Starting phenix.real_space_refine
on Wed Feb  4 18:22:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zjr_60154/02_2026/8zjr_60154.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zjr_60154/02_2026/8zjr_60154.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zjr_60154/02_2026/8zjr_60154.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zjr_60154/02_2026/8zjr_60154.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zjr_60154/02_2026/8zjr_60154.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zjr_60154/02_2026/8zjr_60154.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.091
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     262      5.49       5
     S      14      5.16       5
     C    6858      2.51       5
     N    2302      2.21       5
     O    2777      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12213
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 820
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
      Conformer: "B"
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
          bond proxies already assigned to first conformer: 786
    Chain: "B"
      Number of atoms: 671
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
      Conformer: "B"
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
          bond proxies already assigned to first conformer: 640
    Chain: "C"
      Number of atoms: 814
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 104, 805
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
      Conformer: "B"
        Number of residues, atoms: 104, 805
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
          bond proxies already assigned to first conformer: 805
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 92, 718
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
      Conformer: "B"
        Number of residues, atoms: 92, 718
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
          bond proxies already assigned to first conformer: 709
    Chain: "E"
      Number of atoms: 805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 805
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 687
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 84, 678
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
      Conformer: "B"
        Number of residues, atoms: 84, 678
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
          bond proxies already assigned to first conformer: 676
    Chain: "G"
      Number of atoms: 858
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
      Conformer: "B"
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
          bond proxies already assigned to first conformer: 830
    Chain: "H"
      Number of atoms: 750
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 95, 740
          Classifications: {'peptide': 95}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
      Conformer: "B"
        Number of residues, atoms: 95, 740
          Classifications: {'peptide': 95}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
          bond proxies already assigned to first conformer: 739
    Chain: "I"
      Number of atoms: 2702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 2702
          Classifications: {'DNA': 131}
          Link IDs: {'rna3p': 130}
    Chain: "J"
      Number of atoms: 2669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 2669
          Classifications: {'DNA': 131}
          Link IDs: {'rna3p': 130}
    Chain: "M"
      Number of atoms: 701
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 82, 690
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 3, 'TRANS': 78}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 82, 690
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 3, 'TRANS': 78}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 693
  Residues with excluded nonbonded symmetry interactions: 12
    residue:
      pdb=" N  AARG A  54 " occ=0.56
      ... (20 atoms not shown)
      pdb=" NH2BARG A  54 " occ=0.44
    residue:
      pdb=" N  AARG A 130 " occ=0.40
      ... (20 atoms not shown)
      pdb=" NH2BARG A 130 " occ=0.60
    residue:
      pdb=" N  AGLU B  53 " occ=0.45
      ... (16 atoms not shown)
      pdb=" OE2BGLU B  53 " occ=0.55
    residue:
      pdb=" N  ALYS B  92 " occ=0.53
      ... (16 atoms not shown)
      pdb=" NZ BLYS B  92 " occ=0.47
    residue:
      pdb=" N  ALYS C  96 " occ=0.51
      ... (16 atoms not shown)
      pdb=" NZ BLYS C  96 " occ=0.49
    residue:
      pdb=" N  ALYS D  47 " occ=0.53
      ... (16 atoms not shown)
      pdb=" NZ BLYS D  47 " occ=0.47
    residue:
      pdb=" N  AGLU D 114 " occ=0.62
      ... (16 atoms not shown)
      pdb=" OE2BGLU D 114 " occ=0.38
    residue:
      pdb=" N  ALYS F  78 " occ=0.28
      ... (16 atoms not shown)
      pdb=" NZ BLYS F  78 " occ=0.72
    residue:
      pdb=" N  AGLU G  92 " occ=0.61
      ... (16 atoms not shown)
      pdb=" OE2BGLU G  92 " occ=0.39
    residue:
      pdb=" N  AGLN G 105 " occ=0.17
      ... (16 atoms not shown)
      pdb=" NE2BGLN G 105 " occ=0.83
    residue:
      pdb=" N  AHIS H  83 " occ=0.61
      ... (18 atoms not shown)
      pdb=" NE2BHIS H  83 " occ=0.39
    residue:
      pdb=" N  AARG M  94 " occ=0.48
      ... (20 atoms not shown)
      pdb=" NH2BARG M  94 " occ=0.52
  Time building chain proxies: 4.15, per 1000 atoms: 0.34
  Number of scatterers: 12213
  At special positions: 0
  Unit cell: (75.96, 116.05, 136.095, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     262     15.00
     O    2777      8.00
     N    2302      7.00
     C    6858      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: 1.05
  Conformation dependent library (CDL) restraints added in 566.0 milliseconds
  

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1598

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 11 sheets defined
      68.4% alpha, 4.9% beta
      129 base pairs and 199 stacking pairs defined.
    Time for finding SS restraints: 1.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 58
      removed outlier: 3.617A  pdb=" N   LYS A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   SER A  58 " --> pdb=" O  BARG A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 77
    Processing helix  chain 'A' and resid 88 through 115
    Processing helix  chain 'A' and resid 121 through 133
    Processing helix  chain 'B' and resid 26 through 30
    Processing helix  chain 'B' and resid 31 through 43
      removed outlier: 4.655A  pdb=" N   ARG B  37 " --> pdb=" O   PRO B  33 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   ARG B  40 " --> pdb=" O   ARG B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 77
      removed outlier: 4.032A  pdb=" N   GLU B  54 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 94
      removed outlier: 3.624A  pdb=" N   GLN B  94 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 22
      removed outlier: 3.501A  pdb=" N   ALA C  22 " --> pdb=" O   ARG C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 38
      removed outlier: 3.602A  pdb=" N   VAL C  31 " --> pdb=" O   PRO C  27 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 74
      removed outlier: 3.762A  pdb=" N   ASN C  74 " --> pdb=" O   ALA C  70 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 90
    Processing helix  chain 'C' and resid 91 through 98
    Processing helix  chain 'D' and resid 38 through 50
    Processing helix  chain 'D' and resid 56 through 85
    Processing helix  chain 'D' and resid 91 through 103
    Processing helix  chain 'D' and resid 105 through 124
      removed outlier: 3.631A  pdb=" N   LYS D 109 " --> pdb=" O   GLY D 105 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   SER D 124 " --> pdb=" O   THR D 120 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 57
      removed outlier: 3.868A  pdb=" N   LEU E  49 " --> pdb=" O   GLY E  45 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LYS E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 77
    Processing helix  chain 'E' and resid 86 through 115
    Processing helix  chain 'E' and resid 121 through 132
    Processing helix  chain 'F' and resid 26 through 30
    Processing helix  chain 'F' and resid 31 through 43
    Processing helix  chain 'F' and resid 51 through 77
      removed outlier: 3.789A  pdb=" N   GLY F  57 " --> pdb=" O   GLU F  53 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 94
      removed outlier: 3.658A  pdb=" N   VAL F  87 " --> pdb=" O   THR F  83 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLN F  94 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 22
      removed outlier: 3.524A  pdb=" N   ARG G  21 " --> pdb=" O   THR G  17 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ALA G  22 " --> pdb=" O   ARG G  18 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 17 through 22'
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 74
      removed outlier: 4.489A  pdb=" N   VAL G  50 " --> pdb=" O   ALA G  46 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ASP G  73 " --> pdb=" O   ASN G  69 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ASN G  74 " --> pdb=" O   ALA G  70 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 91
      removed outlier: 3.919A  pdb=" N   ASP G  91 " --> pdb=" O   ALA G  87 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 98
    Processing helix  chain 'H' and resid 38 through 50
      removed outlier: 3.659A  pdb=" N   TYR H  43 " --> pdb=" O   SER H  39 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LYS H  44 " --> pdb=" O   VAL H  40 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 56 through 85
      removed outlier: 3.563A  pdb=" N   GLY H  61 " --> pdb=" O   SER H  57 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ILE H  62 " --> pdb=" O   LYS H  58 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 91 through 103
      removed outlier: 3.514A  pdb=" N   ILE H  95 " --> pdb=" O   THR H  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 105 through 125
    Processing helix  chain 'M' and resid 86 through 99
    Processing helix  chain 'M' and resid 110 through 122
      removed outlier: 3.685A  pdb=" N   TYR M 114 " --> pdb=" O   LYS M 110 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 131 through 143
      removed outlier: 3.950A  pdb=" N   GLY M 136 " --> pdb=" O   THR M 132 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   LYS M 137 " --> pdb=" O   ALA M 133 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85
      removed outlier: 7.745A  pdb=" N   ARG A  84 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120
    Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99
    Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44
      removed outlier: 7.616A  pdb=" N   ARG C  43 " --> pdb=" O   ILE D  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103
      removed outlier: 6.627A  pdb=" N   THR C 102 " --> pdb=" O   TYR F  99 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85
      removed outlier: 7.410A  pdb=" N   ARG E  84 " --> pdb=" O   VAL F  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120
    Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44
      removed outlier: 7.695A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79
    Processing sheet with id=AB2, first strand: chain 'M' and resid 100 through 109
      removed outlier: 3.893A  pdb=" N   GLY M 163 " --> pdb=" O   HIS M 103 " (cutoff:3.500A)
      removed outlier: 8.639A  pdb=" N   ASP M 105 " --> pdb=" O   TYR M 161 " (cutoff:3.500A)
      removed outlier: 9.487A  pdb=" N   TYR M 161 " --> pdb=" O   ASP M 105 " (cutoff:3.500A)
      removed outlier: 9.937A  pdb=" N   CYS M 107 " --> pdb=" O   TYR M 159 " (cutoff:3.500A)
      removed outlier: 10.615A  pdb=" N   TYR M 159 " --> pdb=" O   CYS M 107 " (cutoff:3.500A)

    428 hydrogen bonds defined for protein.
    1274 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      329 hydrogen bonds
      654 hydrogen bond angles
      0 basepair planarities
      129 basepair parallelities
      199 stacking parallelities
  Total time for adding SS restraints: 2.22

  Time building geometry restraints manager: 1.30 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2841
        1.34 -     1.45: 3725
        1.45 -     1.57: 5861
        1.57 -     1.69: 523
        1.69 -     1.81: 25
  Bond restraints: 12975
  Sorted by residual:
  bond pdb=" CB  PRO M 129 "
       pdb=" CG  PRO M 129 "
    ideal  model  delta    sigma   weight residual
    1.492  1.615 -0.123 5.00e-02 4.00e+02 6.02e+00
  bond pdb=" C3'  DG I  77 "
       pdb=" O3'  DG I  77 "
    ideal  model  delta    sigma   weight residual
    1.422  1.463 -0.041 3.00e-02 1.11e+03 1.91e+00
  bond pdb=" C3'  DC I  53 "
       pdb=" O3'  DC I  53 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.70e+00
  bond pdb=" C3'  DT I  57 "
       pdb=" O3'  DT I  57 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.69e+00
  bond pdb=" CB  GLN M 156 "
       pdb=" CG  GLN M 156 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.57e+00
  ... (remaining 12970 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 18283
        1.76 -     3.53: 343
        3.53 -     5.29: 12
        5.29 -     7.05: 6
        7.05 -     8.81: 1
  Bond angle restraints: 18645
  Sorted by residual:
  angle pdb=" CA  PRO M 129 "
        pdb=" N   PRO M 129 "
        pdb=" CD  PRO M 129 "
      ideal   model   delta    sigma   weight residual
     112.00  105.28    6.72 1.40e+00 5.10e-01 2.30e+01
  angle pdb=" C   ARG B  36 "
        pdb=" N   ARG B  37 "
        pdb=" CA  ARG B  37 "
      ideal   model   delta    sigma   weight residual
     121.54  128.38   -6.84 1.91e+00 2.74e-01 1.28e+01
  angle pdb=" CA  GLN M 156 "
        pdb=" CB  GLN M 156 "
        pdb=" CG  GLN M 156 "
      ideal   model   delta    sigma   weight residual
     114.10  120.44   -6.34 2.00e+00 2.50e-01 1.01e+01
  angle pdb=" CB  MET E  91 "
        pdb=" CG  MET E  91 "
        pdb=" SD  MET E  91 "
      ideal   model   delta    sigma   weight residual
     112.70  121.51   -8.81 3.00e+00 1.11e-01 8.63e+00
  angle pdb=" C3'  DG I  77 "
        pdb=" O3'  DG I  77 "
        pdb=" P    DG I  78 "
      ideal   model   delta    sigma   weight residual
     120.20  123.84   -3.64 1.50e+00 4.44e-01 5.89e+00
  ... (remaining 18640 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.31: 5900
       35.31 -    70.61: 1250
       70.61 -   105.92: 15
      105.92 -   141.23: 1
      141.23 -   176.53: 4
  Dihedral angle restraints: 7170
    sinusoidal: 4677
      harmonic: 2493
  Sorted by residual:
  dihedral pdb=" CA  ILE B  35 "
           pdb=" C   ILE B  35 "
           pdb=" N   ARG B  36 "
           pdb=" CA  ARG B  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.22   23.78     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" C4'  DT I  57 "
           pdb=" C3'  DT I  57 "
           pdb=" O3'  DT I  57 "
           pdb=" P    DC I  58 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   36.53 -176.53     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG I  77 "
           pdb=" C3'  DG I  77 "
           pdb=" O3'  DG I  77 "
           pdb=" P    DG I  78 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   47.07  172.93     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 7167 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1517
       0.030 -    0.061: 437
       0.061 -    0.091: 93
       0.091 -    0.122: 47
       0.122 -    0.152: 6
  Chirality restraints: 2100
  Sorted by residual:
  chirality pdb=" C3'  DG I  77 "
            pdb=" C4'  DG I  77 "
            pdb=" O3'  DG I  77 "
            pdb=" C2'  DG I  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.51   -0.15 2.00e-01 2.50e+01 5.77e-01
  chirality pdb=" CA  ASN M  98 "
            pdb=" N   ASN M  98 "
            pdb=" C   ASN M  98 "
            pdb=" CB  ASN M  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.94e-01
  chirality pdb=" CA  ILE B  30 "
            pdb=" N   ILE B  30 "
            pdb=" C   ILE B  30 "
            pdb=" CB  ILE B  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.49e-01
  ... (remaining 2097 not shown)

  Planarity restraints: 1462
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  37 "    0.018 2.00e-02 2.50e+03   3.65e-02 1.33e+01
        pdb=" C   ARG B  37 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   ARG B  37 "    0.023 2.00e-02 2.50e+03
        pdb=" N   LEU B  38 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG M 128 "   -0.036 5.00e-02 4.00e+02   5.15e-02 4.24e+00
        pdb=" N   PRO M 129 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO M 129 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO M 129 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  32 "    0.031 5.00e-02 4.00e+02   4.60e-02 3.39e+00
        pdb=" N   PRO B  33 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO B  33 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B  33 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1459 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1837
        2.76 -     3.29: 10615
        3.29 -     3.83: 23375
        3.83 -     4.36: 26282
        4.36 -     4.90: 40363
  Nonbonded interactions: 102472
  Sorted by model distance:
  nonbonded pdb=" OG  SER M  85 "
            pdb=" N   ASN M  86 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" OG1 THR F  74 "
            pdb=" OD2 ASP F  86 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" N   GLU M  87 "
            pdb=" OE1 GLU M  87 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" N2   DG I 131 "
            pdb=" O2   DT J  18 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" OD2 ASP D  69 "
            pdb=" OH  TYR F  99 "
     model   vdw
     2.258 3.040
  ... (remaining 102467 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 39 through 53 or resid 55 through 129 or resid 131 through \ 
 134))
  selection = (chain 'E' and (resid 39 through 53 or resid 55 through 129 or resid 131 through \ 
 134))
}
ncs_group {
  reference = (chain 'B' and (resid 22 through 52 or resid 54 through 77 or resid 79 through 9 \ 
1 or resid 93 through 102))
  selection = (chain 'F' and (resid 22 through 52 or resid 54 through 77 or resid 79 through 9 \ 
1 or resid 93 through 102))
}
ncs_group {
  reference = (chain 'C' and (resid 16 through 91 or resid 93 through 95 or resid 97 through 1 \ 
04 or resid 106 through 119))
  selection = (chain 'G' and (resid 16 through 91 or resid 93 through 95 or resid 97 through 1 \ 
04 or resid 106 through 119))
}
ncs_group {
  reference = (chain 'D' and (resid 34 through 46 or resid 48 through 82 or resid 84 through 1 \ 
13 or resid 115 through 125))
  selection = (chain 'H' and (resid 34 through 46 or resid 48 through 82 or resid 84 through 1 \ 
13 or resid 115 through 125))
}

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=0.02 max=1.00 mean=0.99
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:             1.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.530
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
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      :  0.004   0.123  12975  Z= 0.155
  Angle     :  0.539   8.813  18645  Z= 0.322
  Chirality :  0.033   0.152   2100
  Planarity :  0.004   0.051   1462
  Dihedral  : 27.699 176.533   5572
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 19.83 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.29), residues: 859
  helix:  1.61 (0.22), residues: 598
  sheet: -5.13 (0.67), residues: 14
  loop : -1.14 (0.36), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG M 118 
 TYR   0.012   0.001   TYR G  58 
 PHE   0.006   0.001   PHE F 101 
 TRP   0.002   0.001   TRP M  95 
 HIS   0.002   0.001   HIS F  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (12975)
  covalent geometry    : angle       0.53888 (18645)
  hydrogen bonds       : bond        0.10459 (  757)
  hydrogen bonds       : angle       3.81033 ( 1928)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.348 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 79
  average time/residue: 0.1560
  time to fit residues: 16.4642
Evaluate side-chains
  74 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  124 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.3980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.4980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  26 ASN
** B  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 ASN
** D  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  26 ASN
** F  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  64 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.182777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.126890 restraints weight = 79278.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 4.94
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3424
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3424 r_free = 0.3424    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3423 r_free = 0.3423    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3423
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.0707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  12975  Z= 0.163
  Angle     :  0.540   6.614  18645  Z= 0.322
  Chirality :  0.034   0.140   2100
  Planarity :  0.004   0.044   1462
  Dihedral  : 30.154 178.826   3850
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 19.97 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.29), residues: 859
  helix:  1.82 (0.21), residues: 605
  sheet: -5.18 (0.66), residues: 14
  loop : -1.12 (0.36), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG M 118 
 TYR   0.011   0.001   TYR H  41 
 PHE   0.010   0.001   PHE E  68 
 TRP   0.001   0.000   TRP M  95 
 HIS   0.003   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (12975)
  covalent geometry    : angle       0.54014 (18645)
  hydrogen bonds       : bond        0.04226 (  757)
  hydrogen bonds       : angle       2.97555 ( 1928)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A   59 THR cc_start: 0.9197 (p) cc_final: 0.8947 (p)
REVERT: A   60 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7354 (pm20)
REVERT: B   75 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7341 (mt-10)
REVERT: C  100 ARG cc_start: 0.7545 (mtp85) cc_final: 0.7238 (mtp85)
REVERT: E   60 GLU cc_start: 0.8343 (pm20) cc_final: 0.8013 (pm20)
REVERT: M  103 HIS cc_start: 0.8666 (t-90) cc_final: 0.8408 (t-170)
  outliers start: 7
  outliers final: 4
  residues processed: 86
  average time/residue: 0.1456
  time to fit residues: 16.7835
Evaluate side-chains
  83 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain F residue   26 ASN
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0010
   chunk 53 optimal weight:    9.9990
   chunk 63 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.7788

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

Flipped N/Q/H residues before XYZ refinement:
B  26 ASN
** B  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 ASN
** D  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.189487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.134510 restraints weight = 79298.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 4.70
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3566
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3566 r_free = 0.3566    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3565 r_free = 0.3565    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3565
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.0858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12975  Z= 0.163
  Angle     :  0.532   6.610  18645  Z= 0.317
  Chirality :  0.034   0.138   2100
  Planarity :  0.004   0.040   1462
  Dihedral  : 30.124 179.818   3849
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 20.53 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.29), residues: 859
  helix:  1.92 (0.21), residues: 604
  sheet: -5.23 (0.63), residues: 14
  loop : -1.19 (0.35), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M 118 
 TYR   0.011   0.001   TYR D  41 
 PHE   0.011   0.001   PHE E  68 
 TRP   0.001   0.000   TRP M  95 
 HIS   0.003   0.001   HIS F  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (12975)
  covalent geometry    : angle       0.53171 (18645)
  hydrogen bonds       : bond        0.04056 (  757)
  hydrogen bonds       : angle       2.88486 ( 1928)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.318 
Fit side-chains
REVERT: C  100 ARG cc_start: 0.7559 (mtp85) cc_final: 0.7252 (mtp85)
  outliers start: 6
  outliers final: 5
  residues processed: 84
  average time/residue: 0.1345
  time to fit residues: 15.2441
Evaluate side-chains
  83 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain E residue   83 LEU
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 74 optimal weight:    5.9990
   chunk 105 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
B  26 ASN
** B  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 ASN
D  64 ASN
** D  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  26 ASN
F  76 HIS
M 103 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.187231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.132606 restraints weight = 75932.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 4.49
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3534
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3534 r_free = 0.3534    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3534 r_free = 0.3534    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3534
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.1104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  12975  Z= 0.195
  Angle     :  0.556   6.663  18645  Z= 0.329
  Chirality :  0.035   0.155   2100
  Planarity :  0.004   0.039   1462
  Dihedral  : 30.239 179.083   3849
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 20.95 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.29), residues: 859
  helix:  1.89 (0.21), residues: 604
  sheet: -5.24 (0.67), residues: 14
  loop : -1.21 (0.35), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG M 165 
 TYR   0.010   0.001   TYR D  41 
 PHE   0.012   0.001   PHE E  68 
 TRP   0.001   0.001   TRP M  95 
 HIS   0.004   0.001   HIS F  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (12975)
  covalent geometry    : angle       0.55571 (18645)
  hydrogen bonds       : bond        0.04321 (  757)
  hydrogen bonds       : angle       2.91634 ( 1928)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.306 
Fit side-chains
REVERT: C  100 ARG cc_start: 0.7601 (mtp85) cc_final: 0.7284 (mtp85)
REVERT: E   60 GLU cc_start: 0.8387 (pm20) cc_final: 0.8145 (pm20)
  outliers start: 12
  outliers final: 9
  residues processed: 87
  average time/residue: 0.1285
  time to fit residues: 15.1456
Evaluate side-chains
  87 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain E residue   83 LEU
Chi-restraints excluded: chain F residue   26 ASN
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 58 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 16 optimal weight:    0.2980
   chunk 49 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 86 optimal weight:    8.9990
   chunk 72 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
B  26 ASN
** B  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 ASN
** D  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  26 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.190241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.135901 restraints weight = 72401.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 4.46
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3577
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3577 r_free = 0.3577    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3577 r_free = 0.3577    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3577
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.1239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12975  Z= 0.151
  Angle     :  0.519   6.684  18645  Z= 0.309
  Chirality :  0.033   0.145   2100
  Planarity :  0.004   0.039   1462
  Dihedral  : 30.081 179.573   3849
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 21.37 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.57 (0.29), residues: 859
  helix:  2.03 (0.21), residues: 607
  sheet: -5.25 (0.67), residues: 14
  loop : -1.20 (0.35), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M 165 
 TYR   0.011   0.001   TYR D  41 
 PHE   0.009   0.001   PHE E  68 
 TRP   0.001   0.000   TRP M  95 
 HIS   0.004   0.001   HIS M 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (12975)
  covalent geometry    : angle       0.51883 (18645)
  hydrogen bonds       : bond        0.03864 (  757)
  hydrogen bonds       : angle       2.77814 ( 1928)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7315 (pm20)
REVERT: C  100 ARG cc_start: 0.7513 (mtp85) cc_final: 0.7285 (mtp85)
  outliers start: 12
  outliers final: 8
  residues processed: 89
  average time/residue: 0.1336
  time to fit residues: 16.1098
Evaluate side-chains
  88 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain F residue   26 ASN
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain G residue   20 SER
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 87 optimal weight:    6.9990
   chunk 98 optimal weight:    0.7980
   chunk 71 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 40 optimal weight:    0.3980
   chunk 86 optimal weight:    8.9990
   chunk 21 optimal weight:    0.7980
   chunk 83 optimal weight:    5.9990
   chunk 103 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  26 ASN
** B  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 ASN
F  26 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.189792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.134820 restraints weight = 63833.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 4.22
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3568
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3568 r_free = 0.3568    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3568 r_free = 0.3568    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3568
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12975  Z= 0.155
  Angle     :  0.520   6.655  18645  Z= 0.310
  Chirality :  0.033   0.139   2100
  Planarity :  0.004   0.039   1462
  Dihedral  : 30.097 179.850   3849
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 21.23 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.66 (0.29), residues: 859
  helix:  2.09 (0.21), residues: 605
  sheet: -5.21 (0.69), residues: 14
  loop : -1.13 (0.36), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M 165 
 TYR   0.011   0.001   TYR D  41 
 PHE   0.010   0.001   PHE E  68 
 TRP   0.001   0.000   TRP M  95 
 HIS   0.003   0.001   HIS M 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (12975)
  covalent geometry    : angle       0.52038 (18645)
  hydrogen bonds       : bond        0.03901 (  757)
  hydrogen bonds       : angle       2.77933 ( 1928)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.206 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7393 (pm20)
REVERT: C  100 ARG cc_start: 0.7554 (mtp85) cc_final: 0.7319 (mtp85)
REVERT: D  100 ARG cc_start: 0.7899 (mtt-85) cc_final: 0.7607 (mtt180)
REVERT: E   60 GLU cc_start: 0.8414 (pm20) cc_final: 0.8123 (pm20)
  outliers start: 12
  outliers final: 8
  residues processed: 86
  average time/residue: 0.1461
  time to fit residues: 16.9750
Evaluate side-chains
  88 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain G residue   20 SER
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain H residue   58 LYS
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 98 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** B  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 ASN
** F  26 ASN ** 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 = 0.4212 r_free = 0.4212 target = 0.188883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.134635 restraints weight = 75385.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 4.56
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3560
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3560 r_free = 0.3560    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3560 r_free = 0.3560    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3560
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12975  Z= 0.173
  Angle     :  0.535   7.784  18645  Z= 0.317
  Chirality :  0.034   0.140   2100
  Planarity :  0.004   0.039   1462
  Dihedral  : 30.132 179.893   3849
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 20.53 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.64 (0.29), residues: 859
  helix:  2.08 (0.21), residues: 605
  sheet: -5.19 (0.70), residues: 14
  loop : -1.14 (0.36), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M 165 
 TYR   0.010   0.001   TYR D  41 
 PHE   0.012   0.001   PHE E  68 
 TRP   0.000   0.000   TRP M  95 
 HIS   0.004   0.001   HIS M 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (12975)
  covalent geometry    : angle       0.53494 (18645)
  hydrogen bonds       : bond        0.04043 (  757)
  hydrogen bonds       : angle       2.81227 ( 1928)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7405 (pm20)
REVERT: C  100 ARG cc_start: 0.7605 (mtp85) cc_final: 0.7369 (mtp85)
REVERT: D   94 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7047 (mp0)
REVERT: D  100 ARG cc_start: 0.7905 (mtt-85) cc_final: 0.7622 (mtt180)
REVERT: E   60 GLU cc_start: 0.8455 (pm20) cc_final: 0.8204 (pm20)
  outliers start: 14
  outliers final: 9
  residues processed: 89
  average time/residue: 0.1390
  time to fit residues: 16.9352
Evaluate side-chains
  89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain D residue   94 GLU
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain G residue   20 SER
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain H residue   58 LYS
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.3188

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

Flipped N/Q/H residues before XYZ refinement:
B  26 ASN
** B  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  32 HIS
C  39 ASN
** F  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.185454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.131717 restraints weight = 74956.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 4.56
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3528
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3528 r_free = 0.3528    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3528 r_free = 0.3528    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3528
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  12975  Z= 0.215
  Angle     :  0.574   7.984  18645  Z= 0.337
  Chirality :  0.036   0.169   2100
  Planarity :  0.004   0.040   1462
  Dihedral  : 30.429 179.381   3849
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 20.67 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.29), residues: 859
  helix:  1.91 (0.21), residues: 606
  sheet: -5.33 (0.66), residues: 14
  loop : -1.16 (0.35), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG M 165 
 TYR   0.010   0.001   TYR D  41 
 PHE   0.015   0.001   PHE E  68 
 TRP   0.002   0.001   TRP M  95 
 HIS   0.003   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 (12975)
  covalent geometry    : angle       0.57429 (18645)
  hydrogen bonds       : bond        0.04497 (  757)
  hydrogen bonds       : angle       2.94629 ( 1928)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.317 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7477 (pm20)
REVERT: C  100 ARG cc_start: 0.7625 (mtp85) cc_final: 0.7394 (mtp85)
REVERT: D   94 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7050 (mp0)
REVERT: H  114 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7914 (mm-30)
  outliers start: 13
  outliers final: 8
  residues processed: 88
  average time/residue: 0.1542
  time to fit residues: 18.2682
Evaluate side-chains
  87 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain D residue   94 GLU
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 86 optimal weight:    8.9990
   chunk 84 optimal weight:    5.9990
   chunk 48 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0770
   chunk 35 optimal weight:    0.5980
   chunk 39 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
B  26 ASN
** B  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 ASN
** F  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.190218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.136534 restraints weight = 68149.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 4.40
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3586
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3587 r_free = 0.3587    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3587
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12975  Z= 0.144
  Angle     :  0.512   8.220  18645  Z= 0.305
  Chirality :  0.033   0.136   2100
  Planarity :  0.004   0.039   1462
  Dihedral  : 30.135 178.194   3849
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 21.37 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.29), residues: 859
  helix:  2.14 (0.21), residues: 608
  sheet: -5.26 (0.66), residues: 14
  loop : -1.18 (0.36), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M 165 
 TYR   0.011   0.001   TYR D  41 
 PHE   0.007   0.001   PHE E  68 
 TRP   0.002   0.001   TRP M  95 
 HIS   0.003   0.001   HIS M 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (12975)
  covalent geometry    : angle       0.51205 (18645)
  hydrogen bonds       : bond        0.03835 (  757)
  hydrogen bonds       : angle       2.74429 ( 1928)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7416 (pm20)
REVERT: C  100 ARG cc_start: 0.7516 (mtp85) cc_final: 0.7301 (mtp85)
REVERT: M  165 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7586 (ptt90)
  outliers start: 10
  outliers final: 7
  residues processed: 87
  average time/residue: 0.1642
  time to fit residues: 18.9162
Evaluate side-chains
  85 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain M residue  165 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 66 optimal weight:    0.5980
   chunk 90 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0470
   chunk 60 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
B  26 ASN
** B  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 ASN
F  26 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.189908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.135352 restraints weight = 62401.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 4.21
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3572
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3572 r_free = 0.3572    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3572 r_free = 0.3572    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3572
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.1674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12975  Z= 0.150
  Angle     :  0.516   8.581  18645  Z= 0.306
  Chirality :  0.033   0.159   2100
  Planarity :  0.004   0.039   1462
  Dihedral  : 30.118 179.018   3849
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 21.09 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.29), residues: 859
  helix:  2.17 (0.21), residues: 608
  sheet: -5.26 (0.66), residues: 14
  loop : -1.14 (0.36), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  78 
 TYR   0.010   0.001   TYR D  41 
 PHE   0.010   0.001   PHE E  68 
 TRP   0.004   0.001   TRP M  95 
 HIS   0.004   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (12975)
  covalent geometry    : angle       0.51559 (18645)
  hydrogen bonds       : bond        0.03863 (  757)
  hydrogen bonds       : angle       2.76705 ( 1928)

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

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

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1718 Ramachandran restraints generated.
    859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7418 (pm20)
REVERT: C  100 ARG cc_start: 0.7516 (mtp85) cc_final: 0.7302 (mtp85)
REVERT: D   94 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.6989 (mp0)
REVERT: D  100 ARG cc_start: 0.7850 (mtt-85) cc_final: 0.7580 (mtt180)
REVERT: E   60 GLU cc_start: 0.8408 (pm20) cc_final: 0.8119 (pm20)
REVERT: M  165 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7492 (ptt90)
  outliers start: 11
  outliers final: 8
  residues processed: 84
  average time/residue: 0.1540
  time to fit residues: 17.4582
Evaluate side-chains
  88 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain C residue   52 LEU
Chi-restraints excluded: chain D residue   94 GLU
Chi-restraints excluded: chain E residue   72 VAL
Chi-restraints excluded: chain F residue   26 ASN
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain M residue  165 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 96 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0970
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B  26 ASN
** B  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 ASN
F  26 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.189796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.135309 restraints weight = 63280.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 4.23
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3573
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3573 r_free = 0.3573    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3573 r_free = 0.3573    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3573
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.1712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12975  Z= 0.152
  Angle     :  0.517   8.704  18645  Z= 0.306
  Chirality :  0.033   0.138   2100
  Planarity :  0.004   0.039   1462
  Dihedral  : 30.093 178.949   3849
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 20.67 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.77 (0.29), residues: 859
  helix:  2.18 (0.21), residues: 608
  sheet: -5.26 (0.67), residues: 14
  loop : -1.12 (0.36), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  78 
 TYR   0.010   0.001   TYR D  41 
 PHE   0.010   0.001   PHE E  68 
 TRP   0.001   0.000   TRP M  95 
 HIS   0.003   0.001   HIS M 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (12975)
  covalent geometry    : angle       0.51728 (18645)
  hydrogen bonds       : bond        0.03886 (  757)
  hydrogen bonds       : angle       2.76407 ( 1928)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2192.59 seconds
wall clock time: 38 minutes 19.34 seconds (2299.34 seconds total)