free = 0.2538    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2538 r_free = 0.2538    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2538
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8883
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  15165  Z= 0.294
  Angle     :  0.627   8.959  21781  Z= 0.362
  Chirality :  0.037   0.147   2489
  Planarity :  0.004   0.058   1746
  Dihedral  : 29.513 173.571   4381
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 18.45 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    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:  1.96 (0.27), residues: 1033
  helix:  2.40 (0.21), residues: 647
  sheet: -1.05 (0.88), residues: 24
  loop : -0.59 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP K  93 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.015   0.002   PHE K  62 
 TYR   0.067   0.002   TYR D  83 
 ARG   0.005   0.000   ARG K 125 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 198
  time to evaluate  : 1.139 
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: A   59 GLU cc_start: 0.9109 (pm20) cc_final: 0.8786 (pm20)
REVERT: A   73 GLU cc_start: 0.9478 (tm-30) cc_final: 0.9178 (tm-30)
REVERT: A   79 LYS cc_start: 0.9160 (tptm) cc_final: 0.8724 (tptp)
REVERT: A   94 GLU cc_start: 0.8872 (tp30) cc_final: 0.8559 (tt0)
REVERT: C   24 GLN cc_start: 0.9395 (mm-40) cc_final: 0.8789 (mp10)
REVERT: C   56 GLU cc_start: 0.9337 (tt0) cc_final: 0.8899 (tt0)
REVERT: E   73 GLU cc_start: 0.8639 (tt0) cc_final: 0.8363 (tt0)
REVERT: E   94 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8934 (mm-30)
REVERT: F   91 LYS cc_start: 0.9460 (ttmt) cc_final: 0.9121 (ttpt)
REVERT: G   61 GLU cc_start: 0.9119 (tp30) cc_final: 0.8838 (mm-30)
REVERT: D   42 TYR cc_start: 0.8722 (t80) cc_final: 0.8497 (t80)
REVERT: D   93 GLU cc_start: 0.8969 (mp0) cc_final: 0.8756 (mp0)
REVERT: H   33 ARG cc_start: 0.8257 (mtp85) cc_final: 0.7580 (ttt90)
REVERT: H   83 TYR cc_start: 0.8575 (m-10) cc_final: 0.8351 (m-10)
REVERT: H  106 LEU cc_start: 0.9398 (mt) cc_final: 0.9108 (mt)
REVERT: H  113 GLU cc_start: 0.9306 (mm-30) cc_final: 0.8889 (mt-10)
REVERT: K    1 MET cc_start: 0.7521 (tmm) cc_final: 0.7144 (tmm)
REVERT: K   38 MET cc_start: 0.9105 (mtt) cc_final: 0.8654 (tpt)
REVERT: K   87 ASP cc_start: 0.8859 (p0) cc_final: 0.8563 (t0)
REVERT: K  125 ARG cc_start: 0.8882 (mtm110) cc_final: 0.8625 (ptp-170)
REVERT: L   50 CYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7592 (t)
  outliers start: 21
  outliers final: 20
  residues processed: 213
  average time/residue: 0.2929
  time to fit residues: 87.7523
Evaluate side-chains
  214 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 193
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   13 LYS
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue   45 TYR
Chi-restraints excluded: chain K residue   70 THR
Chi-restraints excluded: chain K residue   98 THR
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   50 CYS
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain M residue   36 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 125 optimal weight:   10.0000
   chunk 95 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 113 optimal weight:    8.9990
   chunk 11 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9990
   chunk 117 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.049471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.033263 restraints weight = 81500.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.2742 rms_B_bonded: 2.99
r_work: 0.2567 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.2567
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2560
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2560 r_free = 0.2560    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2560 r_free = 0.2560    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2560
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8861
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15165  Z= 0.222
  Angle     :  0.619   8.527  21781  Z= 0.358
  Chirality :  0.036   0.184   2489
  Planarity :  0.004   0.059   1746
  Dihedral  : 29.491 173.137   4381
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.57 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    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:  1.96 (0.27), residues: 1033
  helix:  2.38 (0.21), residues: 649
  sheet: -1.06 (0.87), residues: 24
  loop : -0.57 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K 141 
 HIS   0.004   0.001   HIS F  75 
 PHE   0.013   0.001   PHE E  67 
 TYR   0.074   0.002   TYR D  83 
 ARG   0.008   0.000   ARG K 139 

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 201
  time to evaluate  : 1.322 
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   59 GLU cc_start: 0.9104 (pm20) cc_final: 0.8790 (pm20)
REVERT: A   73 GLU cc_start: 0.9462 (tm-30) cc_final: 0.9173 (tm-30)
REVERT: A   79 LYS cc_start: 0.9103 (tptm) cc_final: 0.8651 (tptp)
REVERT: A   94 GLU cc_start: 0.8836 (tp30) cc_final: 0.8513 (tt0)
REVERT: C   24 GLN cc_start: 0.9374 (mm-40) cc_final: 0.8768 (mp10)
REVERT: C   56 GLU cc_start: 0.9311 (tt0) cc_final: 0.8861 (tt0)
REVERT: C   95 LYS cc_start: 0.9507 (tppt) cc_final: 0.9262 (ttpt)
REVERT: E   73 GLU cc_start: 0.8621 (tt0) cc_final: 0.8329 (tt0)
REVERT: F   53 GLU cc_start: 0.7827 (pm20) cc_final: 0.7420 (pm20)
REVERT: F   91 LYS cc_start: 0.9452 (ttmt) cc_final: 0.9101 (ttpt)
REVERT: G   61 GLU cc_start: 0.9052 (tp30) cc_final: 0.8793 (tp30)
REVERT: D   93 GLU cc_start: 0.8994 (mp0) cc_final: 0.8780 (mp0)
REVERT: H   33 ARG cc_start: 0.8290 (mtp85) cc_final: 0.7657 (ttt90)
REVERT: H  106 LEU cc_start: 0.9383 (mt) cc_final: 0.9093 (mt)
REVERT: H  113 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8892 (mt-10)
REVERT: K    1 MET cc_start: 0.7511 (tmm) cc_final: 0.7198 (tmm)
REVERT: K   38 MET cc_start: 0.9079 (mtt) cc_final: 0.8638 (tpt)
REVERT: K   87 ASP cc_start: 0.8832 (p0) cc_final: 0.8569 (t0)
REVERT: K  120 VAL cc_start: 0.6337 (m) cc_final: 0.5723 (p)
REVERT: K  125 ARG cc_start: 0.8858 (mtm110) cc_final: 0.8486 (ptp-170)
REVERT: L   50 CYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7625 (t)
REVERT: L   55 ARG cc_start: 0.7931 (mmp80) cc_final: 0.7660 (mmp80)
  outliers start: 22
  outliers final: 20
  residues processed: 216
  average time/residue: 0.2976
  time to fit residues: 91.0843
Evaluate side-chains
  218 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 197
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   13 LYS
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue   26 VAL
Chi-restraints excluded: chain K residue   45 TYR
Chi-restraints excluded: chain K residue   70 THR
Chi-restraints excluded: chain K residue   98 THR
Chi-restraints excluded: chain L residue   49 LEU
Chi-restraints excluded: chain L residue   50 CYS
Chi-restraints excluded: chain L residue   74 VAL
Chi-restraints excluded: chain M residue   36 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 17 optimal weight:    8.9990
   chunk 21 optimal weight:    0.7980
   chunk 62 optimal weight:    6.9990
   chunk 113 optimal weight:    8.9990
   chunk 18 optimal weight:    0.6980
   chunk 81 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9990
   chunk 107 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 68 optimal weight:   10.0000
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.050253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.033961 restraints weight = 81508.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.2769 rms_B_bonded: 2.97
r_work: 0.2602 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.2602
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2596
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2596 r_free = 0.2596    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2596 r_free = 0.2596    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
r_final: 0.2596
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8833
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15165  Z= 0.195
  Angle     :  0.621  10.511  21781  Z= 0.356
  Chirality :  0.036   0.162   2489
  Planarity :  0.004   0.060   1746
  Dihedral  : 29.366 172.544   4381
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 20.18 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.40 %
    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:  1.84 (0.27), residues: 1033
  helix:  2.25 (0.21), residues: 655
  sheet: -0.87 (0.89), residues: 24
  loop : -0.61 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP L  61 
 HIS   0.003   0.001   HIS H  82 
 PHE   0.015   0.001   PHE L  40 
 TYR   0.052   0.002   TYR D  83 
 ARG   0.008   0.000   ARG K 136 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7568.28 seconds
wall clock time: 135 minutes 9.61 seconds (8109.61 seconds total)